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Younesian S, Mohammadi MH, Younesian O, Momeny M, Ghaffari SH, Bashash D. DNA methylation in human diseases. Heliyon 2024; 10:e32366. [PMID: 38933971 PMCID: PMC11200359 DOI: 10.1016/j.heliyon.2024.e32366] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2023] [Revised: 05/30/2024] [Accepted: 06/03/2024] [Indexed: 06/28/2024] Open
Abstract
Aberrant epigenetic modifications, particularly DNA methylation, play a critical role in the pathogenesis and progression of human diseases. The current review aims to reveal the role of aberrant DNA methylation in the pathogenesis and progression of diseases and to discuss the original data obtained from international research laboratories on this topic. In the review, we mainly summarize the studies exploring the role of aberrant DNA methylation as diagnostic and prognostic biomarkers in a broad range of human diseases, including monogenic epigenetics, autoimmunity, metabolic disorders, hematologic neoplasms, and solid tumors. The last section provides a general overview of the possibility of the DNA methylation machinery from the perspective of pharmaceutic approaches. In conclusion, the study of DNA methylation machinery is a phenomenal intersection that each of its ways can reveal the mysteries of various diseases, introduce new diagnostic and prognostic biomarkers, and propose a new patient-tailored therapeutic approach for diseases.
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Affiliation(s)
- Samareh Younesian
- Department of Hematology and Blood Banking, School of Allied Medical Sciences, Shahid Beheshti University of Medical Sciences, Tehran, 1971653313 Iran
| | - Mohammad Hossein Mohammadi
- Department of Hematology and Blood Banking, School of Allied Medical Sciences, Shahid Beheshti University of Medical Sciences, Tehran, 1971653313 Iran
| | - Ommolbanin Younesian
- School of Medicine, Tonekabon Branch, Islamic Azad University, Tonekabon, 46841-61167 Iran
| | - Majid Momeny
- The Brown Foundation Institute of Molecular Medicine, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, 77030 TX, USA
| | - Seyed H. Ghaffari
- Hematology, Oncology and Stem Cell Transplantation Research Center, Shariati Hospital, Tehran University of Medical Sciences, Tehran, 1411713135 Iran
| | - Davood Bashash
- Department of Hematology and Blood Banking, School of Allied Medical Sciences, Shahid Beheshti University of Medical Sciences, Tehran, 1971653313 Iran
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Huang C, Aghaei-Zarch SM. From molecular pathogenesis to therapy: Unraveling non-coding RNAs/DNMT3A axis in human cancers. Biochem Pharmacol 2024; 222:116107. [PMID: 38438051 DOI: 10.1016/j.bcp.2024.116107] [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: 11/23/2023] [Revised: 02/03/2024] [Accepted: 03/01/2024] [Indexed: 03/06/2024]
Abstract
Cancer is a comprehensive classification encompassing more than 100 forms of malignancies that manifest in diverse tissues within the human body. Recent studies have provided evidence that aberrant epigenetic modifications are pivotal indicators of cancer. Epigenetics encapsulates DNA methyltransferases as a crucial class of modifiers. DNMTs, including DNMT3A, assume central roles in DNA methylation processes that orchestrate normal biological functions, such as gene transcription, predominantly in mammals. Typically, deviations in DNMT3A function engender distortions in factors that drive tumor growth and progression, thereby exacerbating the malignant phenotype of tumors. Consequently, such abnormalities pose significant challenges in cancer therapy because they impede treatment efficacy. Non-coding RNAs (ncRNAs) represent a group of RNA molecules that cannot encode functional proteins. Recent investigation attests to the crucial significance of regulatory ncRNAs in epigenetic regulation. Notably, recent reports have illuminated the complex interplay between ncRNA expression and epigenetic regulatory machinery, including DNMT3A, particularly in cancer. Recent findings have demonstrated that miRNAs, namely miR-770-5p, miR-101, and miR-145 exhibit the capability to target DNMT3A directly, and their aberration is implicated in diverse cellular abnormalities that predispose to cancer development. This review aims to articulate the interplay between DNMT3A and the ncRNAs, focusing on its impact on the development and progression of cancer, cancer therapy resistance, cancer stem cells, and prognosis. Importantly, the emergence of such reports that suggest a connection between DNMT3A and ncRNAs in several cancers indicates that this connecting axis offers a valuable target with significant therapeutic potential that might be exploited for cancer management.
