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Lawrence EM, Cooray A, Kueh AJ, Pal M, Tai L, Garnham AL, Li-Wai-Suen CSN, Vanyai H, Gouil Q, Lancaster J, Callegari S, Whelan L, Lieschke E, Thomas A, Strasser A, Liao Y, Shi W, Wei AH, Herold MJ. Transcriptomic changes including p53 dysregulation prime DNMT3A mutant cells for transformation. EMBO Rep 2025:10.1038/s44319-025-00450-4. [PMID: 40307617 DOI: 10.1038/s44319-025-00450-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2024] [Revised: 04/02/2025] [Accepted: 04/04/2025] [Indexed: 05/02/2025] Open
Abstract
DNMT3A mutations are prevalent in haematologic malignancies. In our mouse model the murine homologue (R878H) of the human 'hotspot' R882H mutation is introduced into the mouse Dnmt3a locus. This results in globally reduced DNA methylation in all tissues. Mice with heterozygous R878H DNMT3A mutations develop γ-radiation induced thymic lymphoma more rapidly than control mice, suggesting a vulnerability to stress stimuli in Dnmt3aR878H/+ cells. In competitive transplantations, Dnmt3aR878H/+ Lin-Sca-1+Kit+ (LSK) haematopoietic stem/progenitor cells (HSPCs) have a competitive advantage over WT HSPCs, indicating a self-renewal phenotype at the expense of differentiation. RNA sequencing of Dnmt3aR878H/+ LSKs exposed to low dose γ-radiation shows downregulation of the p53 pathway compared to γ-irradiated WT LSKs. Accordingly, reduced PUMA expression is observed by flow cytometry in the bone marrow of γ-irradiated Dnmt3aR878H/+ mice due to impaired p53 signalling. These findings provide new insights into how DNMT3A mutations cause subtle changes in the transcriptome of LSK cells which contribute to their increased self-renewal and propensity for malignant transformation.
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Affiliation(s)
- Erin M Lawrence
- Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, University of Melbourne, Parkville, Victoria, Australia
| | - Amali Cooray
- Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, University of Melbourne, Parkville, Victoria, Australia
| | - Andrew J Kueh
- Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, University of Melbourne, Parkville, Victoria, Australia
- Olivia Newton John Cancer Research Institute, Heidelberg, Australia
- School of Cancer Medicine, La Trobe University, Bundoora, Victoria, Australia
| | - Martin Pal
- Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, University of Melbourne, Parkville, Victoria, Australia
- School of Dentistry and Medical Sciences, Charles Sturt University, Wagga Wagga, NSW, Australia
| | - Lin Tai
- Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Olivia Newton John Cancer Research Institute, Heidelberg, Australia
| | - Alexandra L Garnham
- Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, University of Melbourne, Parkville, Victoria, Australia
| | - Connie S N Li-Wai-Suen
- Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, University of Melbourne, Parkville, Victoria, Australia
| | - Hannah Vanyai
- Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, University of Melbourne, Parkville, Victoria, Australia
| | - Quentin Gouil
- Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, University of Melbourne, Parkville, Victoria, Australia
- Olivia Newton John Cancer Research Institute, Heidelberg, Australia
- School of Cancer Medicine, La Trobe University, Bundoora, Victoria, Australia
| | - James Lancaster
- Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, University of Melbourne, Parkville, Victoria, Australia
| | - Sylvie Callegari
- Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, University of Melbourne, Parkville, Victoria, Australia
| | - Lauren Whelan
- Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, University of Melbourne, Parkville, Victoria, Australia
| | - Elizabeth Lieschke
- Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, University of Melbourne, Parkville, Victoria, Australia
- Oncogene Biology Laboratory, Francis Crick Institute, London, UK
| | - Annabella Thomas
- Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, University of Melbourne, Parkville, Victoria, Australia
| | - Andreas Strasser
- Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, University of Melbourne, Parkville, Victoria, Australia
| | - Yang Liao
- Olivia Newton John Cancer Research Institute, Heidelberg, Australia
- School of Cancer Medicine, La Trobe University, Bundoora, Victoria, Australia
| | - Wei Shi
- Olivia Newton John Cancer Research Institute, Heidelberg, Australia
- School of Cancer Medicine, La Trobe University, Bundoora, Victoria, Australia
| | - Andrew H Wei
- Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, University of Melbourne, Parkville, Victoria, Australia
| | - Marco J Herold
- Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia.
- Department of Medical Biology, University of Melbourne, Parkville, Victoria, Australia.
- Olivia Newton John Cancer Research Institute, Heidelberg, Australia.
- School of Cancer Medicine, La Trobe University, Bundoora, Victoria, Australia.
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2
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Métois A, Bordeleau ME, Theret L, Hajmirza A, Moujaber O, Spinella JF, Chagraoui J, Mayotte N, Boivin I, Audemard É, Aubert L, Lisi V, Khakipoor B, Farah A, Bonneil É, Robert A, Lippens J, Moraitis A, Béliveau F, Feghaly A, Boucher G, Marcotte R, Gendron P, Thibault P, Lemieux S, Richard-Carpentier G, Lavallée VP, Hébert J, Roux PP, Sauvageau G. IL1RAP is an immunotherapeutic target for normal karyotype triple-mutated acute myeloid leukemia. Biomark Res 2025; 13:61. [PMID: 40229904 PMCID: PMC11995633 DOI: 10.1186/s40364-025-00769-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2024] [Accepted: 03/16/2025] [Indexed: 04/16/2025] Open
Abstract
BACKGROUND Surface antigens of potential clinical significance remain under-characterized in AML. The European Leukemia Network classifies normal karyotype AML (NK-AML) mutated for NPM1 (NPM1c) as a distinct entity associated with favorable outcomes if not associated with FLT3-ITD mutation. A subset of NPM1c NK-AML shows additional mutations in 2 genes: FLT3 (FLT3-ITD) and DNMT3 A. These leukemias, also referred to as NK triple mutated AML (NKt-AML), are particularly difficult to eradicate with current treatment options. Therefore, novel therapies are necessary that use proteins specifically expressed at the surface. METHODS In order to identify surface antigens for immunotherapy in NKt-AML, an extensive multi-omic analysis was conducted on primary AML samples. Surface proteome enrichment was performed on 100 primary AML samples, twelve of which were NKt-AML. Transcriptome analysis was carried out on the 691 primary AML samples, and single-cell RNA sequencing was conducted on 23 primary AML samples. RESULTS Herein, using multi-omics data from the Leucegene collection, we identify IL1RAP as a promising antigen for this AML subgroup. We demonstrate that IL1RAP is expressed at the surface of primitive AML cells reminiscent of leukemic stem cells in NKt-AML primary human AML specimens, while showing relatively low expression levels in normal bone marrow HSCs. Furthermore, results indicate that elevated IL1RAP expression associates with poor overall and relapse-free survival in the Leucegene cohort of AML patients and predicts nonresponse to hematopoietic stem cell transplantation. Finally, we show that IL1RAP protein is internalized following exposure to specific antibodies, suggesting that IL1RAP represents an interesting target for antibody-drug conjugate development in NKt-AML. CONCLUSIONS IL1RAP exhibits preferential expression within NKt-AML, correlating with diminished overall survival rates and diminished responsiveness to hematopoietic stem cell transplantation. Moreover, internalization of IL1RAP presents a promising avenue for immunotherapeutic intervention.
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Affiliation(s)
- Arnaud Métois
- The Leucegene Project at Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, Québec, H3 T 1 J4, Canada
| | - Marie-Eve Bordeleau
- The Leucegene Project at Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, Québec, H3 T 1 J4, Canada
| | - Louis Theret
- The Leucegene Project at Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, Québec, H3 T 1 J4, Canada
| | - Azadeh Hajmirza
- The Leucegene Project at Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, Québec, H3 T 1 J4, Canada
| | - Ossama Moujaber
- The Leucegene Project at Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, Québec, H3 T 1 J4, Canada
| | - Jean-François Spinella
- The Leucegene Project at Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, Québec, H3 T 1 J4, Canada
| | - Jalila Chagraoui
- The Leucegene Project at Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, Québec, H3 T 1 J4, Canada
| | - Nadine Mayotte
- The Leucegene Project at Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, Québec, H3 T 1 J4, Canada
| | - Isabel Boivin
- The Leucegene Project at Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, Québec, H3 T 1 J4, Canada
| | - Éric Audemard
- The Leucegene Project at Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, Québec, H3 T 1 J4, Canada
| | - Léo Aubert
- The Leucegene Project at Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, Québec, H3 T 1 J4, Canada
| | - Véronique Lisi
- The Leucegene Project at Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, Québec, H3 T 1 J4, Canada
- Centre Hospitalier Universitaire Sainte-Justine Research Center, Montréal, Québec, H3 T 1 C5, Canada
| | - Banafsheh Khakipoor
- The Leucegene Project at Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, Québec, H3 T 1 J4, Canada
- Centre Hospitalier Universitaire Sainte-Justine Research Center, Montréal, Québec, H3 T 1 C5, Canada
| | - Azer Farah
- The Leucegene Project at Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, Québec, H3 T 1 J4, Canada
- Centre Hospitalier Universitaire Sainte-Justine Research Center, Montréal, Québec, H3 T 1 C5, Canada
| | - Éric Bonneil
- The Leucegene Project at Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, Québec, H3 T 1 J4, Canada
| | - Alma Robert
- Medical Devices Research Center, National Research Council Canada, Montréal, Québec, H4P 2R2, Canada
| | - Julie Lippens
- Medical Devices Research Center, National Research Council Canada, Montréal, Québec, H4P 2R2, Canada
| | - Anna Moraitis
- Medical Devices Research Center, National Research Council Canada, Montréal, Québec, H4P 2R2, Canada
| | - François Béliveau
- The Leucegene Project at Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, Québec, H3 T 1 J4, Canada
- Quebec Leukemia Cell Bank, Maisonneuve-Rosemont Hospital, Montréal, Québec, H1 T 2M4, Canada
| | - Albert Feghaly
- The Leucegene Project at Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, Québec, H3 T 1 J4, Canada
| | - Geneviève Boucher
- The Leucegene Project at Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, Québec, H3 T 1 J4, Canada
| | - Richard Marcotte
- Human Health Therapeutic Research Center National Research Council Canada, Montréal, Québec, H4P 2R2, Canada
| | - Patrick Gendron
- The Leucegene Project at Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, Québec, H3 T 1 J4, Canada
| | - Pierre Thibault
- The Leucegene Project at Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, Québec, H3 T 1 J4, Canada
- Department of Chemistry, Faculty of Arts and Science, Université de Montréal, Montréal, Québec, H3 T 1 J4, Canada
| | - Sébastien Lemieux
- The Leucegene Project at Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, Québec, H3 T 1 J4, Canada
- Department of Biochemistry and Molecular Medicine, Faculty of Medicine, Université de Montréal, Montréal, Québec, H3 T 1 J4, Canada
| | - Guillaume Richard-Carpentier
- The Leucegene Project at Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, Québec, H3 T 1 J4, Canada
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, M5G 2 C1, Canada
- Department of Medicine, Division of Medical Oncology and Hematology, Temerty Faculty of Medicine, University of Toronto, Toronto, ON, M5S 1 A8, Canada
| | - Vincent-Philippe Lavallée
- The Leucegene Project at Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, Québec, H3 T 1 J4, Canada
- Centre Hospitalier Universitaire Sainte-Justine Research Center, Montréal, Québec, H3 T 1 C5, Canada
- Department of Pediatrics, Faculty of Medicine, Université de Montréal, Montréal, Québec, H3 T 1 J4, Canada
- Hematology and Oncology Division, Centre Hospitalier Universitaire Sainte-Justine, Montréal, Québec, H3 T 1 C5, Canada
| | - Josée Hébert
- The Leucegene Project at Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, Québec, H3 T 1 J4, Canada
- Quebec Leukemia Cell Bank, Maisonneuve-Rosemont Hospital, Montréal, Québec, H1 T 2M4, Canada
- Department of Medicine, Faculty of Medicine, Université de Montréal, Montréal, Québec, H3 T 1 J4, Canada
- Division of Hematology-Oncology, Maisonneuve-Rosemont Hospital, Montréal, Québec, H1 T 2M4, Canada
| | - Philippe P Roux
- The Leucegene Project at Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, Québec, H3 T 1 J4, Canada
- Department of Pathology and Cell Biology, Faculty of Medicine, Université de Montréal, Montréal, Québec, H3 T 1 J4, Canada
| | - Guy Sauvageau
- The Leucegene Project at Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, Québec, H3 T 1 J4, Canada.
- Quebec Leukemia Cell Bank, Maisonneuve-Rosemont Hospital, Montréal, Québec, H1 T 2M4, Canada.
- Department of Medicine, Faculty of Medicine, Université de Montréal, Montréal, Québec, H3 T 1 J4, Canada.
- Division of Hematology-Oncology, Maisonneuve-Rosemont Hospital, Montréal, Québec, H1 T 2M4, Canada.
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3
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Kim DJ. The Role of the DNA Methyltransferase Family and the Therapeutic Potential of DNMT Inhibitors in Tumor Treatment. Curr Oncol 2025; 32:88. [PMID: 39996888 PMCID: PMC11854558 DOI: 10.3390/curroncol32020088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2025] [Revised: 02/02/2025] [Accepted: 02/03/2025] [Indexed: 02/26/2025] Open
Abstract
Members of the DNA methyltransferase (DNMT) family have been recognized as major epigenetic regulators of altered gene expression during tumor development. They establish and maintain DNA methylation of the CpG island of promoter and non-CpG region of the genome. The abnormal methylation status of tumor suppressor genes (TSGs) has been associated with tumorigenesis, leading to genomic instability, improper gene silence, and immune evasion. DNMT1 helps preserve methylation patterns during DNA replication, whereas the DNMT3 family is responsible for de novo methylation, creating new methylation patterns. Altered DNA methylation significantly supports tumor growth by changing gene expression patterns. FDA-approved DNMT inhibitors reverse hypermethylation-induced gene repression and improve therapeutic outcomes for cancer. Recent studies indicate that combining DNMT inhibitors with chemotherapies and immunotherapies can have synergistic effects, especially in aggressive metastatic tumors. Improving the treatment schedules, increasing isoform specificity, reducing toxicity, and utilizing genome-wide analyses of CRISPR-based editing to create personalized epigenetic therapies tailored to individual patient needs are promising strategies for enhancing therapeutic outcomes. This review discusses the interaction between DNMT regulators and DNMT1, its binding partners, the connection between DNA methylation and tumors, how these processes contribute to tumor development, and DNMT inhibitors' advancements and pharmacological properties.
