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Jafari PA, Bagheri R, Lavasani S, Goudarzi S. DNMT3A-R882: a mutation with many paradoxes. Ann Hematol 2024:10.1007/s00277-024-05874-x. [PMID: 38969930 DOI: 10.1007/s00277-024-05874-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2024] [Accepted: 07/01/2024] [Indexed: 07/07/2024]
Abstract
Understanding the underlying mechanism of acute myeloid leukemia (AML) has led to the discovery of novel biomarkers to help predict, treat and monitor leukemia. DNA (cytosine-5)-methyltransferase 3 A (DNMT3A) is considered a prognostic and therapeutic epigenetic target in AML patients with a hotspot mutation of R882. R882 mutation is associated with impaired differentiation of Hematopoietic stem cells in the bone marrow and disease progression. The prevalence of R882 mutation varied in different ethnicities and countries, and similarly, its prognostic impact differed among numerous studies. Nevertheless, the co-occurrence of mutations in R882 with NPM1 and FLT3 has been reported more frequently and is associated with a worse prognosis. These studies also suggest diverse results regarding bone marrow transplantation response as a treatment, while chemoresistance is reached as a conclusive outcome These findings highlight the crucial need for an in-depth discussion on the significance of the R882 mutation in AML patients. Understanding its impact on leukemic transformation, prognosis, and treatment is vital for advancing clinical implications.
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Affiliation(s)
| | - Ramin Bagheri
- Mashhad University of Medical Sciences, Mashhad, Iran
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2
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Tabatabaei T, Rezvany MR, Ghasemi B, Vafaei F, Zadeh MK, Zaker F, Salmaninejad A. Effect of DNMT3A R882H Hot Spot Mutations on DDX43 Promoter Methylation in Acute Myeloid Leukemia. BIOMED RESEARCH INTERNATIONAL 2024; 2024:9625043. [PMID: 38807916 PMCID: PMC11132831 DOI: 10.1155/2024/9625043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/16/2024] [Revised: 04/21/2024] [Accepted: 05/06/2024] [Indexed: 05/30/2024]
Abstract
Epigenetic alterations have been observed in many hematological malignancies, including acute myeloid leukemia (AML). Many of these alterations result from mutations in DNA methyl transferase (DNMT) enzymes, disabling them to methylate target genes in a proper way. In this case-control study, we investigated the association between R882H mutation in DNMT3A gene and DDX43 gene methylation in patients with AML. 47 AML patients and 6 controls were included in this study. After DNA extraction, amplification refractory mutation system (ARMS)-PCR was used to evaluate R882H mutations in DNMT3A gene. The high-resolution melting (HRM) method was used to determine the methylation changes of the DDX43 gene promoter. R882H mutation was only found in 10.6% (5 out of 47) of AML patients. The frequency of DDX43 gene methylation was significantly higher in patients without R882H mutations compared to patients with R882H mutations (P < 0.05). The DNMT3A R882H mutation is typically present in a minority of AML patients. Nevertheless, this mutation is associated with a reduced frequency of methylation in the DDX43 promoter region.
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Affiliation(s)
- Tahere Tabatabaei
- Department of Hematology and Blood Transfusion, School of Allied Medical Sciences, Iran University of Medical Sciences, Tehran, Iran
| | - Mohammad Reza Rezvany
- Department of Hematology and Blood Transfusion, School of Allied Medical Sciences, Iran University of Medical Sciences, Tehran, Iran
| | - Bahare Ghasemi
- Department of Hematology and Blood Transfusion, School of Allied Medical Sciences, Iran University of Medical Sciences, Tehran, Iran
| | - Farzane Vafaei
- Blood Transfusion Research Center, High Institute for Research and Education in Transfusion Medicine, Isfahan, Iran
| | - Masoumeh Kiani Zadeh
- Blood Transfusion Research Center, High Institute for Research and Education in Transfusion Medicine, Tehran, Iran
| | - Farhad Zaker
- Department of Hematology and Blood Transfusion, School of Allied Medical Sciences, Iran University of Medical Sciences, Tehran, Iran
| | - Arash Salmaninejad
- Regenerative Medicine, Organ Procurement and Transplantation Multi-Disciplinary Center, Razi Hospital, School of Medicine, Guilan University of Medical Sciences, Rasht, Iran
- Department of Medical Genetics, Faculty of Medicine, Tehran University of Medical Sciences, Tehran, Iran
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3
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Epigenetic regulation in hematopoiesis and its implications in the targeted therapy of hematologic malignancies. Signal Transduct Target Ther 2023; 8:71. [PMID: 36797244 PMCID: PMC9935927 DOI: 10.1038/s41392-023-01342-6] [Citation(s) in RCA: 22] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Revised: 01/03/2023] [Accepted: 01/19/2023] [Indexed: 02/18/2023] Open
Abstract