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Affiliation(s)
- Chunjie Huang
- School of Medicine, Nantong University, Nantong 226001, China
| | - Seyed Mohsen Aghaei-Zarch
- Department of Medical Genetics, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
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3
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Xie X, Su M, Ren K, Ma X, Lv Z, Li Z, Mei Y, Ji P. Clonal hematopoiesis and bone marrow inflammation. Transl Res 2023; 255:159-170. [PMID: 36347490 DOI: 10.1016/j.trsl.2022.11.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Revised: 10/22/2022] [Accepted: 11/01/2022] [Indexed: 11/07/2022]
Abstract
Clonal hematopoiesis (CH) occurs in hematopoietic stem cells with increased risks of progressing to hematologic malignancies. CH mutations are predominantly found in aged populations and correlate with an increased incidence of cardiovascular and other diseases. Increased lines of evidence demonstrate that CH mutations are closely related to the inflammatory bone marrow microenvironment. In this review, we summarize the recent advances in this topic starting from the discovery of CH and its mutations. We focus on the most commonly mutated and well-studied genes in CH and their contributions to the innate immune responses and inflammatory signaling, especially in the hematopoietic cells of bone marrow. We also aimed to discuss the interrelationship between inflammatory bone marrow microenvironment and CH mutations. Finally, we provide our perspectives on the challenges in the field and possible future directions to help understand the pathophysiology of CH.
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Affiliation(s)
- Xinshu Xie
- School of Biomedical Sciences, Hunan University, Changsha, China
| | - Meng Su
- School of Biomedical Sciences, Hunan University, Changsha, China
| | - Kehan Ren
- Department of Pathology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois; Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Chicago, Illinois
| | - Xuezhen Ma
- School of Biomedical Sciences, Hunan University, Changsha, China
| | - Zhiyi Lv
- School of Biomedical Sciences, Hunan University, Changsha, China
| | - Zhaofeng Li
- School of Biomedical Sciences, Hunan University, Changsha, China
| | - Yang Mei
- School of Biomedical Sciences, Hunan University, Changsha, China; Hunan Provincial Key Laboratory of Medical Virology, Hunan University, Changsha, China.
| | - Peng Ji
- Department of Pathology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois; Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Chicago, Illinois.
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Epigenetic regulation in hematopoiesis and its implications in the targeted therapy of hematologic malignancies. Signal Transduct Target Ther 2023; 8:71. [PMID: 36797244 PMCID: PMC9935927 DOI: 10.1038/s41392-023-01342-6] [Citation(s) in RCA: 22] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Revised: 01/03/2023] [Accepted: 01/19/2023] [Indexed: 02/18/2023] Open
Abstract
Hematologic malignancies are one of the most common cancers, and the incidence has been rising in recent decades. The clinical and molecular features of hematologic malignancies are highly heterogenous, and some hematologic malignancies are incurable, challenging the treatment, and prognosis of the patients. However, hematopoiesis and oncogenesis of hematologic malignancies are profoundly affected by epigenetic regulation. Studies have found that methylation-related mutations, abnormal methylation profiles of DNA, and abnormal histone deacetylase expression are recurrent in leukemia and lymphoma. Furthermore, the hypomethylating agents and histone deacetylase inhibitors are effective to treat acute myeloid leukemia and T-cell lymphomas, indicating that epigenetic regulation is indispensable to hematologic oncogenesis. Epigenetic regulation mainly includes DNA modifications, histone modifications, and noncoding RNA-mediated targeting, and regulates various DNA-based processes. This review presents the role of writers, readers, and erasers of DNA methylation and histone methylation, and acetylation in hematologic malignancies. In addition, this review provides the influence of microRNAs and long noncoding RNAs on hematologic malignancies. Furthermore, the implication of epigenetic regulation in targeted treatment is discussed. This review comprehensively presents the change and function of each epigenetic regulator in normal and oncogenic hematopoiesis and provides innovative epigenetic-targeted treatment in clinical practice.