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Affiliation(s)
- Dae Joong Kim
- Department of Microbiology, Immunology & Cancer Biology, The University of Virginia, Charlottesville, VA 20908, USA
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4
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Jiang M, Zhou X, Feng Y, Ding P, Li J, Lu D, Qin J, Bai Y, Wang A, Xia C, Wang J, Yan X, Ma Z, Zhang R. DNMT3a promotes LUAD cell proliferation and metastasis by activating the HDAC7 signalling pathway. Int J Biol Sci 2025; 21:1585-1602. [PMID: 39990668 PMCID: PMC11844290 DOI: 10.7150/ijbs.96509] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2024] [Accepted: 12/28/2024] [Indexed: 02/25/2025] Open
Abstract
Background: Changes in DNA methylation patterns, in which DNA methyltransferases such as DNA methyltransferase 3 alpha (DNMT3a) play important roles, are closely related to the occurrence and development of tumours. However, the role and mechanism of DNMT3a in lung adenocarcinoma (LUAD) remain unknown. The aim of this study was to investigate the potential effect of DNMT3a on LUAD cell proliferation and metastasis and explore the underlying molecular mechanism. Methods: Immunohistochemistry and Kaplan‒Meier survival analysis were used to investigate the relationship between the expression of DNMT3a and histone deacetylase 7 (HDAC7) and the survival, prognosis and clinicopathological features of patients. The effects of DNMT3a on the proliferation and metastasis of LUAD cells were studied in vivo and in vitro. Recombinant lentivirus-mediated in vitro gene overexpression or knockdown, western blotting, Quantitative real-time polymerase chain reaction (qRT‒PCR) and other methods were used in this study to elucidate the potential molecular mechanisms by which DNMT3a promotes LUAD cell proliferation and metastasis. Results: High expression of DNMT3a or HDAC7 was positively correlated with poor prognosis, high AJCC 8th edition stage, and poor tumour differentiation in LUAD patients. LUAD patients with DNMT3a/HDAC7 co-low expression exhibited the worst prognosis. Upregulation of DNMT3a can promote LUAD cell proliferation and metastasis by upregulating HDAC7 and further activating the expression of downstream mediators ZEB1 and c-Myc. Conversely, overexpression of HDAC7 reversed the attenuation of tumour growth and metastasis and the suppression of c-Myc and ZEB1 expression mediated by downregulation of DNMT3a, further indicating the existence of positive feedback regulation between DNMT3a and HDAC7 in LUAD. Conclusion: Our findings first confirmed that DNMT3a acts as a tumour promoter inducing malignant progression of LUAD by upregulating HDAC7 and further inducing upregulation of ZEB1 and c-Myc. Targeting DNMT3a along with HDAC7 might be a promising therapeutic strategy for LUAD.
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Affiliation(s)
- Menglong Jiang
- Department of Thoracic Surgery, the First Affiliated Hospital of Anhui Medical University, Hefei 230022, China
| | - Xin Zhou
- Department of Medical Oncology, Senior Department of Oncology, the Fifth Medical Center, Chinese PLA General Hospital, Beijing 100853, China
- The Second Medical Center, Chinese PLA General Hospital, Beijing 100853, China
| | - Yingtong Feng
- Department of Cardiothoracic Surgery, the Affiliated Huaihai Hospital of Xuzhou Medical University/the 71st Group Army Hospital of PLA, Xuzhou 221004, China
| | - Peng Ding
- Department of Thoracic Surgery, Tangdu Hospital, the Fourth Military Medical University, Xi'an 710038, China
| | - Jinfeng Li
- Department of Medical Oncology, Senior Department of Oncology, the Fifth Medical Center, Chinese PLA General Hospital, Beijing 100853, China
| | - Di Lu
- Department of Medical Oncology, Senior Department of Oncology, the Fifth Medical Center, Chinese PLA General Hospital, Beijing 100853, China
| | - Jiapei Qin
- Department of Medical Oncology, Senior Department of Oncology, the Fifth Medical Center, Chinese PLA General Hospital, Beijing 100853, China
| | - Yibing Bai
- Department of Medical Oncology, Senior Department of Oncology, the Fifth Medical Center, Chinese PLA General Hospital, Beijing 100853, China
| | - An Wang
- Department of Medical Oncology, Senior Department of Oncology, the Fifth Medical Center, Chinese PLA General Hospital, Beijing 100853, China
| | - Chunfang Xia
- Department of Medical Oncology, Senior Department of Oncology, the Fifth Medical Center, Chinese PLA General Hospital, Beijing 100853, China
| | - Jinliang Wang
- Department of Medical Oncology, Senior Department of Oncology, the Fifth Medical Center, Chinese PLA General Hospital, Beijing 100853, China
| | - Xiaolong Yan
- Department of Thoracic Surgery, Tangdu Hospital, the Fourth Military Medical University, Xi'an 710038, China
| | - Zhiqiang Ma
- Department of Medical Oncology, Senior Department of Oncology, the Fifth Medical Center, Chinese PLA General Hospital, Beijing 100853, China
| | - Renquan Zhang
- Department of Thoracic Surgery, the First Affiliated Hospital of Anhui Medical University, Hefei 230022, China
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5
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Chen L, Zeng P, Tang H, Chen G, Xie J, Yang X, Lei X. Routes and molecular mechanisms of central nervous system involvement in acute myeloid leukemia (Review). Oncol Rep 2024; 52:146. [PMID: 39219268 PMCID: PMC11378150 DOI: 10.3892/or.2024.8805] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2024] [Accepted: 08/08/2024] [Indexed: 09/04/2024] Open
Abstract
Acute myeloid leukemia (AML) is a predominant form of leukemia. Central nervous system (CNS) involvement complicates its diagnosis due to limited diagnostic tools, as well as its treatment due to inadequate therapeutic methodologies and poor prognosis. Furthermore, its incidence rate is unclear. The mechanisms of AML cell mobilization from the bone marrow (BM) to the CNS are not fully elucidated, and the molecular factors contributing to CNS infiltration are insufficiently recognized. The present review aimed to enhance the understanding of CNS involvement of AML and its impact on CNS. The latest research on the pathways and mechanisms facilitating AML cells to escape the BM and infiltrate the CNS was reviewed. Additionally, novel therapeutic strategies targeting specific molecules and genes for treating CNS involvement in AML were examined.
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Affiliation(s)
- Liucui Chen
- School of Pharmaceutical Science, Hengyang Medical School, University of South China, Hengyang, Hunan 421001, P.R. China
| | - Piaorong Zeng
- Department of Hematology, The First Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang, Hunan 421001, P.R. China
| | - Huifang Tang
- Hunan Provincial Key Laboratory of Multi‑omics and Artificial Intelligence of Cardiovascular Diseases, University of South China, Hengyang, Hunan 421001, P.R. China
| | - Gang Chen
- Department of Neurology, The Second Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang, Hunan 421001, P.R. China
| | - Juan Xie
- School of Pharmaceutical Science, Hengyang Medical School, University of South China, Hengyang, Hunan 421001, P.R. China
| | - Xiaoyan Yang
- School of Pharmaceutical Science, Hengyang Medical School, University of South China, Hengyang, Hunan 421001, P.R. China
| | - Xiaoyong Lei
- School of Pharmaceutical Science, Hengyang Medical School, University of South China, Hengyang, Hunan 421001, P.R. China
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6
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Tan WY, Nagabhyrava S, Ang-Olson O, Das P, Ladel L, Sailo B, He L, Sharma A, Ahuja N. Translation of Epigenetics in Cell-Free DNA Liquid Biopsy Technology and Precision Oncology. Curr Issues Mol Biol 2024; 46:6533-6565. [PMID: 39057032 PMCID: PMC11276574 DOI: 10.3390/cimb46070390] [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: 05/27/2024] [Revised: 06/21/2024] [Accepted: 06/23/2024] [Indexed: 07/28/2024] Open
Abstract
Technological advancements in cell-free DNA (cfDNA) liquid biopsy have triggered exponential growth in numerous clinical applications. While cfDNA-based liquid biopsy has made significant strides in personalizing cancer treatment, the exploration and translation of epigenetics in liquid biopsy to clinical practice is still nascent. This comprehensive review seeks to provide a broad yet in-depth narrative of the present status of epigenetics in cfDNA liquid biopsy and its associated challenges. It highlights the potential of epigenetics in cfDNA liquid biopsy technologies with the hopes of enhancing its clinical translation. The momentum of cfDNA liquid biopsy technologies in recent years has propelled epigenetics to the forefront of molecular biology. We have only begun to reveal the true potential of epigenetics in both our understanding of disease and leveraging epigenetics in the diagnostic and therapeutic domains. Recent clinical applications of epigenetics-based cfDNA liquid biopsy revolve around DNA methylation in screening and early cancer detection, leading to the development of multi-cancer early detection tests and the capability to pinpoint tissues of origin. The clinical application of epigenetics in cfDNA liquid biopsy in minimal residual disease, monitoring, and surveillance are at their initial stages. A notable advancement in fragmentation patterns analysis has created a new avenue for epigenetic biomarkers. However, the widespread application of cfDNA liquid biopsy has many challenges, including biomarker sensitivity, specificity, logistics including infrastructure and personnel, data processing, handling, results interpretation, accessibility, and cost effectiveness. Exploring and translating epigenetics in cfDNA liquid biopsy technology can transform our understanding and perception of cancer prevention and management. cfDNA liquid biopsy has great potential in precision oncology to revolutionize conventional ways of early cancer detection, monitoring residual disease, treatment response, surveillance, and drug development. Adapting the implementation of liquid biopsy workflow to the local policy worldwide and developing point-of-care testing holds great potential to overcome global cancer disparity and improve cancer outcomes.
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Affiliation(s)
- Wan Ying Tan
- Department of Surgery, Yale School of Medicine, New Haven, CT 06520-8000, USA; (W.Y.T.); (P.D.); (L.L.); (B.S.); (L.H.)
- Department of Internal Medicine, Norwalk Hospital, Norwalk, CT 06850, USA
- Hematology & Oncology, Neag Comprehensive Cancer Center, UConn Health, Farmington, CT 06030, USA
| | | | - Olivia Ang-Olson
- Department of Surgery, Yale School of Medicine, New Haven, CT 06520-8000, USA; (W.Y.T.); (P.D.); (L.L.); (B.S.); (L.H.)
| | - Paromita Das
- Department of Surgery, Yale School of Medicine, New Haven, CT 06520-8000, USA; (W.Y.T.); (P.D.); (L.L.); (B.S.); (L.H.)
| | - Luisa Ladel
- Department of Surgery, Yale School of Medicine, New Haven, CT 06520-8000, USA; (W.Y.T.); (P.D.); (L.L.); (B.S.); (L.H.)
- Department of Internal Medicine, Norwalk Hospital, Norwalk, CT 06850, USA
| | - Bethsebie Sailo
- Department of Surgery, Yale School of Medicine, New Haven, CT 06520-8000, USA; (W.Y.T.); (P.D.); (L.L.); (B.S.); (L.H.)
| | - Linda He
- Department of Surgery, Yale School of Medicine, New Haven, CT 06520-8000, USA; (W.Y.T.); (P.D.); (L.L.); (B.S.); (L.H.)
| | - Anup Sharma
- Department of Surgery, Yale School of Medicine, New Haven, CT 06520-8000, USA; (W.Y.T.); (P.D.); (L.L.); (B.S.); (L.H.)
| | - Nita Ahuja
- Department of Surgery, Yale School of Medicine, New Haven, CT 06520-8000, USA; (W.Y.T.); (P.D.); (L.L.); (B.S.); (L.H.)
- Department of Pathology, Yale School of Medicine, New Haven, CT 06520-8000, USA
- Biological and Biomedical Sciences Program (BBS), Yale University, New Haven, CT 06520-8084, USA
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7
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Zhu C, Hao Z, Liu D. Reshaping the Landscape of the Genome: Toolkits for Precise DNA Methylation Manipulation and Beyond. JACS AU 2024; 4:40-57. [PMID: 38274248 PMCID: PMC10806789 DOI: 10.1021/jacsau.3c00671] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 11/26/2023] [Accepted: 12/01/2023] [Indexed: 01/27/2024]
Abstract
DNA methylation plays a pivotal role in various biological processes and is highly related to multiple diseases. The exact functions of DNA methylation are still puzzling due to its uneven distribution, dynamic conversion, and complex interactions with other substances. Current methods such as chemical- and enzyme-based sequencing techniques have enabled us to pinpoint DNA methylation at single-base resolution, which necessitated the manipulation of DNA methylation at comparable resolution to precisely illustrate the correlations and causal relationships between the functions of DNA methylation and its spatiotemporal patterns. Here a perspective on the past, recent process, and future of precise DNA methylation tools is provided. Specifically, genome-wide and site-specific manipulation of DNA methylation methods is discussed, with an emphasis on their principles, limitations, applications, and future developmental directions.
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Affiliation(s)
- Chenyou Zhu
- Engineering
Research Center of Advanced Rare Earth Materials, Ministry of Education,
Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Ziyang Hao
- School
of Pharmaceutical Sciences, Capital Medical
University, Beijing, 100069, PR China
| | - Dongsheng Liu
- Engineering
Research Center of Advanced Rare Earth Materials, Ministry of Education,
Department of Chemistry, Tsinghua University, Beijing 100084, China
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8
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Feng Q, Duan H, Zhou X, Wang Y, Zhang J, Zhang H, Chen G, Bao X. DNA Methyltransferase 3A: A Significant Target for the Discovery of Inhibitors as Potent Anticancer Drugs. Mini Rev Med Chem 2024; 24:507-520. [PMID: 37642180 DOI: 10.2174/1389557523666230825100246] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Revised: 06/27/2023] [Accepted: 07/18/2023] [Indexed: 08/31/2023]
Abstract
DNA methyltransferase (DNMT) is a conserved family of Cytosine methylases, which plays a crucial role in the regulation of Epigenetics. They have been considered promising therapeutic targets for cancer. Among the DNMT family, mutations in the DNMT3A subtype are particularly important in hematologic malignancies. The development of specific DNMT3A subtype inhibitors to validate the therapeutic potential of DNMT3A in certain diseases is a significant task. In this review, we summarized the small molecule inhibitors of DNMT3A discovered in recent years and their inhibitory activities, and classified them based on their inhibitory mechanisms.