Hematologic malignancies are one of the most common cancers, and the incidence has been rising in recent decades. The clinical and molecular features of hematologic malignancies are highly heterogenous, and some hematologic malignancies are incurable, challenging the treatment, and prognosis of the patients. However, hematopoiesis and oncogenesis of hematologic malignancies are profoundly affected by epigenetic regulation. Studies have found that methylation-related mutations, abnormal methylation profiles of DNA, and abnormal histone deacetylase expression are recurrent in leukemia and lymphoma. Furthermore, the hypomethylating agents and histone deacetylase inhibitors are effective to treat acute myeloid leukemia and T-cell lymphomas, indicating that epigenetic regulation is indispensable to hematologic oncogenesis. Epigenetic regulation mainly includes DNA modifications, histone modifications, and noncoding RNA-mediated targeting, and regulates various DNA-based processes. This review presents the role of writers, readers, and erasers of DNA methylation and histone methylation, and acetylation in hematologic malignancies. In addition, this review provides the influence of microRNAs and long noncoding RNAs on hematologic malignancies. Furthermore, the implication of epigenetic regulation in targeted treatment is discussed. This review comprehensively presents the change and function of each epigenetic regulator in normal and oncogenic hematopoiesis and provides innovative epigenetic-targeted treatment in clinical practice.
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Urabe A, Chi S, Minami Y. The Immuno-Oncology and Genomic Aspects of DNA-Hypomethylating Therapeutics in Acute Myeloid Leukemia. Int J Mol Sci 2023; 24:ijms24043727. [PMID: 36835136 PMCID: PMC9961620 DOI: 10.3390/ijms24043727] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2022] [Revised: 01/30/2023] [Accepted: 02/09/2023] [Indexed: 02/15/2023] Open
Abstract
Hypomethylating agents (HMAs) have been used for decades in the treatment of hematologic neoplasms, and now, have gathered attention again in terms of their combination with potent molecular-targeted agents such as a BCL-6 inhibitor venetoclax and an IDH1 inhibitor ivosidenib, as well as a novel immune-checkpoint inhibitor (anit-CD47 antibody) megrolimab. Several studies have shown that leukemic cells have a distinct immunological microenvironment, which is at least partially due to genetic alterations such as the TP53 mutation and epigenetic dysregulation. HMAs possibly improve intrinsic anti-leukemic immunity and sensitivity to immune therapies such as PD-1/PD-L1 inhibitors and anti-CD47 agents. This review describes the immuno-oncological backgrounds of the leukemic microenvironment and the therapeutic mechanisms of HMAs, as well as current clinical trials of HMAs and/or venetoclax-based combination therapies.
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Affiliation(s)
| | | | - Yosuke Minami
- Correspondence: ; Tel.: +81-4-7133-1111; Fax: +81-7133-6502
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5
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AMLVaran: a software approach to implement variant analysis of targeted NGS sequencing data in an oncological care setting. BMC Med Genomics 2020; 13:17. [PMID: 32019565 PMCID: PMC7001226 DOI: 10.1186/s12920-020-0668-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Accepted: 01/21/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Next-Generation Sequencing (NGS) enables large-scale and cost-effective sequencing of genetic samples in order to detect genetic variants. After successful use in research-oriented projects, NGS is now entering clinical practice. Consequently, variant analysis is increasingly important to facilitate a better understanding of disease entities and prognoses. Furthermore, variant calling allows to adapt and optimize specific treatments of individual patients, and thus is an integral part of personalized medicine.However, the analysis of NGS data typically requires a number of complex bioinformatics processing steps. A flexible and reliable software that combines the variant analysis process with a simple, user-friendly interface is therefore highly desirable, but still lacking. RESULTS With AMLVaran (AML Variant Analyzer), we present a web-based software, that covers the complete variant analysis workflow of targeted NGS samples. The software provides a generic pipeline that allows free choice of variant calling tools and a flexible language (SSDL) for filtering variant lists. AMLVaran's interactive website presents comprehensive annotation data and includes curated information on relevant hotspot regions and driver mutations. A concise clinical report with rule-based diagnostic recommendations is generated.An AMLVaran configuration with eight variant calling tools and a complex scoring scheme, based on the somatic variant calling pipeline appreci8, was used to analyze three datasets from AML and MDS studies with 402 samples in total. Maximum sensitivity and positive predictive values were 1.0 and 0.96, respectively. The tool's usability was found to be satisfactory by medical professionals. CONCLUSION Coverage analysis, reproducible variant filtering and software usability are important for clinical assessment of variants. AMLVaran performs reliable NGS variant analyses and generates reports fulfilling the requirements of a clinical setting. Due to its generic design, the software can easily be adapted for use with different targeted panels for other tumor entities, or even for whole-exome data. AMLVaran has been deployed to a public web server and is distributed with Docker scripts for local use.