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Aladily TN, Qiqieh JF, Alshorman A, Alhyari S, Khader M. PAX5 and TDT-Negative B-Acute Lymphoblastic Leukemia with Unusual Genetic Mutations: A Case Report. Avicenna J Med 2022; 12:186-190. [PMID: 36570429 PMCID: PMC9771627 DOI: 10.1055/s-0042-1758387] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
B-acute lymphoblastic leukemia (B-ALL) is commonly encountered in clinical practice. Patients present with increased percentage of lymphoblasts in bone marrow and/or peripheral blood. Immunophenotypic study by flow cytometry or immunohistochemistry is essential to establish the diagnosis. Paired box-5 (PAX5) is a B cell lineage protein and terminal deoxynucleotidyl transferase (TDT) is an immature marker, both of which are routinely tested in the pathologic workup of acute leukemia. In this report, we describe a case of B-ALL in a 37-year-old woman in which both PAX5 and TDT were negative. Next-generation sequencing test detected mutations in DNA methyltransferase 3 α and Fms related receptor tyrosine kinase 3 genes, which are frequently mutated in acute myeloid leukemia rather than B-ALL. The constellation of these rare findings in a single case signifies the importance of examining a wide panel of markers when the diagnosis of ALL is suspected.
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Affiliation(s)
- Tariq N. Aladily
- Department of Hematopathology, The University of Jordan, Amman, Jordan,Address for correspondence Tariq N. Aladily, MD Department of Hematopathology, The University of JordanAmman 11814Jordan
| | - Jamil F. Qiqieh
- Department of Hematopathology, The University of Jordan, Amman, Jordan
| | - Alaa Alshorman
- Department of Hematology and Oncology, The University of Jordan, Amman, Jordan
| | - Salem Alhyari
- Department of Hematology and Oncology, The University of Jordan, Amman, Jordan
| | - Majd Khader
- Department of Pathology, King Hussein Cancer Center, Amman, Jordan
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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 drives daunorubicin resistance in acute myeloid leukemia via regulating NRF2/NQO1 pathway. Cell Commun Signal 2022; 20:168. [PMID: 36303144 PMCID: PMC9615155 DOI: 10.1186/s12964-022-00978-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Accepted: 09/24/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND DNA methyltransferase 3A (DNMT3A) often mutate on arginine 882 (DNMT3AR882) in acute myeloid leukemia (AML). AML patients with DNMT3A R882 mutation are usually resistant to daunorubicin treatment; however, the associated mechanism is still unclear. Therefore, it is urgent to investigate daunorubicin resistance in AML patients with DNMT3A R882 mutant. METHOD AML cell lines with DNMT3A-wild type (DNMT3A-WT), and DNMT3A-Arg882His (DNMT3A-R882H) mutation were constructed to investigate the role of DNMT3A R882H mutation on cell proliferation, apoptosis and cells' sensitivity to Danunorubin. Bioinformatics was used to analyze the role of nuclear factor-E2-related factor (NRF2) in AML patients with DNMT3A R882 mutation. The regulatory mechanism of DNMT3A R882H mutation on NRF2 was studied by Bisulfite Sequencing and CO-IP. NRF2 inhibitor Brusatol (Bru) was used to explore the role of NRF2 in AML cells carried DNMT3A R882H mutation. RESULTS AML cells with a DNMT3A R882H mutation showed high proliferative and anti-apoptotic activities. In addition, mutant cells were less sensitive to daunorubicin and had a higher NRF2 expression compared with those in WT cells. Furthermore, the NRF2/NQO1 pathway was activated in mutant cells in response to daunorubicin treatment. DNMT3A R882H mutation regulated the expression of NRF2 via influencing protein stability rather than decreasing methylation of NRF2 promoter. Also, NRF2/NQO1 pathway inhibition improved mutant cells' sensitivity to daunorubicin significantly. CONCLUSION Our findings identified NRF2 as an important player in the regulation of cell apoptosis through which helps mediate chemoresistance to daunorubicin in AML cells with DNMT3A R882H mutation. Targeting NRF2 might be a novel therapeutic approach to treat AML patients with a DNMT3A R882H mutation. Video abstract.