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Affiliation(s)
- Qixun Feng
- Key Laboratory of Structure-Based Drugs Design and Discovery of Ministry of Education, Shenyang Pharmaceutical University, Shenyang, China
| | - Honggao Duan
- Key Laboratory of Structure-Based Drugs Design and Discovery of Ministry of Education, Shenyang Pharmaceutical University, Shenyang, China
| | - Xinglong Zhou
- Key Laboratory of Structure-Based Drugs Design and Discovery of Ministry of Education, Shenyang Pharmaceutical University, Shenyang, China
| | - Yuning Wang
- Key Laboratory of Structure-Based Drugs Design and Discovery of Ministry of Education, Shenyang Pharmaceutical University, Shenyang, China
| | - Jinda Zhang
- Key Laboratory of Structure-Based Drugs Design and Discovery of Ministry of Education, Shenyang Pharmaceutical University, Shenyang, China
| | - Haoge Zhang
- Key Laboratory of Structure-Based Drugs Design and Discovery of Ministry of Education, Shenyang Pharmaceutical University, Shenyang, China
| | - Guoliang Chen
- Key Laboratory of Structure-Based Drugs Design and Discovery of Ministry of Education, Shenyang Pharmaceutical University, Shenyang, China
| | - Xuefei Bao
- Key Laboratory of Structure-Based Drugs Design and Discovery of Ministry of Education, Shenyang Pharmaceutical University, Shenyang, China
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9
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Qin Y, Shen K, Liu T, Ma H. Prognostic value of IDH2R140 and IDH2R172 mutations in patients with acute myeloid leukemia: a systematic review and meta-analysis. BMC Cancer 2023; 23:527. [PMID: 37291515 DOI: 10.1186/s12885-023-11034-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2023] [Accepted: 05/31/2023] [Indexed: 06/10/2023] Open
Abstract
BACKGROUND Whether isocitrate dehydrogenase 2 (IDH2) R140 and R172 gene mutations affect the prognosis of patients with acute myeloid leukemia (AML) is controversial. Here, we performed a meta-analysis to assess their prognostic value. METHODS Eligible studies were systematically searched from PubMed, Embase, the Cochrane Library and Chinese databases up to June 1, 2022. We extracted the hazard ratios (HRs) and their 95% confidence intervals (CIs) of overall survival (OS) and progression-free survival (PFS) to carry out a meta-analysis by a fixed effect model or random effect model according to the heterogeneity between studies. RESULTS A total of 12725 AML patients from 11 studies were included in this meta-analysis, of which 1111 (8.7%) and 305 (2.4%) had IDH2R140 and IDH2R172 mutations, respectively. The results revealed that both IDH2R140 and IDH2R172 mutations had no significant effect on OS (IDH2R140: HR = 0.92, 95% CI: 0.77-1.10, P = 0.365; IDH2R172: HR = 0.91, 95% CI: 0.65-1.28, P = 0.590) or PFS (IDH2R140: HR = 1.02, 95% CI: 0.75-1.40, P = 0.881; IDH2R172: HR = 1.31, 95% CI: 0.78-2.22, P = 0.306) in AML patients. Subgroup analysis of AML patients with IDH2R140 mutation revealed that studies from the USA (HR = 0.60, 95% CI: 0.41-0.89, P = 0.010) and ≤ 50 years old (HR = 0.63, 95% CI: 0.50-0.80, P = 0.000) had longer OS. However, studies from Sweden (HR = 1.94, 95% CI: 1.07-3.53, P = 0.030) had shorter OS. Meanwhile, subgroup analysis of AML patients with IDH2R172 mutation showed that studies from Germany/Austria (HR = 0.76, 95% CI: 0.61-0.94, P = 0.012) and from Sweden (HR = 0.22, 95% CI: 0.07-0.74, P = 0.014) had longer OS, whereas studies from the UK (HR = 1.49, 95% CI: 1.13-1.96, P = 0.005) and studies with nonmultivariate analysis of data type (HR = 1.35, 95% CI: 1.06-1.73, P = 0.014) had shorter OS. In addition, our study also found that patients with IDH2R140 mutation had significantly longer OS (HR = 0.61, 95% CI: 0.39-0.96, P = 0.032) and PFS (HR = 0.31, 95% CI: 0.18-0.52, P = 0.021) than patients with IDH2R172 mutation, despite some degree of heterogeneity. CONCLUSIONS This meta-analysis demonstrates that IDH2R140 mutation improves OS in younger AML patients and that the prognostic value of IDH2R172 mutation is significantly heterogeneous. Differences in region and data type have a significant impact on the prognosis of AML patients with IDH2R140 and/or IDH2R172 mutations. Additionally, AML patients with IDH2R140 mutation have a better prognosis than those with IDH2R172 mutations, albeit with some degree of heterogeneity.
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Affiliation(s)
- Yao Qin
- Department of Hematology, West China Hospital, Sichuan University, No. 37 Guo Xue Xiang, Wuhou District, Chengdu, 610041, Sichuan, China
| | - Kai Shen
- Department of Hematology, West China Hospital, Sichuan University, No. 37 Guo Xue Xiang, Wuhou District, Chengdu, 610041, Sichuan, China
| | - Ting Liu
- Department of Hematology, West China Hospital, Sichuan University, No. 37 Guo Xue Xiang, Wuhou District, Chengdu, 610041, Sichuan, China
| | - Hongbing Ma
- Department of Hematology, West China Hospital, Sichuan University, No. 37 Guo Xue Xiang, Wuhou District, Chengdu, 610041, Sichuan, China.
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10
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Zhang J, Yang T, Han M, Wang X, Yang W, Guo N, Ren Y, Cui W, Li S, Zhao Y, Zhai X, Jia L, Yang J, Wu C, Wang L. Gain-of-function mutations in the catalytic domain of DOT1L promote lung cancer malignant phenotypes via the MAPK/ERK signaling pathway. SCIENCE ADVANCES 2023; 9:eadc9273. [PMID: 37256945 PMCID: PMC10413674 DOI: 10.1126/sciadv.adc9273] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Accepted: 04/25/2023] [Indexed: 06/02/2023]
Abstract
Lung cancer is a lethal malignancy lacking effective therapies. Emerging evidence suggests that epigenetic enzyme mutations are closely related to the malignant phenotype of lung cancer. Here, we identified a series of gain-of-function mutations in the histone methyltransferase DOT1L. The strongest of them is R231Q, located in the catalytic DOT domain. R231Q can enhance the substrate binding ability of DOT1L. Moreover, R231Q promotes cell growth and drug resistance of lung cancer cells in vitro and in vivo. Mechanistic studies also revealed that the R231Q mutant specifically activates the MAPK/ERK signaling pathway by enriching H3K79me2 on the RAF1 promoter and epigenetically regulating the expression of downstream targets. The combination of a DOT1L inhibitor (SGC0946) and a MAPK/ERK axis inhibitor (binimetinib) can effectively reverse the R231Q-induced phenomena. Our results reveal gain-of-function mutations in an epigenetic enzyme and provide promising insights for the precise treatment of lung cancer patients.
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Affiliation(s)
- Jiayu Zhang
- Department of Pharmacology, Shenyang Pharmaceutical University, Shenyang 110016, China
- Benxi Institute of Pharmaceutical Research, Shenyang Pharmaceutical University, Benxi 117004, China
| | - Ting Yang
- Department of Pharmacology, Shenyang Pharmaceutical University, Shenyang 110016, China
- Benxi Institute of Pharmaceutical Research, Shenyang Pharmaceutical University, Benxi 117004, China
| | - Mei Han
- Department of Pharmacology, Shenyang Pharmaceutical University, Shenyang 110016, China
- Benxi Institute of Pharmaceutical Research, Shenyang Pharmaceutical University, Benxi 117004, China
| | - Xiaoxuan Wang
- Department of Pharmacology, Shenyang Pharmaceutical University, Shenyang 110016, China
- Benxi Institute of Pharmaceutical Research, Shenyang Pharmaceutical University, Benxi 117004, China
| | - Weiming Yang
- Department of Pharmacology, Shenyang Pharmaceutical University, Shenyang 110016, China
- Benxi Institute of Pharmaceutical Research, Shenyang Pharmaceutical University, Benxi 117004, China
| | - Ning Guo
- Department of Pharmacology, Shenyang Pharmaceutical University, Shenyang 110016, China
- Benxi Institute of Pharmaceutical Research, Shenyang Pharmaceutical University, Benxi 117004, China
| | - Yong Ren
- Department of Pathology, General Hospital of Central Theater Command of People's Liberation Army, Wuhan 430070, China
| | - Wei Cui
- Department of Pharmacology, Shenyang Pharmaceutical University, Shenyang 110016, China
| | - Shangxiao Li
- Department of Biochemistry and Molecular Biology, Shenyang Pharmaceutical University, Shenyang 110016, China
| | - Yongshan Zhao
- Department of Biochemistry and Molecular Biology, Shenyang Pharmaceutical University, Shenyang 110016, China
| | - Xin Zhai
- Key Laboratory of Structure-Based Drug Design and Discovery, Ministry of Education, Shenyang Pharmaceutical University, Shenyang 110016, China
| | - Lina Jia
- Department of Pharmacology, Shenyang Pharmaceutical University, Shenyang 110016, China
| | - Jingyu Yang
- Department of Pharmacology, Shenyang Pharmaceutical University, Shenyang 110016, China
| | - Chunfu Wu
- Department of Pharmacology, Shenyang Pharmaceutical University, Shenyang 110016, China
| | - Lihui Wang
- Department of Pharmacology, Shenyang Pharmaceutical University, Shenyang 110016, China
- Benxi Institute of Pharmaceutical Research, Shenyang Pharmaceutical University, Benxi 117004, China
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11
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Chu X, Zhong L, Dan W, Wang X, Zhang Z, Liu Z, Lu Y, Shao X, Zhou Z, Chen S, Liu B. DNMT3A R882H mutation promotes acute leukemic cell survival by regulating glycolysis through the NRF2/NQO1 axis. Cell Signal 2023; 105:110626. [PMID: 36758683 DOI: 10.1016/j.cellsig.2023.110626] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2022] [Revised: 01/30/2023] [Accepted: 02/03/2023] [Indexed: 02/09/2023]
Abstract
BACKGROUND Studies have confirmed that acute myeloid leukemia (AML) cells with DNA methyltransferase 3A Arg882His (DNMT3A R882H) mutation show an increased proliferation capability. However, the associated mechanism is still unclear. Glycolysis is involved in regulating malignant proliferation of cancer cell. Hence, we analyzed whether the DNMT3A R882H mutation interferes with glycolysis and thereby influences AML cell proliferation. METHODS We generated AML cell line carrying a DNMT3A-R882H mutation and compared it with the wild type (DNMT3A-WT) with regard to glycolysis regulation. Moreover, we analyzed the cell line's proliferation and apoptosis by a CCK-8 assay, western blotting, and flow cytometry. The role of NRF2/NQO1 signaling in regulating glycolysis was investigated by NRF2-knockdown and Brusatol (specific inhibitor of NRF2) treatment. RESULTS DNMT3A R882H cells had a higher glucose transport capacity compared to WT cells and their viability could be reduced by glucose deprivation. Moreover, daunorubicin had a slight inhibitory effect on glycolysis while glycolysis inhibition re-sensitized mutant cells to daunorubicin. Obviously, DNMT3A R882H mutation activated the NRF2/NQO1 pathway and enhanced the glycolytic activity in mutant cells. CONCLUSION Taken together, these results suggest a novel mechanism by which a DNMT3A R882H mutation promotes glycolysis via activation of NRF2/NQO1 pathway. A parallel glycolysis inhibition adds to the anticancer effects of daunorubicin which might lead to a novel therapeutic approach for the treatment of AML patients carrying a DNMT3A R882H mutation.
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Affiliation(s)
- Xuan Chu
- Central Laboratory of Yong-Chuan Hospital, Chongqing Medical University, Chongqing 402160, China
| | - Liang Zhong
- Key Laboratory of Laboratory Medical Diagnostics, Ministry of Education, Department of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, China.
| | - Wenran Dan
- Central Laboratory of Yong-Chuan Hospital, Chongqing Medical University, Chongqing 402160, China
| | - Xiao Wang
- Central Laboratory of Yong-Chuan Hospital, Chongqing Medical University, Chongqing 402160, China
| | - Zhonghui Zhang
- Central Laboratory of Yong-Chuan Hospital, Chongqing Medical University, Chongqing 402160, China
| | - Zhenyan Liu
- Central Laboratory of Yong-Chuan Hospital, Chongqing Medical University, Chongqing 402160, China
| | - Yang Lu
- Central Laboratory of Yong-Chuan Hospital, Chongqing Medical University, Chongqing 402160, China
| | - Xin Shao
- Central Laboratory of Yong-Chuan Hospital, Chongqing Medical University, Chongqing 402160, China
| | - Ziwei Zhou
- Central Laboratory of Yong-Chuan Hospital, Chongqing Medical University, Chongqing 402160, China
| | - Shuyu Chen
- Central Laboratory of Yong-Chuan Hospital, Chongqing Medical University, Chongqing 402160, China
| | - Beizhong Liu
- Central Laboratory of Yong-Chuan Hospital, Chongqing Medical University, Chongqing 402160, China; Key Laboratory of Laboratory Medical Diagnostics, Ministry of Education, Department of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, China.
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12
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Zhao A, Zhou H, Yang J, Li M, Niu T. 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: 50] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [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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Affiliation(s)
- Ailin Zhao
- Department of Hematology, West China Hospital, Sichuan University, 610041, Chengdu, Sichuan, China
| | - Hui Zhou
- Department of Hematology, West China Hospital, Sichuan University, 610041, Chengdu, Sichuan, China
| | - Jinrong Yang
- Department of Hematology, West China Hospital, Sichuan University, 610041, Chengdu, Sichuan, China
| | - Meng Li
- Department of Hematology, West China Hospital, Sichuan University, 610041, Chengdu, Sichuan, China
| | - Ting Niu
- Department of Hematology, West China Hospital, Sichuan University, 610041, Chengdu, Sichuan, China.