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Liang S, Zhou X, Pan H, Yang Y, Shi L, Wang L. Prognostic value of DNMT3A mutations in myelodysplastic syndromes: a meta-analysis. ACTA ACUST UNITED AC 2020; 24:613-622. [PMID: 31482762 DOI: 10.1080/16078454.2019.1657613] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Objectives: Although DNA (cytosine-5)-methyltransferase 3 alpha (DNMT3A) gene mutations have been widely reported in myelodysplastic syndromes (MDS), the prognostic significance of DNMT3A mutations is still controversial. In this study, we conducted a meta-analysis to determine the prognostic effect of DNMT3A mutations in patients with MDS. Methods: Eligible studies from PubMed, Embase, Web of Science, Clinical Trials and the Cochrane Library were searched. Hazard ratios (HRs) and their 95% confidence intervals (CIs) for overall survival (OS) and leukemia-free survival (LFS) were pooled to assess the effect of DNMT3A mutations on the prognosis in MDS patients. Results: A total of 12 studies with 2236 patients were included in this meta-analysis. The pooled HRs for OS and LFS revealed that MDS patients with DNMT3A mutations had a significantly poor prognosis as compared with those without mutations (OS: HR = 1.654, 95% CI = 1.387-1.973, p < 0.001; LFS: HR = 4.624, 95% CI = 3.121-6.851, p < 0.001). Discussion and Conclusion: This meta-analysis showed an adverse prognostic effect of DNMT3A mutations in patients with MDS, which will contribute to risk stratification and prognostic assessment in the disease.
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Affiliation(s)
- Simin Liang
- Department of Hematology, The First Affiliated Hospital of Chongqing Medical University , Chongqing , People's Republic of China
| | - Xiaojia Zhou
- Department of Hematology, The First Affiliated Hospital of Chongqing Medical University , Chongqing , People's Republic of China
| | - Hui Pan
- Department of Hematology, The First Affiliated Hospital of Chongqing Medical University , Chongqing , People's Republic of China
| | - Yichun Yang
- Department of Hematology, The First Affiliated Hospital of Chongqing Medical University , Chongqing , People's Republic of China
| | - Lin Shi
- Department of Hematology, The First Affiliated Hospital of Chongqing Medical University , Chongqing , People's Republic of China
| | - Li Wang
- Department of Hematology, The First Affiliated Hospital of Chongqing Medical University , Chongqing , People's Republic of China
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7
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Study of DNA methyl transferase 3A mutation in acute myeloid leukemic patients. EGYPTIAN JOURNAL OF MEDICAL HUMAN GENETICS 2018. [DOI: 10.1016/j.ejmhg.2018.05.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
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8
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Yang X, Shi J, Zhang X, Zhang G, Zhang J, Yang S, Wang J, Ke X, Fu L. Biological and clinical influences of NPM1 in acute myeloid leukemia patients with DNMT3A mutations. Cancer Manag Res 2018; 10:2489-2497. [PMID: 30122998 PMCID: PMC6086113 DOI: 10.2147/cmar.s166714] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022] Open
Abstract
Purpose DNMT3A and NPM1 mutations are known to impact the prognosis of acute myeloid leukemia (AML). DNMT3A mutations are negative prognostic factors, while NPM1 mutations are low-risk factors and inclined to concurrently appear with DNMT3A mutations. In this study, we aimed to find out how NPM1 mutations affect patients’ outcomes in the background of DNMT3A mutations. Patients and methods We screened The Cancer Genome Atlas (TCGA) database and found 51 AML patients with DNMT3A mutations. Of them, 28 patients had a combination of NPM1 mutations. Results In all, NPM1 had the highest mutation frequency (n=28, 54.9%). DNMT3Amut/NPM1mut patients had higher bone marrow (BM) blasts (P=0.015), higher FLT3-ITD/TKD rate (P=0.004), and lower IDH2 mutation rate (P=0.014) than the DNMT3Amut/NPM1wild patients, while their prognoses were the same as the DNMT3Amut/NPM1wild patients (P>0.1). All 51 patients benefited from hematopoietic stem cell transplantation (HSCT) treatment (P=0.005 and 0.001 for event-free survival [EFS] and overall survival [OS], respectively). In the 23 patients with DNMT3Amut/NPM1wild, those who received HSCT had prolonged EFS and OS (P=0.043 and 0.008, respectively), while HSCT treatment did not produce a positive impact on EFS and OS in the remaining 28 patients with DNMT3Amut/NPM1mut (P=0.056 and 0.053, respectively). Conclusion Our study found that NPM1 mutations influenced BM blasts’ percentage, FLT3-ITD/TKD rate, and IDH2 mutation rate in AML patients with DNMT3A mutations but made little difference to the overall prognosis. While HSCT treatments benefited all DNMT3Amut patients, it was better for DNMT3Amut/NPM1wild patients to extend their EFS and OS.