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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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Muylaert C, Van Hemelrijck LA, Maes A, De Veirman K, Menu E, Vanderkerken K, De Bruyne E. Aberrant DNA methylation in multiple myeloma: A major obstacle or an opportunity? Front Oncol 2022; 12:979569. [PMID: 36059621 PMCID: PMC9434119 DOI: 10.3389/fonc.2022.979569] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Accepted: 07/22/2022] [Indexed: 11/30/2022] Open
Abstract
Drug resistance (DR) of cancer cells leading to relapse is a huge problem nowadays to achieve long-lasting cures for cancer patients. This also holds true for the incurable hematological malignancy multiple myeloma (MM), which is characterized by the accumulation of malignant plasma cells in the bone marrow (BM). Although new treatment approaches combining immunomodulatory drugs, corticosteroids, proteasome inhibitors, alkylating agents, and monoclonal antibodies have significantly improved median life expectancy, MM remains incurable due to the development of DR, with the underlying mechanisms remaining largely ill-defined. It is well-known that MM is a heterogeneous disease, encompassing both genetic and epigenetic aberrations. In normal circumstances, epigenetic modifications, including DNA methylation and posttranslational histone modifications, play an important role in proper chromatin structure and transcriptional regulation. However, in MM, numerous epigenetic defects or so-called ‘epimutations’ have been observed and this especially at the level of DNA methylation. These include genome-wide DNA hypomethylation, locus specific hypermethylation and somatic mutations, copy number variations and/or deregulated expression patterns in DNA methylation modifiers and regulators. The aberrant DNA methylation patterns lead to reduced gene expression of tumor suppressor genes, genomic instability, DR, disease progression, and high-risk disease. In addition, the frequency of somatic mutations in the DNA methylation modifiers seems increased in relapsed patients, again suggesting a role in DR and relapse. In this review, we discuss the recent advances in understanding the involvement of aberrant DNA methylation patterns and/or DNA methylation modifiers in MM development, progression, and relapse. In addition, we discuss their involvement in MM cell plasticity, driving myeloma cells to a cancer stem cell state characterized by a more immature and drug-resistant phenotype. Finally, we briefly touch upon the potential of DNA methyltransferase inhibitors to prevent relapse after treatment with the current standard of care agents and/or new, promising (immuno) therapies.
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Plasticity of Cancer Stem Cell: Origin and Role in Disease Progression and Therapy Resistance. Stem Cell Rev Rep 2021; 16:397-412. [PMID: 31965409 DOI: 10.1007/s12015-019-09942-y] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
In embryonic development and throughout life, there are some cells can exhibit phenotypic plasticity. Phenotypic plasticity is the ability of cells to differentiate into multiple lineages. In normal development, plasticity is highly regulated whereas cancer cells re-activate this dynamic ability for their own progression. The re-activation of these mechanisms enables cancer cells to acquire a cancer stem cell (CSC) phenotype- a subpopulation of cells with increased ability to survive in a hostile environment and resist therapeutic insults. There are several contributors fuel CSC plasticity in different stages of disease progression such as a complex network of tumour stroma, epidermal microenvironment and different sub-compartments within tumour. These factors play a key role in the transformation of tumour cells from a stable condition to a progressive state. In addition, flexibility in the metabolic state of CSCs helps in disease progression. Moreover, epigenetic changes such as chromatin, DNA methylation could stimulate the phenotypic change of CSCs. Development of resistance to therapy due to highly plastic behaviour of CSCs is a major cause of treatment failure in cancers. However, recent studies explored that plasticity can also expose the weaknesses in CSCs, thereby could be utilized for future therapeutic development. Therefore, in this review, we discuss how cancer cells acquire the plasticity, especially the role of the normal developmental process, tumour microenvironment, and epigenetic changes in the development of plasticity. We further highlight the therapeutic resistance property of CSCs attributed by plasticity. Also, outline some potential therapeutic options against plasticity of CSCs. Graphical Abstract .