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13
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Epigenetic Modification of Cytosines in Hematopoietic Differentiation and Malignant Transformation. Int J Mol Sci 2023; 24:ijms24021727. [PMID: 36675240 PMCID: PMC9863985 DOI: 10.3390/ijms24021727] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2022] [Revised: 01/13/2023] [Accepted: 01/13/2023] [Indexed: 01/18/2023] Open
Abstract
The mammalian DNA methylation landscape is established and maintained by the combined activities of the two key epigenetic modifiers, DNA methyltransferases (DNMT) and Ten-eleven-translocation (TET) enzymes. Once DNMTs produce 5-methylcytosine (5mC), TET proteins fine-tune the DNA methylation status by consecutively oxidizing 5mC to 5-hydroxymethylcytosine (5hmC) and further oxidized derivatives. The 5mC and oxidized methylcytosines are essential for the maintenance of cellular identity and function during differentiation. Cytosine modifications with DNMT and TET enzymes exert pleiotropic effects on various aspects of hematopoiesis, including self-renewal of hematopoietic stem/progenitor cells (HSPCs), lineage determination, differentiation, and function. Under pathological conditions, these enzymes are frequently dysregulated, leading to loss of function. In particular, the loss of DNMT3A and TET2 function is conspicuous in diverse hematological disorders, including myeloid and lymphoid malignancies, and causally related to clonal hematopoiesis and malignant transformation. Here, we update recent advances in understanding how the maintenance of DNA methylation homeostasis by DNMT and TET proteins influences normal hematopoiesis and malignant transformation, highlighting the potential impact of DNMT3A and TET2 dysregulation on clonal dominance and evolution of pre-leukemic stem cells to full-blown malignancies. Clarification of the normal and pathological functions of DNA-modifying epigenetic regulators will be crucial to future innovations in epigenetic therapies for treating hematological disorders.
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14
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The R736H cancer mutation in DNMT3A modulates the properties of the FF-subunit interface. Biochimie 2022; 208:66-74. [PMID: 36528185 DOI: 10.1016/j.biochi.2022.12.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2022] [Revised: 11/21/2022] [Accepted: 12/12/2022] [Indexed: 12/23/2022]
Abstract
The DNMT3A DNA methyltransferase is an important epigenetic enzyme that is frequently mutated in cancers, particularly in AML. The heterozygous R736H mutation in the FF-interface of the tetrameric enzyme is the second most frequently observed DNMT3A cancer mutation, but its pathogenic mechanism is unclear. We show here that R736H leads to a moderate reduction in catalytic activity of 20-40% depending on the substrate, but no changes in CpG specificity, flanking sequence preferences and subnuclear localization. Strikingly, R736H showed a very strong stimulation by DNMT3L and the R736H/DNMT3L complex was 3-fold more active than WT/DNMT3L. Similarly, formation of mixed R736H/DNMT3A WT FF-interfaces led to an increased activity. R736H/DNMT3L and mixed R736H/DNMT3A WT FF-interfaces were less stable than interfaces not involving R736H, suggesting that an increased flexibility of the mixed interfaces stimulates catalytic activity. Our data suggest that aberrant activity of DNMT3A R736H may lead to DNA hypermethylation in cancer cells which could cause changes in gene expression.
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15
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Nam AS, Dusaj N, Izzo F, Murali R, Myers RM, Mouhieddine TH, Sotelo J, Benbarche S, Waarts M, Gaiti F, Tahri S, Levine R, Abdel-Wahab O, Godley LA, Chaligne R, Ghobrial I, Landau DA. Single-cell multi-omics of human clonal hematopoiesis reveals that DNMT3A R882 mutations perturb early progenitor states through selective hypomethylation. Nat Genet 2022; 54:1514-1526. [PMID: 36138229 PMCID: PMC10068894 DOI: 10.1038/s41588-022-01179-9] [Citation(s) in RCA: 67] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Accepted: 07/29/2022] [Indexed: 12/13/2022]
Abstract
Somatic mutations in cancer genes have been detected in clonal expansions across healthy human tissue, including in clonal hematopoiesis. However, because mutated and wild-type cells are admixed, we have limited ability to link genotypes with phenotypes. To overcome this limitation, we leveraged multi-modality single-cell sequencing, capturing genotype, transcriptomes and methylomes in progenitors from individuals with DNMT3A R882 mutated clonal hematopoiesis. DNMT3A mutations result in myeloid over lymphoid bias, and an expansion of immature myeloid progenitors primed toward megakaryocytic-erythroid fate, with dysregulated expression of lineage and leukemia stem cell markers. Mutated DNMT3A leads to preferential hypomethylation of polycomb repressive complex 2 targets and a specific CpG flanking motif. Notably, the hypomethylation motif is enriched in binding motifs of key hematopoietic transcription factors, serving as a potential mechanistic link between DNMT3A mutations and aberrant transcriptional phenotypes. Thus, single-cell multi-omics paves the road to defining the downstream consequences of mutations that drive clonal mosaicism.
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Affiliation(s)
- Anna S Nam
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
- New York Genome Center, New York, NY, USA
| | - Neville Dusaj
- New York Genome Center, New York, NY, USA
- Division of Hematology and Medical Oncology, Department of Medicine and Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
- Tri-Institutional MD-PhD Program, Weill Cornell Medicine, Rockefeller University, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Franco Izzo
- New York Genome Center, New York, NY, USA
- Division of Hematology and Medical Oncology, Department of Medicine and Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
| | - Rekha Murali
- New York Genome Center, New York, NY, USA
- Division of Hematology and Medical Oncology, Department of Medicine and Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
| | - Robert M Myers
- New York Genome Center, New York, NY, USA
- Division of Hematology and Medical Oncology, Department of Medicine and Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
- Tri-Institutional MD-PhD Program, Weill Cornell Medicine, Rockefeller University, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Tarek H Mouhieddine
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Jesus Sotelo
- New York Genome Center, New York, NY, USA
- Division of Hematology and Medical Oncology, Department of Medicine and Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
| | - Salima Benbarche
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Michael Waarts
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Federico Gaiti
- New York Genome Center, New York, NY, USA
- Division of Hematology and Medical Oncology, Department of Medicine and Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
| | - Sabrin Tahri
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Ross Levine
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Omar Abdel-Wahab
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Lucy A Godley
- Section of Hematology/Oncology, Departments of Medicine and Human Genetics, The University of Chicago, Chicago, IL, USA
| | - Ronan Chaligne
- New York Genome Center, New York, NY, USA
- Division of Hematology and Medical Oncology, Department of Medicine and Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
| | - Irene Ghobrial
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.
| | - Dan A Landau
- New York Genome Center, New York, NY, USA.
- Division of Hematology and Medical Oncology, Department of Medicine and Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA.
- Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA.
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16
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Higo T, Suzuki Y, Sato M, Koya J, Mizuno H, Miyauchi M, Masamoto Y, Kataoka K, Sumitomo Y, Tsuruta-Kishino T, Sato T, Kurokawa M. Heterozygous Dnmt3a R878C Induces Expansion of Quiescent Hematopoietic Stem Cell Pool. Exp Hematol 2022; 109:45-54. [PMID: 35245608 DOI: 10.1016/j.exphem.2022.02.006] [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: 12/22/2020] [Revised: 02/08/2022] [Accepted: 02/15/2022] [Indexed: 11/29/2022]
Abstract
Somatic mutation of DNMT3A (DNA methyltransferase 3 alpha) is implicated in the development of a wide range of hematological disorders, including clonal hematopoiesis indeterminant potential. To elucidate the functional roles of endogenous levels of a DNMT3A R882 mutant, we generated a novel Dnmt3a R878C conditional knock-in mouse model. In contrast to viable heterozygotes, mice homozygous for the Dnmt3a R878C mutation in the hematopoietic system were not viable (Dnmt3a R878C is homologous to human DNMT3A R882C). Hematopoietic cell-specific heterozygous expression of Dnmt3a R878C led to significant expansion of adult quiescent hematopoietic stem cells (HSCs); however, these mice had no incidence of hematological malignancies. The expanding HSC population in heterozygous Dnmt3a R878C knock-in mice showed an accumulation of G0 phase cells. In contrast to aberrantly enhanced self-renewal capacity in vitro, heterozygous Dnmt3a R878C knock-in HSCs had no competitive repopulating advantage in vivo over wild-type HSCs. Considering the capacity of the heterozygous Dnmt3a R878C mutant for HSC pool expansion, our Dnmt3a R878C knock-in mouse line is a useful platform to dissect the pathophysiology of clonal hematopoiesis. This mouse line can also help to elucidate the biological and molecular actions of DNMT3A mutations in the malignant transformation of normal HSCs.
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Affiliation(s)
- Takashi Higo
- Department of Hematology and Oncology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Yutaro Suzuki
- Department of Hematology and Oncology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Michiaki Sato
- Department of Hematology and Oncology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Junji Koya
- Department of Hematology and Oncology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Hideaki Mizuno
- Department of Hematology and Oncology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Masashi Miyauchi
- Department of Hematology and Oncology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Yosuke Masamoto
- Department of Hematology and Oncology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Keisuke Kataoka
- Department of Hematology and Oncology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Yoshiki Sumitomo
- Department of Hematology and Oncology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Takako Tsuruta-Kishino
- Department of Hematology and Oncology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Tomohiko Sato
- Department of Hematology and Oncology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Mineo Kurokawa
- Department of Hematology and Oncology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan; Department of Cell Therapy and Transplantation, The University of Tokyo Hospital, Tokyo, Japan.
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17
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Mack A, Emperle M, Schnee P, Adam S, Pleiss J, Bashtrykov P, Jeltsch A. Preferential self-interaction of DNA methyltransferase DNMT3A subunits containing the R882H cancer mutation leads to dominant changes of flanking sequence preferences. J Mol Biol 2022; 434:167482. [DOI: 10.1016/j.jmb.2022.167482] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Revised: 01/31/2022] [Accepted: 01/31/2022] [Indexed: 11/30/2022]
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18
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Liao M, Chen R, Yang Y, He H, Xu L, Jiang Y, Guo Z, He W, Jiang H, Wang J. Aging-elevated inflammation promotes DNMT3A R878H-driven clonal hematopoiesis. Acta Pharm Sin B 2022; 12:678-691. [PMID: 35256939 PMCID: PMC8897035 DOI: 10.1016/j.apsb.2021.09.015] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Revised: 07/07/2021] [Accepted: 08/25/2021] [Indexed: 12/20/2022] Open
Abstract
Aging-elevated DNMT3A R882H-driven clonal hematopoiesis (CH) is a risk factor for myeloid malignancies remission and overall survival. Although some studies were conducted to investigate this phenomenon, the exact mechanism is still under debate. In this study, we observed that DNMT3A R878H bone marrow cells (human allele: DNMT3A R882H) displayed enhanced reconstitution capacity in aged bone marrow milieu and upon inflammatory insult. DNMT3A R878H protects hematopoietic stem and progenitor cells from the damage induced by chronic inflammation, especially TNFα insults. Mechanistically, we identified that RIPK1–RIPK3–MLKL-mediated necroptosis signaling was compromised in R878H cells in response to proliferation stress and TNFα insults. Briefly, we elucidated the molecular mechanism driving DNMT3A R878H-based clonal hematopoiesis, which raises clinical value for treating DNMT3A R882H-driven clonal hematopoiesis and myeloid malignancies with aging.
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19
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Chattopadhyaya S, Ghosal S. DNA methylation: a saga of genome maintenance in hematological perspective. Hum Cell 2022; 35:448-461. [DOI: 10.1007/s13577-022-00674-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Accepted: 01/13/2022] [Indexed: 12/21/2022]
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20
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Mouse Models of Frequently Mutated Genes in Acute Myeloid Leukemia. Cancers (Basel) 2021; 13:cancers13246192. [PMID: 34944812 PMCID: PMC8699817 DOI: 10.3390/cancers13246192] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 11/24/2021] [Accepted: 11/30/2021] [Indexed: 01/19/2023] Open
Abstract
Acute myeloid leukemia is a clinically and biologically heterogeneous blood cancer with variable prognosis and response to conventional therapies. Comprehensive sequencing enabled the discovery of recurrent mutations and chromosomal aberrations in AML. Mouse models are essential to study the biological function of these genes and to identify relevant drug targets. This comprehensive review describes the evidence currently available from mouse models for the leukemogenic function of mutations in seven functional gene groups: cell signaling genes, epigenetic modifier genes, nucleophosmin 1 (NPM1), transcription factors, tumor suppressors, spliceosome genes, and cohesin complex genes. Additionally, we provide a synergy map of frequently cooperating mutations in AML development and correlate prognosis of these mutations with leukemogenicity in mouse models to better understand the co-dependence of mutations in AML.
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21
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Mensah IK, Norvil AB, AlAbdi L, McGovern S, Petell CJ, He M, Gowher H. Misregulation of the expression and activity of DNA methyltransferases in cancer. NAR Cancer 2021; 3:zcab045. [PMID: 34870206 PMCID: PMC8634572 DOI: 10.1093/narcan/zcab045] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Revised: 10/29/2021] [Accepted: 11/10/2021] [Indexed: 12/15/2022] Open
Abstract
In mammals, DNA methyltransferases DNMT1 and DNMT3's (A, B and L) deposit and maintain DNA methylation in dividing and nondividing cells. Although these enzymes have an unremarkable DNA sequence specificity (CpG), their regional specificity is regulated by interactions with various protein factors, chromatin modifiers, and post-translational modifications of histones. Changes in the DNMT expression or interacting partners affect DNA methylation patterns. Consequently, the acquired gene expression may increase the proliferative potential of cells, often concomitant with loss of cell identity as found in cancer. Aberrant DNA methylation, including hypermethylation and hypomethylation at various genomic regions, therefore, is a hallmark of most cancers. Additionally, somatic mutations in DNMTs that affect catalytic activity were mapped in Acute Myeloid Leukemia cancer cells. Despite being very effective in some cancers, the clinically approved DNMT inhibitors lack specificity, which could result in a wide range of deleterious effects. Elucidating distinct molecular mechanisms of DNMTs will facilitate the discovery of alternative cancer therapeutic targets. This review is focused on: (i) the structure and characteristics of DNMTs, (ii) the prevalence of mutations and abnormal expression of DNMTs in cancer, (iii) factors that mediate their abnormal expression and (iv) the effect of anomalous DNMT-complexes in cancer.