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Affiliation(s)
- Xinrui Yang
- Department of Hematology and Lymphoma Research Center, Peking University, Third Hospital, Beijing 100191, China,
| | - Jinlong Shi
- Department of Biomedical Engineering, Chinese PLA General Hospital, Beijing 100853, China
| | - Xinpei Zhang
- Department of Hematology and Lymphoma Research Center, Peking University, Third Hospital, Beijing 100191, China,
| | - Gaoqi Zhang
- Department of Hematology and Lymphoma Research Center, Peking University, Third Hospital, Beijing 100191, China,
| | - Jilei Zhang
- Department of Hematology and Lymphoma Research Center, Peking University, Third Hospital, Beijing 100191, China,
| | - Siyuan Yang
- Department of Hematology and Lymphoma Research Center, Peking University, Third Hospital, Beijing 100191, China,
| | - Jing Wang
- Department of Hematology and Lymphoma Research Center, Peking University, Third Hospital, Beijing 100191, China,
| | - Xiaoyan Ke
- Department of Hematology and Lymphoma Research Center, Peking University, Third Hospital, Beijing 100191, China,
| | - Lin Fu
- Department of Hematology and Lymphoma Research Center, Peking University, Third Hospital, Beijing 100191, China,
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9
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Mevatee P, Tantiworawit A, Traisathit P, Puaninta C, Mevatee U, Angsuchawan S, Bumroongkit K. FLT3-ITD, NPM1, and DNMT3A Gene Mutations and Risk Factors in Normal Karyotype Acute Myeloid Leukemia and Myelodysplastic Syndrome Patients in Upper Northern Thailand. Asian Pac J Cancer Prev 2017; 18:3031-3039. [PMID: 29172276 PMCID: PMC5773788 DOI: 10.22034/apjcp.2017.18.11.3031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
Objective: Approximately 40-45% of AML and MDS patients have a cytogenetically normal karyotype (CN-AML and CN-MDS). The frequency and types of gene mutations in these cases may differ among various populations. The objective of this study was to identify frequencies and types of FLT3-ITD, NPM1, and DNMT3A mutations, and associations of them with clinical data and risk factors in CN-AML and CN-MDS cases in upper Northern Thailand. Methods: Bone marrow samples of 40 CN-AML and 60 CN-MDS patients were analyzed for gene mutations by direct sequencing. In addition, data for potential risk factors were obtained for comparison. Results: Frequencies of FLT3-ITD, NPM1, and DNMT3A mutations were 25.0%, 17.5%, and 10.0%, respectively in CN-AML, but all zero in CN-MDS cases. NPM1 mutations were found at a median age older than the wild type (58 vs 47 years) while DNMT3A mutations were associated with an increase in the white blood cell count. In all patients, factors for the mutations of these three genes included age ≤ 60 years, and a history of hypertension. Conclusion: When considering mutations in only normal karyotype patients, the frequency of FLT3-ITD, NPM1, DNMT3A mutations in CN-AML patients in upper Northern Thailand were found to occur at lower rates than in Western patients and to differ from other Asian populations including parts of Thailand. No mutations were observed in CN-MDS cases. Some types of gene mutations differed from previous studies, possibly attributable to differences in geography, lifestyle and genetic backgrounds. Links with age ≤ 60 years and history of hypertension were found. Investigation of these three genes in an intermediate risk group with a normal karyotype is useful for a better understanding of molecular leukemogenetic steps in CN-AML and CN-MDS patients and may be beneficial for planning treatment and prevention in the population of upper Northern Thailand.