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Veiga CB, Lawrence EM, Murphy AJ, Herold MJ, Dragoljevic D. Myelodysplasia Syndrome, Clonal Hematopoiesis and Cardiovascular Disease. Cancers (Basel) 2021; 13:cancers13081968. [PMID: 33921778 PMCID: PMC8073047 DOI: 10.3390/cancers13081968] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Revised: 04/12/2021] [Accepted: 04/14/2021] [Indexed: 12/19/2022] Open
Abstract
Simple Summary The development of blood cancers is a complex process that involves the acquisition of specific blood disorders that precede cancer. These blood disorders are often driven by the accumulation of genetic abnormalities, which are discussed in this review. Likewise, predicting the rate of progression of these diseases is difficult, but it appears to be linked to which specific gene mutations are present in blood cells. In this review, we discuss a variety of genetic abnormalities that drive blood cancer, conditions that precede clinical symptoms of blood cancer, and how alterations in these genes change blood cell function. Additionally, we discuss the novel links between blood cancer development and heart disease. Abstract The development of myelodysplasia syndromes (MDS) is multiphasic and can be driven by a plethora of genetic mutations and/or abnormalities. MDS is characterized by a hematopoietic differentiation block, evidenced by increased immature hematopoietic cells, termed blast cells and decreased mature circulating leukocytes in at least one lineage (i.e., cytopenia). Clonal hematopoiesis of indeterminate potential (CHIP) is a recently described phenomenon preceding MDS development that is driven by somatic mutations in hemopoietic stem cells (HSCs). These mutant HSCs have a competitive advantage over healthy cells, resulting in an expansion of these clonal mutated leukocytes. In this review, we discuss the multiphasic development of MDS, the common mutations found in both MDS and CHIP, how a loss-of-function in these CHIP-related genes can alter HSC function and leukocyte development and the potential disease outcomes that can occur with dysfunctional HSCs. In particular, we discuss the novel connections between MDS development and cardiovascular disease.
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Affiliation(s)
- Camilla Bertuzzo Veiga
- Division of Immunometabolism, Baker Heart and Diabetes Institute, Melbourne, VIC 3004, Australia; (C.B.V.); (A.J.M.)
- Department of Anatomy and Physiology, University of Melbourne, Parkville, Melbourne, VIC 3010, Australia
| | - Erin M. Lawrence
- Walter and Eliza Hall Institute of Medical Research, 1 G Royal Parade, Parkville, Melbourne, VIC 3052, Australia; (E.M.L.); (M.J.H.)
- Department of Medical Biology, University of Melbourne, Parkville, Melbourne, VIC 3052, Australia
| | - Andrew J. Murphy
- Division of Immunometabolism, Baker Heart and Diabetes Institute, Melbourne, VIC 3004, Australia; (C.B.V.); (A.J.M.)
- Department of Diabetes, Department of Immunology, Monash University, Clayton, VIC 3004, Australia
- Baker Department of Cardiometabolic Health, University of Melbourne, Melbourne, VIC 3052, Australia
| | - Marco J. Herold
- Walter and Eliza Hall Institute of Medical Research, 1 G Royal Parade, Parkville, Melbourne, VIC 3052, Australia; (E.M.L.); (M.J.H.)
- Department of Medical Biology, University of Melbourne, Parkville, Melbourne, VIC 3052, Australia
| | - Dragana Dragoljevic
- Division of Immunometabolism, Baker Heart and Diabetes Institute, Melbourne, VIC 3004, Australia; (C.B.V.); (A.J.M.)