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Affiliation(s)
- Isaiah K Mensah
- Department of Biochemistry, Purdue University, West Lafayette, IN 47907, USA
| | | | - Lama AlAbdi
- Department of Zoology, Collage of Science, King Saud University, Riyadh, Saudi Arabia
| | - Sarah McGovern
- Department of Biochemistry, Purdue University, West Lafayette, IN 47907, USA
| | | | - Ming He
- Department of Biochemistry, Purdue University, West Lafayette, IN 47907, USA
| | - Humaira Gowher
- Department of Biochemistry, Purdue University, West Lafayette, IN 47907, USA
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22
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Liao M, Dong Q, Chen R, Xu L, Jiang Y, Guo Z, Xiao M, He W, Cao C, Hu R, Sun W, Jiang H, Wang J. Oridonin inhibits DNMT3A R882 mutation-driven clonal hematopoiesis and leukemia by inducing apoptosis and necroptosis. Cell Death Discov 2021; 7:297. [PMID: 34663800 PMCID: PMC8523644 DOI: 10.1038/s41420-021-00697-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2021] [Revised: 09/14/2021] [Accepted: 10/05/2021] [Indexed: 01/10/2023] Open
Abstract
DNA (cytosine-5)-methyltransferase 3A (DNMT3A) mutations occur in ~20% of de novo acute myeloid leukemia (AML) patients, and >50% of these mutations in AML samples are heterozygous missense alterations within the methyltransferase domain at residue R882. DNMT3A R882 mutations in AML patients promote resistance to anthracycline chemotherapy and drive relapse. In this study, we performed high-throughput screening and identified that oridonin, an ent-kaurene diterpenoid extracted from the Chinese herb Rabdosia rubescens, inhibits DNMT3A R882 mutant leukemic cells at a low-micromolar concentration (IC50 = 2.1 µM) by activating both RIPK1-Caspase-8-Caspase-3-mediated apoptosis and RIPK1-RIPK3-MLKL-mediated necroptosis. The inhibitory effect of oridonin against DNMT3A R882 mutant leukemia cells can also be observed in vivo. Furthermore, oridonin inhibits clonal hematopoiesis of hematopoietic stem cells (HSCs) with Dnmt3a R878H mutation comparing to normal HSCs by inducing apoptosis and necroptosis. Overall, oridonin is a potential and promising drug candidate or lead compound targeting DNMT3A R882 mutation-driven clonal hematopoiesis and leukemia.
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Affiliation(s)
- Min Liao
- School of Pharmaceutical Sciences, Tsinghua University, 100084, Beijing, China
| | - Qiongye Dong
- Key Laboratory of Intelligent Information Processing, Advanced Computer Research Center, Institute of Computing Technology, Chinese Academy of Sciences, 100190, Beijing, China
| | - Ruiqing Chen
- School of Pharmaceutical Sciences, Tsinghua University, 100084, Beijing, China
| | - Liqian Xu
- School of Pharmaceutical Sciences, Tsinghua University, 100084, Beijing, China
| | - Yuxuan Jiang
- School of Pharmaceutical Sciences, Tsinghua University, 100084, Beijing, China
| | - Zhenxing Guo
- Department of Hematology/Oncology, First Hospital of Tsinghua University, 100016, Beijing, China
| | - Min Xiao
- Department of Hematology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, 430030, Wuhan, China
| | - Wei He
- School of Pharmaceutical Sciences, Tsinghua University, 100084, Beijing, China
| | - Changcai Cao
- Shandong Hongmai Biotechnology Co., Ltd. Room 1201, building B, Research Institute of Tianjin University, No. 51, Lutai Avenue, Zibo High tech Zone, 255000, Tianjin, China
| | - Ronghua Hu
- Department of Hematology, Xuanwu Hospital, Capital Medical University, 100053, Beijing, China
| | - Wanling Sun
- Department of Hematology, Xuanwu Hospital, Capital Medical University, 100053, Beijing, China.
| | - Hong Jiang
- Kidney Disease Center, the First Affiliated Hospital, College of Medicine, Zhejiang University, 310003, Hangzhou, China.
| | - Jianwei Wang
- School of Pharmaceutical Sciences, Tsinghua University, 100084, Beijing, China.
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23
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Epigenetic Regulation of Cancer Immune Cells. Semin Cancer Biol 2021; 83:377-383. [PMID: 34182142 DOI: 10.1016/j.semcancer.2021.06.022] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Revised: 05/06/2021] [Accepted: 06/23/2021] [Indexed: 12/17/2022]
Abstract
The epigenetic regulation of immune response involves reversible and heritable changes that do not alter the DNA sequence. Though there have been extensive studies accomplished relating to epigenetic changes in cancer cells, recent focus has been shifted on epigenetic-mediated changes in the immune cells including T cells, Macrophages, Natural Killer cells and anti-tumor immune responses. This review compiles the most relevant and recent literature related to the role of epigenetic mechanisms including DNA methylation and histone modifications in immune cells of wide range of cancers. We also include recent research with respect to role of the most relevant transcription factors that epigenetically control the anti-tumor immune response. Finally, a statement of future direction that promises to look forward for strategies to improve immunotherapy in cancer.
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24
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Hu X, Wang B, Chen Q, Huang A, Fu W, Liu L, Zhang Y, Tang G, Cheng H, Ni X, Gao L, Chen J, Chen L, Zhang W, Yang J, Cao S, Yu L, Wang J. A clinical prediction model identifies a subgroup with inferior survival within intermediate risk acute myeloid leukemia. J Cancer 2021; 12:4912-4923. [PMID: 34234861 PMCID: PMC8247394 DOI: 10.7150/jca.57231] [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: 12/27/2020] [Accepted: 05/19/2021] [Indexed: 12/19/2022] Open
Abstract
Intermediate risk acute myeloid leukemia (AML) comprises around 50% of AML patients and is featured with heterogeneous clinical outcomes. The study aimed to generate a prediction model to identify intermediate risk AML patients with an inferior survival. We performed targeted next generation sequencing analysis for 121 patients with 2017 European LeukemiaNet-defined intermediate risk AML, revealing 122 mutated genes, with 24 genes mutated in > 10% of patients. A prognostic nomogram characterized by white blood cell count ≥10×109/L at diagnosis, mutated DNMT3A and genes involved in signaling pathways was developed for 110 patients who were with clinical outcomes. Two subgroups were identified: intermediate low risk (ILR; 43.6%, 48/110) and intermediate high risk (IHR; 56.4%, 62/110). The model was prognostic of overall survival (OS) and relapse-free survival (RFS) (OS: Concordance index [C-index]: 0.703, 95%CI: 0.643-0.763; RFS: C-index: 0.681, 95%CI 0.620-0.741), and was successfully validated with two independent cohorts. Allogeneic hematopoietic stem cell transplantation (alloHSCT) reduced the relapse risk of IHR patients (3-year RFS: alloHSCT: 40.0±12.8% vs. chemotherapy: 8.6±5.8%, P= 0.010). The prediction model can help identify patients with an unfavorable prognosis and refine risk-adapted therapy for intermediate risk AML patients.
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Affiliation(s)
- Xiaoxia Hu
- Department of Hematology, Institute of Hematology, Changhai Hospital, Shanghai 200433, China
| | - Bianhong Wang
- Department of Hematology, Beijing Tsinghua Changgung Hospital, School of Clinical Medicine, Tsinghua University, Beijing 102218, China.,Department of Hematology, Chinese PLA General Hospital, Beijing, 100853, China
| | - Qi Chen
- Department of Health Statistics, Second Military Medical University, Shanghai 200433, China
| | - Aijie Huang
- Department of Hematology, Institute of Hematology, Changhai Hospital, Shanghai 200433, China
| | - Weijia Fu
- Department of Hematology, Institute of Hematology, Changhai Hospital, Shanghai 200433, China
| | - Lixia Liu
- Acornmed Biotechnology Co., Ltd. Beijing, 100176, China
| | - Ying Zhang
- Department of Hematology, Institute of Hematology, Changhai Hospital, Shanghai 200433, China
| | - Gusheng Tang
- Department of Hematology, Institute of Hematology, Changhai Hospital, Shanghai 200433, China
| | - Hui Cheng
- Department of Hematology, Institute of Hematology, Changhai Hospital, Shanghai 200433, China
| | - Xiong Ni
- Department of Hematology, Institute of Hematology, Changhai Hospital, Shanghai 200433, China
| | - Lei Gao
- Department of Hematology, Institute of Hematology, Changhai Hospital, Shanghai 200433, China
| | - Jie Chen
- Department of Hematology, Institute of Hematology, Changhai Hospital, Shanghai 200433, China
| | - Li Chen
- Department of Hematology, Institute of Hematology, Changhai Hospital, Shanghai 200433, China
| | - Weiping Zhang
- Department of Hematology, Institute of Hematology, Changhai Hospital, Shanghai 200433, China
| | - Jianmin Yang
- Department of Hematology, Institute of Hematology, Changhai Hospital, Shanghai 200433, China
| | - Shanbo Cao
- Acornmed Biotechnology Co., Ltd. Beijing, 100176, China
| | - Li Yu
- Department of Hematology, Chinese PLA General Hospital, Beijing, 100853, China.,Department of Hematology and Oncology, Shenzhen University General Hospital; Shenzhen University International Cancer Center, Shenzhen University Health Science Center, Shenzhen, 518000, China
| | - Jianmin Wang
- Department of Hematology, Institute of Hematology, Changhai Hospital, Shanghai 200433, China
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25
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Yang Y, Dai Y, Yang X, Wu S, Wang Y. DNMT3A Mutation-Induced CDK1 Overexpression Promotes Leukemogenesis by Modulating the Interaction between EZH2 and DNMT3A. Biomolecules 2021; 11:biom11060781. [PMID: 34067359 PMCID: PMC8224654 DOI: 10.3390/biom11060781] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Revised: 05/14/2021] [Accepted: 05/19/2021] [Indexed: 12/22/2022] Open
Abstract
DNMT3A mutations are frequently identified in acute myeloid leukemia (AML) and indicate poor prognosis. Previously, we found that the hotspot mutation DNMT3A R882H could upregulate CDK1 and induce AML in conditional knock-in mice. However, the mechanism by which CDK1 is involved in leukemogenesis of DNMT3A mutation-related AML, and whether CDK1 could be a therapeutic target, remains unclear. In this study, using fluorescence resonance energy transfer and immunoprecipitation analysis, we discovered that increased CDK1 could compete with EZH2 to bind to the PHD-like motif of DNMT3A, which may disturb the protein interaction between EZH2 and DNMT3A. Knockdown of CDK1 in OCI-AML3 cells with DNMT3A mutation markedly inhibited proliferation and induced apoptosis. CDK1 selective inhibitor CGP74514A (CGP) and the pan-CDK inhibitor flavopiridol (FLA) arrested OCI-AML3 cells in the G2/M phase, and induced cell apoptosis. CGP significantly increased CD163-positive cells. Moreover, the combined application of CDK1 inhibitor and traditional chemotherapy drugs synergistically inhibited proliferation and induced apoptosis of OCI-AML3 cells. In conclusion, this study highlights CDK1 overexpression as a pathogenic factor and a potential therapeutic target for DNMT3A mutation-related AML.
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26
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Que Y, Li H, Lin L, Zhu X, Xiao M, Wang Y, Zhu L, Li D. Study on the Immune Escape Mechanism of Acute Myeloid Leukemia With DNMT3A Mutation. Front Immunol 2021; 12:653030. [PMID: 34093541 PMCID: PMC8173207 DOI: 10.3389/fimmu.2021.653030] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Accepted: 05/05/2021] [Indexed: 12/28/2022] Open
Abstract
DNA (cytosine-5)-methyltransferase 3A (DNMT3A)-mutated acute myeloid leukemia (AML) has a poor prognosis, but the exact mechanism is still unclear. Here, we aimed to explore the mechanism of immune escape in AML with DNMT3A mutation. We constructed a DNMT3A knockout clone and DNMT3A-R882H-mutated clones. RNA-seq results showed that transcription factors and macrophage inflammatory proteins were significantly downregulated in the DNMT3A mutant clones. KEGG enrichment and gene set enrichment analysis (GSEA) showed that a large number of genes were enriched in inflammatory immune-related pathways, such as the toll-like receptor signaling pathway. Therefore, we co-cultured AML cells with macrophages. The DNMT3A-mutated AML cells attenuated M1 macrophage polarization and resisted its killing effect in vitro and in vivo. In xenografts, the tumor volumes in the experimental group were significantly larger than those in the control group, and the proportion of M2 macrophages was significantly higher. After the co-culture, the increase in pro-inflammatory cytokine expression in the mutant cells was significantly lower than that in the control group, while that in immunosuppressive factors was not significantly different. In co-cultivated supernatants, the concentration of inflammatory factors in the experimental group was significantly lower than that in the control group, while that of immunosuppressive factors was significantly higher. Resistin significantly promoted the expression of inflammatory proteins in AML cells. It relieved the inhibitory effect of DNMT3A mutation, promoted the phenotypic recovery of the co-cultured macrophages, eliminated resistance, and regulated the immune microenvironment. Thus, resistin may serve as an ancillary drug for patients with DNMT3A-mutated AML.