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Affiliation(s)
- Piyanan Mevatee
- Department of Anatomy, Faculty of Medicine, Chiang Mai University, Thailand.
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10
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Li W, Cui L, Gao C, Liu S, Zhao X, Zhang R, Zheng H, Wu M, Li Z. DNMT3A mutations in Chinese childhood acute myeloid leukemia. Medicine (Baltimore) 2017; 96:e7620. [PMID: 28767575 PMCID: PMC5626129 DOI: 10.1097/md.0000000000007620] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
BACKGROUND DNA methyltransferase 3A (DNMT3A) mutations have been found in approximately 20% of adult acute myeloid leukemia (AML) patients and in 0% to 1.4% of children with AML, and the hotspots of mutations are mainly located in the catalytic methyltransferase domain, hereinto, mutation R882 accounts for 60%. Although the negative effect of DNMT3A on treatment outcome is well known, the prognostic significance of other DNMT3A mutations in AML is still unclear. Here, we tried to determine the incidence and prognostic significance of DNMT3A mutations in a large cohort in Chinese childhood AML. METHODS We detected the mutations in DNMT3A exon 23 by polymerase chain reaction and direct sequencing in 342 children with AML (0-16 years old) from January 2005 to June 2013, treated on BCH-2003 AML protocol. The correlation of DNMT3A mutations with clinical characteristics, fusion genes, other molecular anomalies (FLT3 internal tandem duplication [FLT3-ITD], Nucleophosmin 1, C-KIT (KIT proto-oncogene receptor tyrosine kinase), and Wilms tumor 1 mutations), and treatment outcome were analyzed. RESULTS DNMT3A mutations were detected in 4 out of 342 (1.2%) patients. Two patients were PML-RARA positive and 1 patient was FLT3-ITD positive. The mutations in coding sequences included S892S, V912A, R885G, and Q886R. Furthermore, there was 1 intronic mutation (c.2739+55A>C) found in 1 patient. No association of DNMT3A mutations with common clinical features was found. Two patients with DNMT3A mutations died of relapse or complications during treatment. One patient gave up treatment due to remission induction failure in day 33. Only 1 patient achieved continuous complete remission. CONCLUSIONS DNMT3A mutations were rare in Chinese children with AML including PML-RARA positive APL. The mutation positions were different from the hotspots reported in adult AML. DNMT3A mutations may have adverse impact on prognosis of children with AML.
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Affiliation(s)
- Weijing Li
- Hematology & Oncology Laboratory, Beijing Pediatric Research Institute
- Beijing Key Laboratory of Pediatric Hematology Oncology
- Key Laboratory of Major Diseases in Children
- National Key Discipline of Pediatrics, Ministry of Education
| | - Lei Cui
- Hematology & Oncology Laboratory, Beijing Pediatric Research Institute
- Beijing Key Laboratory of Pediatric Hematology Oncology
- Key Laboratory of Major Diseases in Children
- National Key Discipline of Pediatrics, Ministry of Education
| | - Chao Gao
- Beijing Key Laboratory of Pediatric Hematology Oncology
- Key Laboratory of Major Diseases in Children
- National Key Discipline of Pediatrics, Ministry of Education
- Hematology & Oncology Center, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, China
| | - Shuguang Liu
- Beijing Key Laboratory of Pediatric Hematology Oncology
- Key Laboratory of Major Diseases in Children
- National Key Discipline of Pediatrics, Ministry of Education
- Hematology & Oncology Center, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, China
| | - Xiaoxi Zhao
- Beijing Key Laboratory of Pediatric Hematology Oncology
- Key Laboratory of Major Diseases in Children
- National Key Discipline of Pediatrics, Ministry of Education
- Hematology & Oncology Center, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, China
| | - Ruidong Zhang
- Beijing Key Laboratory of Pediatric Hematology Oncology
- Key Laboratory of Major Diseases in Children
- National Key Discipline of Pediatrics, Ministry of Education
- Hematology & Oncology Center, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, China
| | - Huyong Zheng
- Beijing Key Laboratory of Pediatric Hematology Oncology
- Key Laboratory of Major Diseases in Children
- National Key Discipline of Pediatrics, Ministry of Education
- Hematology & Oncology Center, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, China
| | - Minyuan Wu
- Beijing Key Laboratory of Pediatric Hematology Oncology
- Key Laboratory of Major Diseases in Children
- National Key Discipline of Pediatrics, Ministry of Education
- Hematology & Oncology Center, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, China