- Department of Diabetes, Department of Immunology, Monash University, Clayton, VIC 3004, Australia
- Baker Department of Cardiometabolic Health, University of Melbourne, Melbourne, VIC 3052, Australia
- Correspondence:
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Sarkar S, Chaudhuri T, Roy S, Bose S. A rare synchronous presentation of double primary malignancies – lung and prostate. J Cancer Res Ther 2021; 17:1576-1579. [DOI: 10.4103/jcrt.jcrt_822_17] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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11
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Jiang D, Shu C, Lei C, Wan Y, Sun L. Early-onset colorectal cancer: A distinct entity with unique genetic features. Oncol Lett 2020; 20:33. [PMID: 32774506 PMCID: PMC7406876 DOI: 10.3892/ol.2020.11894] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Accepted: 06/26/2020] [Indexed: 02/05/2023] Open
Abstract
The aim of the present study was to elucidate the genetic features of early-onset colorectal cancer (CRC), particularly the genetic mutations that may be regarded as prognostic and/or predictive markers in CRC and other malignancies. In total, 40 patients with non-polyposis CRC aged 35 or younger were selected. The formalin-fixed, paraffin-embedded tumors acquired were subjected to mismatch repair (MMR) protein immunochemical staining and gene analysis with next-generation sequencing (44 exons, 17 genes; Ion Torrent Sequencing Platform). A total of 11 (27.5%) tumors presented with MMR protein deficiency (dMMR) and 26 (65%) tumors harbored one or more genetic mutations, including K-RAS proto-oncogene (35%), phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit alpha (PIK3CA; 20%), B-Raf proto-oncogene (5%), erb-b2 receptor tyrosine kinase 2 (5%), discoidin domain receptor tyrosine kinase 2 (5%), N-RAS proto-oncogene (2.5%), KIT proto-oncogene (2.5%), TSC complex subunit 1 (2.5%), DNA methyltransferase 3 alpha (2.5%) and ABL proto-oncogene 1 (2.5%). Of the dMMR tumors, 81.8% (9/11) of cases presented with mutations in the tested genes, while only 58.6% (17/29) of the MMR-proficient (pMMR) tumors presented with these (P=0.158). PI3KCA was frequently mutated in dMMR tumors compared to pMMR tumors (P=0.025). In a subgroup with a family history of CRC, the dMMR status (P<0.001) and PIK3CA genetic mutation status (P=0.01) were more frequently observed compared to the other two groups (with a family history of other cancer types or no malignancy). Almost all patients who had relatives with CRC presented with both dMMR and other genetic mutations, while this was not observed in the patients who had relatives with other types of carcinoma. Certain genetic mutations that are rarely reported in CRC were only identified in those patients with a family history of carcinoma. In conclusion, non-polyposis CRC in young adults presents as a distinct entity with a unique set of genetic features. However, investigation of more cases in further studies is required to verify the present results.
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Affiliation(s)
- Dan Jiang
- Department of Pathology, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, P.R. China
| | - Chang Shu
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Chengdu, Sichuan 610041, P.R. China
| | - Chuanfen Lei
- Department of Pathology, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, P.R. China
| | - Ying Wan
- Department of Pathology, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, P.R. China
| | - Linyong Sun
- Department of Pathology, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, P.R. China
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Tsankov AM, Wadsworth MH, Akopian V, Charlton J, Allon SJ, Arczewska A, Mead BE, Drake RS, Smith ZD, Mikkelsen TS, Shalek AK, Meissner A. Loss of DNA methyltransferase activity in primed human ES cells triggers increased cell-cell variability and transcriptional repression. Development 2019; 146:dev174722. [PMID: 31515224 PMCID: PMC6803377 DOI: 10.1242/dev.174722] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2018] [Accepted: 08/12/2019] [Indexed: 01/23/2023]
Abstract
Maintenance of pluripotency and specification towards a new cell fate are both dependent on precise interactions between extrinsic signals and transcriptional and epigenetic regulators. Directed methylation of cytosines by the de novo methyltransferases DNMT3A and DNMT3B plays an important role in facilitating proper differentiation, whereas DNMT1 is essential for maintaining global methylation levels in all cell types. Here, we generated single-cell mRNA expression data from wild-type, DNMT3A, DNMT3A/3B and DNMT1 knockout human embryonic stem cells and observed a widespread increase in cellular and transcriptional variability, even with limited changes in global methylation levels in the de novo knockouts. Furthermore, we found unexpected transcriptional repression upon either loss of the de novo methyltransferase DNMT3A or the double knockout of DNMT3A/3B that is further propagated upon differentiation to mesoderm and ectoderm. Taken together, our single-cell RNA-sequencing data provide a high-resolution view into the consequences of depleting the three catalytically active DNMTs in human pluripotent stem cells.