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Affiliation(s)
- Yimei Que
- Department of Hematology, Tongji Hospital Affiliated with Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Huimin Li
- Department of Hematology, Tongji Hospital Affiliated with Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Liman Lin
- Department of Hematology, Tongji Hospital Affiliated with Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Xiaojian Zhu
- Department of Hematology, Tongji Hospital Affiliated with Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Min Xiao
- Department of Hematology, Tongji Hospital Affiliated with Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Ying Wang
- Department of Hematology, Tongji Hospital Affiliated with Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Li Zhu
- Department of Hematology, Tongji Hospital Affiliated with Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Dengju Li
- Department of Hematology, Tongji Hospital Affiliated with Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
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27
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Huang AJ, Gao L, Ni X, Hu XX, Tang GS, Cheng H, Chen J, Chen L, Liu LX, Wang CC, Zhang WP, Yang JM, Wang JM. [Spectrum of gene mutations and clinical features in adult acute myeloid leukemia with normal karyotype]. ZHONGHUA XUE YE XUE ZA ZHI = ZHONGHUA XUEYEXUE ZAZHI 2021; 42:420-424. [PMID: 35790467 PMCID: PMC8293012 DOI: 10.3760/cma.j.issn.0253-2727.2021.05.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Indexed: 12/24/2022]
Affiliation(s)
- A J Huang
- Department of Hematology, Institute of Hematology, the First Affiliated Hospital of Navy Military Medical University (Changhai Hospital), Shanghai 200433
| | - L Gao
- Department of Hematology, Institute of Hematology, the First Affiliated Hospital of Navy Military Medical University (Changhai Hospital), Shanghai 200433
| | - X Ni
- Department of Hematology, Institute of Hematology, the First Affiliated Hospital of Navy Military Medical University (Changhai Hospital), Shanghai 200433
| | - X X Hu
- Department of Hematology, Institute of Hematology, the First Affiliated Hospital of Navy Military Medical University (Changhai Hospital), Shanghai 200433
| | - G S Tang
- Department of Hematology, Institute of Hematology, the First Affiliated Hospital of Navy Military Medical University (Changhai Hospital), Shanghai 200433
| | - H Cheng
- Department of Hematology, Institute of Hematology, the First Affiliated Hospital of Navy Military Medical University (Changhai Hospital), Shanghai 200433
| | - J Chen
- Department of Hematology, Institute of Hematology, the First Affiliated Hospital of Navy Military Medical University (Changhai Hospital), Shanghai 200433
| | - L Chen
- Department of Hematology, Institute of Hematology, the First Affiliated Hospital of Navy Military Medical University (Changhai Hospital), Shanghai 200433
| | - L X Liu
- Acornmed Biotechnology Co., Ltd. Beijing, 100176
| | - C C Wang
- Acornmed Biotechnology Co., Ltd. Beijing, 100176
| | - W P Zhang
- Department of Hematology, Institute of Hematology, the First Affiliated Hospital of Navy Military Medical University (Changhai Hospital), Shanghai 200433
| | - J M Yang
- Department of Hematology, Institute of Hematology, the First Affiliated Hospital of Navy Military Medical University (Changhai Hospital), Shanghai 200433
| | - J M Wang
- Department of Hematology, Institute of Hematology, the First Affiliated Hospital of Navy Military Medical University (Changhai Hospital), Shanghai 200433
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28
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Clonal hematopoiesis: mechanisms driving dominance of stem cell clones. Blood 2021; 136:1590-1598. [PMID: 32746453 DOI: 10.1182/blood.2020006510] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Accepted: 05/14/2020] [Indexed: 12/16/2022] Open
Abstract
The discovery of clonal hematopoiesis (CH) in older individuals has changed the way hematologists and stem cell biologists view aging. Somatic mutations accumulate in stem cells over time. While most mutations have no impact, some result in subtle functional differences that ultimately manifest in distinct stem cell behaviors. With a large pool of stem cells and many decades to compete, some of these differences confer advantages under specific contexts. Approximately 20 genes are recurrently found as mutated in CH, indicating they confer some advantage. The impact of these mutations has begun to be analyzed at a molecular level by modeling in cell lines and in mice. Mutations in epigenetic regulators such as DNMT3A and TET2 confer an advantage by enhancing self-renewal of stem and progenitor cells and inhibiting their differentiation. Mutations in other genes involved in the DNA damage response may simply enhance cell survival. Here, we review proposed mechanisms that lead to CH, specifically in the context of stem cell biology, based on our current understanding of the function of some of the CH-associated genes.
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29
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Sharma A, Liu H, Herwig-Carl MC, Chand Dakal T, Schmidt-Wolf IGH. Epigenetic Regulatory Enzymes: mutation Prevalence and Coexistence in Cancers. Cancer Invest 2021; 39:257-273. [PMID: 33411587 DOI: 10.1080/07357907.2021.1872593] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Epigenetic regulation is an important layer of transcriptional control with the particularity to affect the broad spectrum of genome. Over the years, largely due to the substantial number of recurrent mutations, there have been hundreds of novel driver genes characterized in various cancers. Additionally, the relative contribution of two dysregulated epigenomic entities (DNA methylation and histone modifications) that gradually drive the cancer phenotype remains in the research focus. However, a complex scenario arises when the disease phenotype does not harbor any relevant mutation or an abnormal transcription level. Although the cancer landscape involves the contribution of multiple genetic and non-genetic factors, herein, we discuss specifically the mutation spectrum of epigenetically-related enzymes in cancer. In addition, we address the coexistence of these two epigenetic entities in malignant human diseases, especially cancer. We suggest that the study of epigenetically-related somatic mutations in the early cellular differentiation stage of embryonic development might help to understand their later-staged footprints in the cancer genome. Furthermore, understanding the co-occurrence and/or inverse association of different disease types and redefining the general definition of "healthy" controls could provide insights into the genome reorganization.
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Affiliation(s)
- Amit Sharma
- Department of Integrated Oncology, CIO Bonn, University Hospital Bonn, Bonn, Germany.,Department of Neurology, University Hospital Bonn, Bonn, Germany
| | - Hongde Liu
- State Key Laboratory of Bioelectronics, School of Biological Science & Medical Engineering, Southeast University, Nanjing, China
| | | | - Tikam Chand Dakal
- Department of Biotechnology, Mohanlal Sukhadia University, Rajasthan, India
| | - Ingo G H Schmidt-Wolf
- Department of Integrated Oncology, CIO Bonn, University Hospital Bonn, Bonn, Germany
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30
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Al-Yozbaki M, Jabre I, Syed NH, Wilson CM. Targeting DNA methyltransferases in non-small-cell lung cancer. Semin Cancer Biol 2021; 83:77-87. [PMID: 33486076 DOI: 10.1016/j.semcancer.2021.01.005] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Revised: 01/14/2021] [Accepted: 01/17/2021] [Indexed: 12/30/2022]
Abstract
Despite the advances in treatment using chemotherapy or targeted therapies, due to static survival rates, non-small cell lung cancer (NSCLC) is the major cause of cancer-related deaths worldwide. Epigenetic-based therapies have been developed for NSCLC by targeting DNA methyltransferases (DNMTs) and histone-modifying enzymes. However, treatment using single epigenetic agents on solid tumours has been inadequate; whereas, treatment with a combination of DNMTs inhibitors with chemotherapy and immunotherapy has shown great promise. Dietary sources of phytochemicals could also inhibit DNMTs and cancer stem cells, representing a novel and promising way to prevent and treat cancer. Herein, we will discuss the different DNMTs, DNA methylation profiling in NSCLC as well as current demethylating agents in ongoing clinical trials. Therefore, providing a concise overview of future developments in the field of epigenetic therapy in NSCLC.
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Affiliation(s)
- Minnatallah Al-Yozbaki
- Canterbury Christ Church University, School of Human and Life Sciences, Life Sciences Industry Liaison Lab, Sandwich, UK
| | - Ibtissam Jabre
- Dept. of Microbial Sciences, School of Biosciences and Medicine, Faculty of Health and Medical Sciences, University of Surrey, Guildford, GU2 7XH, UK
| | - Naeem H Syed
- Canterbury Christ Church University, School of Human and Life Sciences, Life Sciences Industry Liaison Lab, Sandwich, UK
| | - Cornelia M Wilson
- Canterbury Christ Church University, School of Human and Life Sciences, Life Sciences Industry Liaison Lab, Sandwich, UK; University of Liverpool, Institute of Translation Medicine, Dept of Molecular & Clinical Cancer Medicine, UK.
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31
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Abstract
Mouse models of human myeloid malignancies support the detailed and focused investigation of selected driver mutations and represent powerful tools in the study of these diseases. Carefully developed murine models can closely recapitulate human myeloid malignancies in vivo, enabling the interrogation of a number of aspects of these diseases including their preclinical course, interactions with the microenvironment, effects of pharmacological agents, and the role of non-cell-autonomous factors, as well as the synergy between co-occurring mutations. Importantly, advances in gene-editing technologies, particularly CRISPR-Cas9, have opened new avenues for the development and study of genetically modified mice and also enable the direct modification of mouse and human hematopoietic cells. In this review we provide a concise overview of some of the important mouse models that have advanced our understanding of myeloid leukemogenesis with an emphasis on models relevant to clonal hematopoiesis, myelodysplastic syndromes, and acute myeloid leukemia with a normal karyotype.
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Affiliation(s)
- Faisal Basheer
- Wellcome-MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, Department of Haematology, University of Cambridge, Cambridge CB2 0AW, United Kingdom
- Haematological Cancer Genetics, Wellcome Trust Sanger Institute, Cambridge CB10 1SA, United Kingdom
- Department of Haematology, Cambridge University Hospitals NHS Foundation Trust, Cambridge CB2 0QQ, United Kingdom
| | - George Vassiliou
- Wellcome-MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, Department of Haematology, University of Cambridge, Cambridge CB2 0AW, United Kingdom
- Haematological Cancer Genetics, Wellcome Trust Sanger Institute, Cambridge CB10 1SA, United Kingdom
- Department of Haematology, Cambridge University Hospitals NHS Foundation Trust, Cambridge CB2 0QQ, United Kingdom
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32
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Castro-Piedras I, Vartak D, Sharma M, Pandey S, Casas L, Molehin D, Rasha F, Fokar M, Nichols J, Almodovar S, Rahman RL, Pruitt K. Identification of Novel MeCP2 Cancer-Associated Target Genes and Post-Translational Modifications. Front Oncol 2020; 10:576362. [PMID: 33363010 PMCID: PMC7758440 DOI: 10.3389/fonc.2020.576362] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Accepted: 10/26/2020] [Indexed: 12/23/2022] Open
Abstract
Abnormal regulation of DNA methylation and its readers has been associated with a wide range of cellular dysfunction. Disruption of the normal function of DNA methylation readers contributes to cancer progression, neurodevelopmental disorders, autoimmune disease and other pathologies. One reader of DNA methylation known to be especially important is MeCP2. It acts a bridge and connects DNA methylation with histone modifications and regulates many gene targets contributing to various diseases; however, much remains unknown about how it contributes to cancer malignancy. We and others previously described novel MeCP2 post-translational regulation. We set out to test the hypothesis that MeCP2 would regulate novel genes linked with tumorigenesis and that MeCP2 is subject to additional post-translational regulation not previously identified. Herein we report novel genes bound and regulated by MeCP2 through MeCP2 ChIP-seq and RNA-seq analyses in two breast cancer cell lines representing different breast cancer subtypes. Through genomics analyses, we localize MeCP2 to novel gene targets and further define the full range of gene targets within breast cancer cell lines. We also further examine the scope of clinical and pre-clinical lysine deacetylase inhibitors (KDACi) that regulate MeCP2 post-translationally. Through proteomics analyses, we identify many additional novel acetylation sites, nine of which are mutated in Rett Syndrome. Our study provides important new insight into downstream targets of MeCP2 and provide the first comprehensive map of novel sites of acetylation associated with both pre-clinical and FDA-approved KDACi used in the clinic. This report examines a critical reader of DNA methylation and has important implications for understanding MeCP2 regulation in cancer models and identifying novel molecular targets associated with epigenetic therapies.
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Affiliation(s)
- Isabel Castro-Piedras
- Department of Immunology and Molecular Microbiology, Texas Tech University Health Sciences Center, Lubbock, TX, United States
| | - David Vartak
- Department of Immunology and Molecular Microbiology, Texas Tech University Health Sciences Center, Lubbock, TX, United States
| | - Monica Sharma
- Department of Immunology and Molecular Microbiology, Texas Tech University Health Sciences Center, Lubbock, TX, United States
| | - Somnath Pandey
- Department of Immunology and Molecular Microbiology, Texas Tech University Health Sciences Center, Lubbock, TX, United States
| | - Laura Casas
- Department of Immunology and Molecular Microbiology, Texas Tech University Health Sciences Center, Lubbock, TX, United States
| | - Deborah Molehin
- Department of Immunology and Molecular Microbiology, Texas Tech University Health Sciences Center, Lubbock, TX, United States
| | - Fahmida Rasha
- Department of Immunology and Molecular Microbiology, Texas Tech University Health Sciences Center, Lubbock, TX, United States
| | - Mohamed Fokar
- Center for Biotechnology & Genomics, Texas Tech University, Lubbock, TX, United States
| | - Jacob Nichols
- Department of Internal Medicine, Texas Tech University, Lubbock, TX, United States
| | - Sharilyn Almodovar
- Department of Immunology and Molecular Microbiology, Texas Tech University Health Sciences Center, Lubbock, TX, United States
| | | | - Kevin Pruitt
- Department of Immunology and Molecular Microbiology, Texas Tech University Health Sciences Center, Lubbock, TX, United States
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33
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Saravanaraman P, Selvam M, Ashok C, Srijyothi L, Baluchamy S. De novo methyltransferases: Potential players in diseases and new directions for targeted therapy. Biochimie 2020; 176:85-102. [PMID: 32659446 DOI: 10.1016/j.biochi.2020.07.004] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2019] [Revised: 06/06/2020] [Accepted: 07/07/2020] [Indexed: 12/16/2022]
Abstract
Epigenetic modifications govern gene expression by guiding the human genome on 'what to express and what not to'. DNA methyltransferases (DNMTs) establish methylation patterns on DNA, particularly in CpG islands, and such patterns play a major role in gene silencing. DNMTs are a family of proteins/enzymes (DNMT1, 2, 3A, 3B, and 3L), among which, DNMT1 (maintenance methyltransferase) and DNMT3 (de novo methyltransferases) that direct mammalian development and genome imprinting are highly investigated. In recent decades, many studies revealed a strong association of DNA methylation patterns with gene expression in various clinical conditions. Differential expression of DNMT3 family proteins and their splice variants result in changes in methylation patterns and such alterations have been associated with the initiation and progression of various diseases, especially cancer. This review will discuss the aberrant modifications generated by DNMT3 proteins under various clinical conditions, suggesting a potential signature for de novo methyltransferases in targeted disease therapy. Further, this review discusses the possibility of using 'CpG island methylation signatures' as promising biomarkers and emphasizes 'targeted hypomethylation' by disrupting the interaction of specific DNMT-protein complexes as the future of cancer therapeutics.