| | - Zhigang Li
- Hematology & Oncology Laboratory, Beijing Pediatric Research Institute
- Beijing Key Laboratory of Pediatric Hematology Oncology
- Key Laboratory of Major Diseases in Children
- National Key Discipline of Pediatrics, Ministry of Education
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Xu Y, Li Y, Xu Q, Chen Y, Lv N, Jing Y, Dou L, Bo J, Hou G, Guo J, Wang X, Wang L, Li Y, Chen C, Yu L. Implications of mutational spectrum in myelodysplastic syndromes based on targeted next-generation sequencing. Oncotarget 2017; 8:82475-82490. [PMID: 29137279 PMCID: PMC5669905 DOI: 10.18632/oncotarget.19628] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2017] [Accepted: 06/30/2017] [Indexed: 02/01/2023] Open
Abstract
Myelodysplastic syndromes (MDS) are a group of myeloid hematological malignancies, with a high risk of progression to acute myeloid leukemia (AML). To explore the role of acquired mutations in MDS, 111 MDS-associated genes were screened using next-generation sequencing (NGS), in 125 patients. One or more mutations were detected in 84% of the patients. Some gene mutations are specific for MDS and were associated with disease subtypes, and the patterns of mutational pathways could be associated with progressive MDS. The patterns, frequencies and functional pathways of gene mutations are different, but somehow related, between MDS and AML. Multivariate analysis suggested that patients with ≥ 2 mutations had poor progression-free survival, while GATA1/GATA2, DNMT3A and KRAS/NRAS mutations were associated with poor overall survival. Based on a novel system combining IPSS-R and molecular markers, these MDS patients were further divided into 3 more accurate prognostic subgroups. A panel of 11 target genes was proposed for genetic profiling of MDS. The study offers new insights into the molecular signatures of MDS and the genetic consistency between MDS and AML. Furthermore, results indicate that MDS could be classified by mutation combinations to guide the administration of individualized therapeutic interventions.
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Affiliation(s)
- Yuanyuan Xu
- Department of Hematology and BMT center, Chinese PLA General Hospital, Beijing 100853, China.,Department of Hematology, Hainan Branch of Chinese PLA General Hospital, Sanya 572013, Hainan Province, China
| | - Yan Li
- Department of Hematology and BMT center, Chinese PLA General Hospital, Beijing 100853, China.,Department of Hematology, Hainan Branch of Chinese PLA General Hospital, Sanya 572013, Hainan Province, China
| | - Qingyu Xu
- Department of Hematology and BMT center, Chinese PLA General Hospital, Beijing 100853, China.,Medical school of Nankai University, Tianjin 300071, China
| | - Yuelong Chen
- Annoroad Gene Technology Co. Ltd, Beijing 100176, China
| | - Na Lv
- Department of Hematology and BMT center, Chinese PLA General Hospital, Beijing 100853, China
| | - Yu Jing
- Department of Hematology and BMT center, Chinese PLA General Hospital, Beijing 100853, China
| | - Liping Dou
- Department of Hematology and BMT center, Chinese PLA General Hospital, Beijing 100853, China
| | - Jian Bo
- Department of Hematology and BMT center, Chinese PLA General Hospital, Beijing 100853, China
| | - Guangyuan Hou
- Annoroad Gene Technology Co. Ltd, Beijing 100176, China
| | - Jing Guo
- Annoroad Gene Technology Co. Ltd, Beijing 100176, China
| | - Xiuli Wang
- Annoroad Gene Technology Co. Ltd, Beijing 100176, China
| | - Lili Wang
- Department of Hematology and BMT center, Chinese PLA General Hospital, Beijing 100853, China
| | - Yonghui Li
- Department of Hematology and BMT center, Chinese PLA General Hospital, Beijing 100853, China
| | | | - Li Yu
- Department of Hematology and BMT center, Chinese PLA General Hospital, Beijing 100853, China.,Department of Hematology, General Hospital of Shenzhen University, Shenzhen 518060, China
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12
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Yuan XQ, Zhang DY, Yan H, Yang YL, Zhu KW, Chen YH, Li X, Yin JY, Li XL, Zeng H, Chen XP. Evaluation of DNMT3A genetic polymorphisms as outcome predictors in AML patients. Oncotarget 2016; 7:60555-60574. [PMID: 27528035 PMCID: PMC5312402 DOI: 10.18632/oncotarget.11143] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2016] [Accepted: 07/26/2016] [Indexed: 12/15/2022] Open
Abstract
DNMT3A mutation is known as a recurrent event in acute myelogenous leukemia (AML) patients. However, association between DNMT3A genetic polymorphisms and AML patients' outcomes is unknown. DNMT3A 11 SNPs (rs11695471, rs2289195, rs734693, rs2276598, rs1465825, rs7590760, rs13401241, rs7581217, rs749131, rs41284843 and rs7560488) were genotyped in 344 diagnostic non-FAB-M3 AML patients from southern China. Patients underwent combined chemotherapy with cytarabine and anthracyclines. DNMT3A mRNA expression was analyzed in PBMCs from randomly selected AML patients. Multivariate analysis and combined genotype analysis showed that rs2276598 was associated with increased while rs11695471 and rs734693 were associated with decreased chemosensitivity (P<0.05), while rs11695471 (worse for OS), rs2289195 (favorable for OS and DFS) and rs2276598 (favorable for DFS) were significantly associated with disease prognosis (P<0.05). In conclusion, DNMT3A polymorphisms may be potential predictive markers for AML patients' outcomes, which might improve prognostic stratification of AML.
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Affiliation(s)
- Xiao-Qing Yuan
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha 410008, P. R. China
- Institute of Clinical Pharmacology, Central South University, Hunan Key Laboratory of Pharmacogenetics, Changsha 410078, P. R. China
| | - Dao-Yu Zhang
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha 410008, P. R. China
- Institute of Clinical Pharmacology, Central South University, Hunan Key Laboratory of Pharmacogenetics, Changsha 410078, P. R. China
| | - Han Yan
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha 410008, P. R. China
- Institute of Clinical Pharmacology, Central South University, Hunan Key Laboratory of Pharmacogenetics, Changsha 410078, P. R. China
| | - Yong-Long Yang
- Department of Pharmacy, Haikou People's Hospital and Affiliated Haikou Hospital of Xiangya Medical School, Central South University, Haikou 570311, P. R. China
| | - Ke-Wei Zhu
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha 410008, P. R. China
- Institute of Clinical Pharmacology, Central South University, Hunan Key Laboratory of Pharmacogenetics, Changsha 410078, P. R. China
| | - Yan-Hong Chen
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha 410008, P. R. China
- Institute of Clinical Pharmacology, Central South University, Hunan Key Laboratory of Pharmacogenetics, Changsha 410078, P. R. China
| | - Xi Li
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha 410008, P. R. China
- Institute of Clinical Pharmacology, Central South University, Hunan Key Laboratory of Pharmacogenetics, Changsha 410078, P. R. China
| | - Ji-Ye Yin
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha 410008, P. R. China
- Institute of Clinical Pharmacology, Central South University, Hunan Key Laboratory of Pharmacogenetics, Changsha 410078, P. R. China
| | - Xiao-Lin Li
- Department of Hematology, Xiangya Hospital, Central South University, Changsha 410008, P. R. China
| | - Hui Zeng
- Department of Hematology, Xiangya Hospital, Central South University, Changsha 410008, P. R. China
| | - Xiao-Ping Chen
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha 410008, P. R. China
- Institute of Clinical Pharmacology, Central South University, Hunan Key Laboratory of Pharmacogenetics, Changsha 410078, P. R. China
- Hunan Province Cooperation Innovation Center for Molecular Target New Drug Study, Hengyang 421001, P. R. China
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Prada-Arismendy J, Arroyave JC, Röthlisberger S. Molecular biomarkers in acute myeloid leukemia. Blood Rev 2016; 31:63-76. [PMID: 27639498 DOI: 10.1016/j.blre.2016.08.005] [Citation(s) in RCA: 181] [Impact Index Per Article: 22.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2015] [Revised: 08/24/2016] [Accepted: 08/26/2016] [Indexed: 12/11/2022]
Abstract
Acute myeloid leukemia (AML) is the most common acute leukemia in adults. The pathophysiology of this disease is just beginning to be understood at the cellular and molecular level, and currently cytogenetic markers are the most important for risk stratification and treatment of AML patients. However, with the advent of new technologies, the detection of other molecular markers such as point mutations and characterization of epigenetic and proteomic profiles, have begun to play an important role in how the disease is approached. Recent evidence shows that the identification of new AML biomarkers contributes to a better understanding of the molecular basis of the disease, is significantly useful in screening, diagnosis, prognosis and monitoring of AML, as well as the possibility of predicting each individual's response to treatment. This review summarizes the most relevant molecular (genetic, epigenetic, and protein) biomarkers associated with acute myeloid leukemia and discusses their clinical importance in terms of risk prediction, diagnosis and prognosis.