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Affiliation(s)
- Ponne Saravanaraman
- Department of Biotechnology, Pondicherry Central University, Pondicherry, 605014, India
| | - Murugan Selvam
- Department of Biotechnology, Pondicherry Central University, Pondicherry, 605014, India
| | - Cheemala Ashok
- Department of Biotechnology, Pondicherry Central University, Pondicherry, 605014, India
| | - Loudu Srijyothi
- Department of Biotechnology, Pondicherry Central University, Pondicherry, 605014, India
| | - Sudhakar Baluchamy
- Department of Biotechnology, Pondicherry Central University, Pondicherry, 605014, India.
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34
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Li X, Zhang Y, Pei W, Zhang M, Yang H, Zhong M, Kong X, Xu Y, Zhu X, Chen T, Ye J, Lv K. LncRNA Dnmt3aos regulates Dnmt3a expression leading to aberrant DNA methylation in macrophage polarization. FASEB J 2020; 34:5077-5091. [PMID: 32052888 DOI: 10.1096/fj.201902379r] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Revised: 01/07/2020] [Accepted: 01/27/2020] [Indexed: 01/18/2023]
Abstract
Long non-coding RNAs (lncRNAs) play key roles in various biological processes. However, the roles of lncRNAs in macrophage polarization remain largely unexplored. In this study, thousands of lncRNAs were identified that are differentially expressed in distinct polarized bone marrow-derived macrophages. Among them, Dnmt3aos (DNA methyltransferase 3A, opposite strand), as a known lncRNA, locates on the antisense strand of Dnmt3a. Functional experiments further confirmed that Dnmt3aos were highly expressed in M(IL-4) macrophages and participated in the regulation of Dnmt3a expression, and played a key role in macrophage polarization. The DNA methylation profiles between the Dnmt3aos knockdown group and the control group in M(IL-4) macrophages were determined by MeDIP-seq technique for the first time, and the Dnmt3aos-Dnmt3a axis-mediated DNA methylation modification-regulated macrophage polarization- related gene IFN-γ was identified. Our study will help to enrich our knowledge of the mechanism of macrophage polarization.
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Affiliation(s)
- Xueqin Li
- Key Laboratory of Non-coding RNA Transformation Research of Anhui Higher Education Institutes, Wannan Medical College, Wuhu, PR China.,Central Laboratory of Yijishan Hospital, Wannan Medical College, Wuhu, PR China
| | - Yingying Zhang
- Key Laboratory of Non-coding RNA Transformation Research of Anhui Higher Education Institutes, Wannan Medical College, Wuhu, PR China.,Laboratory Medicine of Yijishan Hospital, Wannan Medical College, Wuhu, PR China
| | - Weiya Pei
- Key Laboratory of Non-coding RNA Transformation Research of Anhui Higher Education Institutes, Wannan Medical College, Wuhu, PR China.,Central Laboratory of Yijishan Hospital, Wannan Medical College, Wuhu, PR China
| | - Mengying Zhang
- Key Laboratory of Non-coding RNA Transformation Research of Anhui Higher Education Institutes, Wannan Medical College, Wuhu, PR China.,Central Laboratory of Yijishan Hospital, Wannan Medical College, Wuhu, PR China
| | - Hui Yang
- Key Laboratory of Non-coding RNA Transformation Research of Anhui Higher Education Institutes, Wannan Medical College, Wuhu, PR China.,Central Laboratory of Yijishan Hospital, Wannan Medical College, Wuhu, PR China
| | - Min Zhong
- Key Laboratory of Non-coding RNA Transformation Research of Anhui Higher Education Institutes, Wannan Medical College, Wuhu, PR China.,Central Laboratory of Yijishan Hospital, Wannan Medical College, Wuhu, PR China
| | - Xiang Kong
- Key Laboratory of Non-coding RNA Transformation Research of Anhui Higher Education Institutes, Wannan Medical College, Wuhu, PR China.,Central Laboratory of Yijishan Hospital, Wannan Medical College, Wuhu, PR China
| | - Yang Xu
- Key Laboratory of Non-coding RNA Transformation Research of Anhui Higher Education Institutes, Wannan Medical College, Wuhu, PR China.,Central Laboratory of Yijishan Hospital, Wannan Medical College, Wuhu, PR China
| | - Xiaolong Zhu
- Key Laboratory of Non-coding RNA Transformation Research of Anhui Higher Education Institutes, Wannan Medical College, Wuhu, PR China.,Central Laboratory of Yijishan Hospital, Wannan Medical College, Wuhu, PR China
| | - Tianbing Chen
- Key Laboratory of Non-coding RNA Transformation Research of Anhui Higher Education Institutes, Wannan Medical College, Wuhu, PR China.,Central Laboratory of Yijishan Hospital, Wannan Medical College, Wuhu, PR China
| | - Jingjing Ye
- Key Laboratory of Non-coding RNA Transformation Research of Anhui Higher Education Institutes, Wannan Medical College, Wuhu, PR China.,Central Laboratory of Yijishan Hospital, Wannan Medical College, Wuhu, PR China
| | - Kun Lv
- Key Laboratory of Non-coding RNA Transformation Research of Anhui Higher Education Institutes, Wannan Medical College, Wuhu, PR China.,Central Laboratory of Yijishan Hospital, Wannan Medical College, Wuhu, PR China
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35
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The epigenetic face of lupus: Focus on antigen-presenting cells. Int Immunopharmacol 2020; 81:106262. [PMID: 32045873 DOI: 10.1016/j.intimp.2020.106262] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2019] [Revised: 01/23/2020] [Accepted: 01/27/2020] [Indexed: 12/19/2022]
Abstract
In recent years, epigenetic mechanisms became widely known due to their ability to regulate and maintain physiological processes such as cell growth, development, differentiation and genomic stability. When dysregulated, epigenetic mechanisms, may introduce gene expression changes and disturbance in immune homeostasis leading to autoimmune diseases. Systemic lupus erythematosus (SLE), the most extensively studied autoimmune disorder, has already been correlated with epigenetic modifications, especially in T cells. Since these cell rely on antigen presentation, it may be assumed that erroneous activity of antigen-presenting cells (APCs), culminates in T cell abnormalities. In this review we summarize and discuss the epigenetic modifications in SLE affected APCs, with the focus on dendritic cells (DCs), B cells and monocytes. Unravelling this aspect of SLE pathogenesis, might result in identification of new disease biomarkers and putative therapeutic approaches.
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36
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Shi X, Yang Y, Shang S, Wu S, Zhang W, Peng L, Huang T, Zhang R, Ren R, Mi J, Wang Y. Cooperation of Dnmt3a R878H with Nras G12D promotes leukemogenesis in knock-in mice: a pilot study. BMC Cancer 2019; 19:1072. [PMID: 31703632 PMCID: PMC6842226 DOI: 10.1186/s12885-019-6207-y] [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: 06/14/2018] [Accepted: 09/25/2019] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND DNMT3A R882H, a frequent mutation in acute myeloid leukemia (AML), plays a critical role in malignant hematopoiesis. Recent findings suggest that DNMT3A mutant acts as a founder mutation and requires additional genetic events to induce full-blown AML. Here, we investigated the cooperation of mutant DNMT3A and NRAS in leukemogenesis by generating a double knock-in (DKI) mouse model harboring both Dnmt3a R878H and Nras G12D mutations. METHODS DKI mice with both Dnmt3a R878H and Nras G12D mutations were generated by crossing Dnmt3a R878H knock-in (KI) mice and Nras G12D KI mice. Routine blood test, flow cytometry analysis and morphological analysis were performed to determine disease phenotype. RNA-sequencing (RNA-seq), RT-PCR and Western blot were carried out to reveal the molecular mechanism. RESULTS The DKI mice developed a more aggressive AML with a significantly shortened lifespan and higher percentage of blast cells compared with KI mice expressing Dnmt3a or Nras mutation alone. RNA-seq analysis showed that Dnmt3a and Nras mutations collaboratively caused abnormal expression of a series of genes related to differentiation arrest and growth advantage. Myc transcription factor and its target genes related to proliferation and apoptosis were up-regulated, thus contributing to promote the process of leukemogenesis. CONCLUSION This study showed that cooperation of DNMT3A mutation and NRAS mutation could promote the onset of AML by synergistically disturbing the transcriptional profiling with Myc pathway involvement in DKI mice.
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Affiliation(s)
- Xiaodong Shi
- State Key Laboratory of Medical Genomics, Shanghai Institute of Hematology, Rui Jin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Ying Yang
- State Key Laboratory of Medical Genomics, Shanghai Institute of Hematology, Rui Jin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Siqi Shang
- State Key Laboratory of Medical Genomics, Shanghai Institute of Hematology, Rui Jin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Songfang Wu
- State Key Laboratory of Medical Genomics, Shanghai Institute of Hematology, Rui Jin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Weina Zhang
- State Key Laboratory of Medical Genomics, Shanghai Institute of Hematology, Rui Jin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Lijun Peng
- State Key Laboratory of Medical Genomics, Shanghai Institute of Hematology, Rui Jin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Ting Huang
- State Key Laboratory of Medical Genomics, Shanghai Institute of Hematology, Rui Jin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Ruihong Zhang
- State Key Laboratory of Medical Genomics, Shanghai Institute of Hematology, Rui Jin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Ruibao Ren
- State Key Laboratory of Medical Genomics, Shanghai Institute of Hematology, Rui Jin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Jianqing Mi
- State Key Laboratory of Medical Genomics, Shanghai Institute of Hematology, Rui Jin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
| | - Yueying Wang
- State Key Laboratory of Medical Genomics, Shanghai Institute of Hematology, Rui Jin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
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37
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Sandoval JE, Reich NO. The R882H substitution in the human de novo DNA methyltransferase DNMT3A disrupts allosteric regulation by the tumor supressor p53. J Biol Chem 2019; 294:18207-18219. [PMID: 31640986 DOI: 10.1074/jbc.ra119.010827] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Revised: 10/18/2019] [Indexed: 12/14/2022] Open
Abstract
A myriad of protein partners modulate the activity of the human DNA methyltransferase 3A (DNMT3A), whose interactions with these other proteins are frequently altered during oncogenesis. We show here that the tumor suppressor p53 decreases DNMT3A activity by forming a heterotetramer complex with DNMT3A. Mutational and modeling experiments suggested that p53 interacts with the same region in DNMT3A as does the structurally characterized DNMT3L. We observed that the p53-mediated repression of DNMT3A activity is blocked by amino acid substitutions within this interface, but surprisingly, also by a distal DNMT3A residue, R882H. DNMT3A R882H occurs frequently in various cancers, including acute myeloid leukemia, and our results suggest that the effects of R882H and other DNMT3A mutations may go beyond changes in DNMT3A methylation activity. To further understand the dynamics of how protein-protein interactions modulate DNMT3A activity, we determined that p53 has a greater affinity for DNMT3A than for DNMT3L and that p53 readily displaces DNMT3L from the DNMT3A:DNMT3L heterotetramer. Interestingly, this occurred even when the preformed DNMT3A:DNMT3L complex was actively methylating DNA. The frequently identified p53 substitutions (R248W and R273H), whereas able to regulate DNMT3A function when forming the DNMT3A:p53 heterotetramer, no longer displaced DNMT3L from the DNMT3A:DNMT3L heterotetramer. The results of our work highlight the complex interplay between DNMT3A, p53, and DNMT3L and how these interactions are further modulated by clinically derived mutations in each of the interacting partners.
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Affiliation(s)
- Jonathan E Sandoval
- Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, California 93106-9510
| | - Norbert O Reich
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106-9510.
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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: 3.3] [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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Epigenetic Abnormalities in Acute Myeloid Leukemia and Leukemia Stem Cells. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019. [PMID: 31338820 DOI: 10.1007/978-981-13-7342-8_8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/28/2023]
Abstract
Recently advances in cancer genomics revealed the unexpected high frequencies of epigenetic abnormalities in human acute myeloid leukemia (AML). Accumulating data suggest that these leukemia-associated epigenetic factors play critical roles in both normal hematopoietic stem cells (HSCs) and leukemia stem cells (LSCs). In turn, these abnormalities result in susceptibilities of LSC and related diseases to epigenetic inhibitors. In this chapter, we will focus on the mutations of epigenetic factors in AML, their functional roles and mechanisms in normal hematopoiesis and leukemia genesis, especially in LSC, and potential treatment opportunities specifically for AML with epigenetic dysregulations.
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40
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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: 39] [Impact Index Per Article: 6.5] [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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Zhang Y, Gu H, Chen Q, Zhang Y, Cheng H, Yang J, Wang J, Hu X. Low Platelet Counts at Diagnosis Predict Better Survival for Patients with Intermediate-Risk Acute Myeloid Leukemia. Acta Haematol 2019; 143:9-18. [PMID: 31167182 DOI: 10.1159/000500230] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Accepted: 04/08/2019] [Indexed: 12/19/2022]
Abstract
BACKGROUND Aggressive growth of primitive and immature cells in the bone marrow results in reductions in megakaryocyte and platelet (PLT) counts, leading to thrombocytopenia in acute myeloid leukemia (AML). However, not all AML patients show thrombocytopenia at the time of diagnosis, and the association of PLT count with patient survival is largely unknown. METHODS A retrospective study was performed to determine PLT counts at diagnosis in the peripheral blood in 291 newly diagnosed AML patients and assess the association of PLT counts with the overall survival (OS) and disease-free survival (DFS) of these patients. RESULTS Low PLT counts (≤40 × 109/L) were associated with better outcomes for the whole cohort (5-year OS, 55.1 ± 3.8 vs. 35.3 ± 3.5%, p < 0.001; 5-year DFS, 49.1 ± 3.8 vs. 25.7 ± 4.0%, p < 0.001) and intermediate-risk patients (5-year OS, 64.5 ± 5.4 vs. 41.0 ± 4.8%, p < 0.001; 5-year DFS, 60.8 ± 5.6 vs. 28.6 ± 5.6%, p < 0.001). Moreover, low PLT counts were related to deeper molecular remission. Low PLT counts correlated with better survival of intermediate-risk AML patients treated with chemotherapy only. Allogeneic hematopoietic stem cell transplantation attenuated the negative impact of high PLT counts on the survival of intermediate-risk patients. Furthermore, univariate and multivariate analyses demonstrated that PLT count at diagnosis was an independent prognostic factor for intermediate-risk AML. CONCLUSION PLT count at diagnosis predicts survival for patients with intermediate-risk AML.