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MESH Headings
- Biomarkers, Tumor
- DNA Methylation
- Disease Susceptibility
- Epigenesis, Genetic
- Genetic Variation
- Humans
- Leukemia, Myeloid, Acute/diagnosis
- Leukemia, Myeloid, Acute/genetics
- Leukemia, Myeloid, Acute/metabolism
- Leukemia, Myeloid, Acute/mortality
- Mutation
- Prognosis
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Affiliation(s)
- Jeanette Prada-Arismendy
- Grupo de Investigación e Innovación Biomédica, Instituto Tecnológico Metropolitano, Medellín, Colombia.
| | - Johanna C Arroyave
- Grupo de Investigación e Innovación Biomédica, Instituto Tecnológico Metropolitano, Medellín, Colombia
| | - Sarah Röthlisberger
- Grupo de Investigación e Innovación Biomédica, Instituto Tecnológico Metropolitano, Medellín, Colombia
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Ahn JS, Kim HJ, Kim YK, Lee SS, Jung SH, Yang DH, Lee JJ, Kim NY, Choi SH, Jung CW, Jang JH, Kim HJ, Moon JH, Sohn SK, Won JH, Kim SH, Kim DDH. DNMT3A R882 Mutation with FLT3-ITD Positivity Is an Extremely Poor Prognostic Factor in Patients with Normal-Karyotype Acute Myeloid Leukemia after Allogeneic Hematopoietic Cell Transplantation. Biol Blood Marrow Transplant 2016; 22:61-70. [DOI: 10.1016/j.bbmt.2015.07.030] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2015] [Accepted: 07/28/2015] [Indexed: 12/17/2022]
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Lin P, Falini B. Acute Myeloid Leukemia With Recurrent Genetic Abnormalities Other Than Translocations. Am J Clin Pathol 2015; 144:19-28. [PMID: 26071459 DOI: 10.1309/ajcp97bjbevzeuin] [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] [Indexed: 10/25/2022] Open
Abstract
OBJECTIVES Session 2 of the workshop focused on cases of acute myeloid leukemia (AML) with gene mutations in the setting of a normal karyotype. METHODS Among 22 AML cases submitted, 14 had the NPM1 mutation, most also accompanied by mutations of other genes such as FLT3-ITD, DNMT3A, or, rarely, TP53; three cases had the heterozygous CEBPA mutation; and two cases had MYC amplification. RESULTS We explored prognostic implications of gene mutations such as DNMT3A, issues related to the classification of AML cases with the NPM1 mutation, and myelodysplasia-related changes arising from chronic myelomonocytic leukemia after a short latency interval. Disparate patterns of treatment response to targeted therapy using an FLT3 inhibitor, designated as cytotoxic or differentiation, and their genetic underpinnings were described. Finally, a minimal screening panel for gene mutations and the optimal approach for monitoring minimal residual disease were discussed. CONCLUSIONS In aggregate, this session highlighted the need for a refined molecular classification of AML as well as improved risk stratification based on systematic assessment for genetic alterations and their evolution over time.
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A tale of two siblings: two cases of AML arising from a single pre-leukemic DNMT3A mutant clone. Leukemia 2015; 29:2101-4. [PMID: 25748685 PMCID: PMC4687467 DOI: 10.1038/leu.2015.67] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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