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Affiliation(s)
- Yimin Zhang
- Department of Hematology, Institute of Hematology, Changhai Hospital, Shanghai, China
| | - Haihui Gu
- Department of Transfusion Medicine, Changhai Hospital, Shanghai, China
| | - Qi Chen
- Department of Health Statistics, Second Military Medical University, Shanghai, China
| | - Ying Zhang
- Department of Hematology, Institute of Hematology, Changhai Hospital, Shanghai, China
| | - Hui Cheng
- Department of Hematology, Institute of Hematology, Changhai Hospital, Shanghai, China
| | - Jianmin Yang
- Department of Hematology, Institute of Hematology, Changhai Hospital, Shanghai, China
| | - Jianmin Wang
- Department of Hematology, Institute of Hematology, Changhai Hospital, Shanghai, China
| | - Xiaoxia Hu
- Department of Hematology, Institute of Hematology, Changhai Hospital, Shanghai, China,
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42
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Han M, Jia L, Lv W, Wang L, Cui W. Epigenetic Enzyme Mutations: Role in Tumorigenesis and Molecular Inhibitors. Front Oncol 2019; 9:194. [PMID: 30984620 PMCID: PMC6449417 DOI: 10.3389/fonc.2019.00194] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2018] [Accepted: 03/06/2019] [Indexed: 12/19/2022] Open
Abstract
Epigenetic modifications, such as DNA methylation and histone modification, result in heritable changes in gene expression without changing the DNA sequence. Epigenetic regulatory enzymes such as DNA methyltransferases, histone methyltransferases, and histone deacetylases are involved in epigenetic modification. Studies have shown that the dysregulation caused by changes in the amino acid sequence of these enzymes is closely correlated with tumor onset and progression. In addition, certain amino acid changes in the metabolic enzyme isocitrate dehydrogenase (IDH) are linked to altered epigenetic modifications in tumors. Some small molecule inhibitors targeting these aberrant enzymes have shown promising anti-cancer efficacy in preclinical and clinical trials. For example, the small molecule inhibitor ivosidenib, which targets IDH1 with a mutation at R132, has been approved by the FDA for the clinical treatment of acute myeloid leukemia. In this review, we summarize the recurrent “hotspot” mutations in these enzymes in various tumors and their role in tumorigenesis. We also describe candidate inhibitors of the mutant enzymes which show potential therapeutic value. In addition, we introduce some previously unreported mutation sites in these enzymes, which may be related to tumor development and provide opportunities for future study.
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Affiliation(s)
- Mei Han
- Department of Pharmacology, Shenyang Pharmaceutical University, Shenyang, China
| | - Lina Jia
- Department of Pharmacology, Shenyang Pharmaceutical University, Shenyang, China
| | - Wencai Lv
- Department of Pharmacology, Shenyang Pharmaceutical University, Shenyang, China
| | - Lihui Wang
- Department of Pharmacology, Shenyang Pharmaceutical University, Shenyang, China
| | - Wei Cui
- Department of Pharmacology, Shenyang Pharmaceutical University, Shenyang, China
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43
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Sequentially inducible mouse models reveal that Npm1 mutation causes malignant transformation of Dnmt3a-mutant clonal hematopoiesis. Leukemia 2019; 33:1635-1649. [PMID: 30692594 PMCID: PMC6609470 DOI: 10.1038/s41375-018-0368-6] [Citation(s) in RCA: 88] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Revised: 11/27/2018] [Accepted: 12/13/2018] [Indexed: 12/21/2022]
Abstract
Clonal hematopoiesis (CH) is a common aging-associated condition with increased risk of hematologic malignancy. Knowledge of the mechanisms driving evolution from CH to overt malignancy has been hampered by a lack of in vivo models that orthogonally activate mutant alleles. Here, we develop independently regulatable mutations in DNA methyltransferase 3A (Dnmt3a) and nucleophosmin 1 (Npm1), observed in human CH and AML, respectively. We find Dnmt3a mutation expands hematopoietic stem and multipotent progenitor cells (HSC/MPPs), modeling CH. Induction of mutant Npm1 after development of Dnmt3a-mutant CH causes progression to myeloproliferative disorder (MPD), and more aggressive MPD is observed with longer latency between mutations. MPDs uniformly progress to acute myeloid leukemia (AML) following transplant, accompanied by a decrease in HSC/MPPs and an increase in myeloid-restricted progenitors, the latter of which propagate AML in tertiary recipient mice. At a molecular level, progression of CH to MPD is accompanied by selection for mutations activating Ras/Raf/MAPK signaling. Progression to AML is characterized by additional oncogenic signaling mutations (Ptpn11, Pik3r1, Flt3) and/or mutations in epigenetic regulators (Hdac1, Idh1, Arid1a). Together, our study demonstrates that Npm1 mutation drives evolution of Dnmt3a-mutant CH to AML and rate of disease progression is accelerated with longer latency of CH.
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44
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Liu L, Shi T, Houk KN, Zhao YL. Understanding the R882H mutation effects of DNA methyltransferase DNMT3A: a combination of molecular dynamics simulations and QM/MM calculations. RSC Adv 2019; 9:31425-31434. [PMID: 35527972 PMCID: PMC9072302 DOI: 10.1039/c9ra06791d] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Accepted: 09/17/2019] [Indexed: 01/15/2023] Open
Abstract
The AML-related high-frequent R882H mutation of DNA (cytosine-5)-methyltransferase 3A (DNMT3A), a key enzyme forde novoepigenetic methylation in human beings, was characterized by a disturbing conformation ofS-adenosylmethionine (SAM).
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Affiliation(s)
- Lanxuan Liu
- State Key Laboratory of Microbial Metabolism
- Joint International Research Laboratory of Metabolic and Developmental Sciences
- School of Life Sciences and Biotechnology
- Shanghai Jiao Tong University
- Shanghai 200240
| | - Ting Shi
- State Key Laboratory of Microbial Metabolism
- Joint International Research Laboratory of Metabolic and Developmental Sciences
- School of Life Sciences and Biotechnology
- Shanghai Jiao Tong University
- Shanghai 200240
| | - Kendall N. Houk
- Department of Chemistry and Biochemistry
- University of California
- Los Angeles
- USA
| | - Yi-Lei Zhao
- State Key Laboratory of Microbial Metabolism
- Joint International Research Laboratory of Metabolic and Developmental Sciences
- School of Life Sciences and Biotechnology
- Shanghai Jiao Tong University
- Shanghai 200240
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45
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Genetic and Epigenetic Perturbations by DNMT3A-R882 Mutants Impaired Apoptosis through Augmentation of PRDX2 in Myeloid Leukemia Cells. Neoplasia 2018; 20:1106-1120. [PMID: 30245403 PMCID: PMC6153424 DOI: 10.1016/j.neo.2018.08.013] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Revised: 08/30/2018] [Accepted: 08/31/2018] [Indexed: 01/02/2023] Open
Abstract
DNA methyltransferase 3A (DNMT3A) is mutated in various myeloid neoplasms including acute myeloid leukemia (AML), especially at the Arg882 and associated with inferior outcomes. Here, we report that the DNMT3A-Arg882His/Cys (R882H/C) mutations led to inactivation of apoptosis through DNA damage signaling following the impairment of differentiation of myeloid leukemia cells. Gene expression profiling analysis revealed aberrant expression of several cell-cycle and apoptosis-related genes, and the DNA methylation assay identified both hypo- and hypermethylation features in different regions throughout the whole genome of DNMT3A mutants-transduced myeloid cells. We found that DNMT3A-R882H/C mutations upregulated the expression of an antioxidant protein, pyroxiredoxin-2 (PRDX2), at the mRNA and protein levels with decreased accumulation of reactive oxygen species (ROS). Augmentation of ROS generation by ROS accumulating agent or by knockdown of PRDX2 from myeloid cells effectively increased drug sensitivity and apoptosis as a consequence of reduced cell proliferation. DNMT3A-R882C/H mutations decreased apoptosis induction in part by increasing the antioxidant capacity of the cell owing to upregulation of PRDX2. Molecularly, both DNMT3A-WT and R882H/C mutants interacted with PRDX2; and R882C/H mutation-induced hypomethylation increased PRDX2 expression which enhanced cell proliferation and growth with impairment of apoptosis, thereby contributing to leukemogenesis.
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46
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Chen D, Christopher M, Helton NM, Ferguson I, Ley TJ, Spencer DH. DNMT3A R882-associated hypomethylation patterns are maintained in primary AML xenografts, but not in the DNMT3A R882C OCI-AML3 leukemia cell line. Blood Cancer J 2018; 8:38. [PMID: 29618788 PMCID: PMC5884841 DOI: 10.1038/s41408-018-0072-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Revised: 02/09/2018] [Accepted: 02/26/2018] [Indexed: 02/07/2023] Open
Affiliation(s)
- David Chen
- Division of Dermatology, and Section of Stem Cell Biology, Department of Internal Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Matthew Christopher
- Division of Oncology, Section of Stem Cell Biology, Department of Internal Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Nichole M Helton
- Division of Oncology, Section of Stem Cell Biology, Department of Internal Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Ian Ferguson
- Division of Oncology, Section of Stem Cell Biology, Department of Internal Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Timothy J Ley
- Division of Oncology, Section of Stem Cell Biology, Department of Internal Medicine, Washington University School of Medicine, St. Louis, MO, USA.,McDonnell Genome Institute, Washington University, St. Louis, MO, USA
| | - David H Spencer
- Division of Oncology, Section of Stem Cell Biology, Department of Internal Medicine, Washington University School of Medicine, St. Louis, MO, USA. .,McDonnell Genome Institute, Washington University, St. Louis, MO, USA.
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47
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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: 15] [Impact Index Per Article: 2.1] [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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48
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Utx loss causes myeloid transformation. Leukemia 2018; 32:1458-1465. [PMID: 29479066 DOI: 10.1038/s41375-018-0011-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2017] [Revised: 12/11/2017] [Accepted: 12/14/2017] [Indexed: 01/08/2023]
Abstract
Recurrent somatic loss-of-function mutations in histone demethylases are frequently detected in cancer. However, whether loss of a histone demethylase can cause cancer has not been determined. Here, we report that knockout of the histone demethylase Utx in mice causes a chronic myelomonocytic leukemia (CMML)-like disease with splenomegaly, monocytosis, and extramedullary hematopoiesis. Mutational analysis of patient data indicated that UTX mutations occur simultaneously with TP53 mutations in myeloid malignancies, and combined inactivation of Utx and Trp53 accelerated the development of CMML in a cell-autonomous manner. Utx loss caused increased self-renewal of hematopoietic stem cells and predisposed hematopoietic stem cells to differentiate into myeloid-derived lineages. Transcriptome and chromatin immunoprecipitation analyses revealed that Utx activates key transcriptional factors required for erythroid differentiation by modulating histone H3 lysine 27 and lysine 4 trimethylation. Our results suggest that Utx suppresses CMML formation by controlling hematopoietic stem cell self-renewal and differentiation.
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49
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Liao M, Wang J. Mechanisms of Hematopoietic Stem Cell Ageing and Targets for Hematopoietic Tumour Prevention. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2018; 1086:117-140. [PMID: 30232756 DOI: 10.1007/978-981-13-1117-8_8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Hematopoietic stem cells represent a rare population in the bone marrow, with the capacity of generating all blood lineage and themselves at the same time. With aging, the reconstitution capacity of hematopoietic stem cells decreases accompanying with differentiation skewing wherein the myeloid branch dominates in both mouse and human. In recent years, various molecular mechanisms that induce functional decline of HSC during aging were disclosed including DNA damage accumulation, metabolic alteration, defects in protein homeostasis, and aging-induced changes in the blood circulatory environment. Deciphering the nature of HSC aging could improve our knowledge of HSC aging-related diseases and furthermore promote the developing of therapeutic interventions for human HSC aging and diseases.
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Affiliation(s)
- Min Liao
- School of Pharmaceutical Sciences, Tsinghua University, Beijing, China
| | - Jianwei Wang
- School of Pharmaceutical Sciences, Tsinghua University, Beijing, China.
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50
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Zhao J, Wang Y, Liang Q, Xu Y, Sang J. MAGEA1 inhibits the expression of BORIS via increased promoter methylation. J Cell Sci 2018; 132:jcs.218628. [DOI: 10.1242/jcs.218628] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Accepted: 11/23/2018] [Indexed: 12/13/2022] Open
Abstract
Melanoma-associated antigen A1 (MAGEA1) and BORIS are members of the cancer testis antigens (CTA) family. Their functions and expression regulation mechanisms are not fully understood. In this study, we revealed new functions and regulatory mechanisms of MAGEA1 and BORIS in breast cancer cells, which were investigated in parental and genetically manipulated breast cancer cells via gene overexpression or siRNA interference-mediated down-regulation. We identified the interaction between MAGEA1 and CTCF, which was required for the binding of MAGEA1 to BORIS promoter and critical for the recruitment of DNMT3a. A protein complex containing MAGEA1, CTCF and DNMT3a will be formed before or after the conjunction with BORIS promoter. The binding of this complex to the BORIS promoter accounts for the hypermethylation and repression of BORIS expression, which results in cell death in the breast cancer cell lines tested. Multiple approaches are employed, including co-IP, GST-pull down, co-localization, cell death analyses using the Annexin V-FITC/PI double staining and caspase3 activation assays, ChIP and bisulfite sequencing PCR assays for methylation. These results have implications in the development of strategies in CTA-based immune therapeutics.
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Affiliation(s)
- Jizhong Zhao
- Key Laboratory of Cell Proliferation and Regulation, College of Life Sciences, Beijing Normal University, Beijing, China
| | - Yueqing Wang
- Key Laboratory of Cell Proliferation and Regulation, College of Life Sciences, Beijing Normal University, Beijing, China
| | - Qianjin Liang
- Key Laboratory of Cell Proliferation and Regulation, College of Life Sciences, Beijing Normal University, Beijing, China
| | - Yan Xu
- Department of Obstetrics and Gynecology, Indiana University School of Medicine, 1044 W. Walnut St. R4-W037, Indianapolis, IN 46202, USA
| | - Jianli Sang
- Key Laboratory of Cell Proliferation and Regulation, College of Life Sciences, Beijing Normal University, Beijing, China
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