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Affiliation(s)
- Alexander M Tsankov
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Marc H Wadsworth
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Institute for Medical Engineering & Science (IMES), Department of Chemistry and Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Veronika Akopian
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA
| | - Jocelyn Charlton
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA
- Department of Genome Regulation, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | - Samuel J Allon
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Institute for Medical Engineering & Science (IMES), Department of Chemistry and Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Aleksandra Arczewska
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA
- Department of Genome Regulation, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | - Benjamin E Mead
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Institute for Medical Engineering & Science (IMES), Department of Chemistry and Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Riley S Drake
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Institute for Medical Engineering & Science (IMES), Department of Chemistry and Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Zachary D Smith
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA
| | | | - Alex K Shalek
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Institute for Medical Engineering & Science (IMES), Department of Chemistry and Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Alexander Meissner
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA
- Department of Genome Regulation, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
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13
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Jing W, Otsuka T, Nakamura M, Sakurai N, Takano H, Hayashi T, Ota M, Nomura T, Hayashi R, Shimasaki T, Tahara T, Shibata T, Arisawa T. Association of genetic polymorphisms in DNMT3A with the progression of gastric mucosal atrophy and susceptibility to gastric cancer in Japan. Oncol Lett 2019; 17:3482-3488. [PMID: 30867787 DOI: 10.3892/ol.2019.9948] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Accepted: 01/02/2019] [Indexed: 01/19/2023] Open
Abstract
The aim of the present study was to investigate whether single nucleotide polymorphisms in the DNMT3A gene are associated with susceptibility to gastric cancer in the Japanese population. The present case-control study examined the associations between single nucleotide polymorphisms (rs6733868 and rs13428812) in DNMT3A and cancer susceptibility in 343 patients with gastric cancer and 708 subjects without gastric malignancies on upper gastro-duodenal endoscopy. Of 708 controls, 409 were classified into two groups histologically: 99 cases with and 310 cases without gastric mucosal atrophy. Overall, homozygosity for the DNMT3A rs6733868 minor allele was significantly associated with a reduced risk of gastric cancer (odds ratio [OR], 0.621; 95% confidence interval [CI], 0.402-0.958; P=0.031), especially of the intestinal type (OR, 0.494; 95% CI, 0.274-0.890; P=0.019). In subjects >60 years, rs6733868 minor allele homozygosity was significantly associated with gastric cancer susceptibility. Carriers of the rs6733868 minor allele had a reduced risk of severe gastric mucosal atrophy (OR, 0.495; 95% CI, 0.299-0.826; P=0.0069). In addition, the number of minor alleles of both rs6733868 and rs13428812 was significantly correlated with the risk of Helicobacter pylori (HP) infection (P=0.0070 and P=0.0050, respectively). However, rs13428812 was not associated with severe gastric mucosal atrophy or gastric carcinogenesis. The present results suggest that DNMT3A polymorphisms serve roles in the progression from HP infection to gastric mucosal atrophy and gastric carcinogenesis in terms of degree and manner.
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Affiliation(s)
- Wu Jing
- Department of Gastroenterology, Kanazawa Medical University, Uchinada-machi, Ishikawa 920-0293, Japan
| | - Toshimi Otsuka
- Department of Gastroenterology, Kanazawa Medical University, Uchinada-machi, Ishikawa 920-0293, Japan
| | - Masakatsu Nakamura
- Department of Gastroenterology, Kanazawa Medical University, Uchinada-machi, Ishikawa 920-0293, Japan
| | - Naoko Sakurai
- Department of Gastroenterology, Kanazawa Medical University, Uchinada-machi, Ishikawa 920-0293, Japan
| | - Hikaru Takano
- Department of Gastroenterology, Kanazawa Medical University, Uchinada-machi, Ishikawa 920-0293, Japan
| | - Tasuku Hayashi
- Department of Gastroenterology, Kanazawa Medical University, Uchinada-machi, Ishikawa 920-0293, Japan
| | - Masafumi Ota
- Department of Gastroenterology, Kanazawa Medical University, Uchinada-machi, Ishikawa 920-0293, Japan
| | - Tomoe Nomura
- Department of Gastroenterology, Kanazawa Medical University, Uchinada-machi, Ishikawa 920-0293, Japan
| | - Ranji Hayashi
- Department of Gastroenterology, Kanazawa Medical University, Uchinada-machi, Ishikawa 920-0293, Japan
| | - Takeo Shimasaki
- Department of Gastroenterology, Kanazawa Medical University, Uchinada-machi, Ishikawa 920-0293, Japan
| | - Tomomitsu Tahara
- Department of Gastroenterology, Fujita Health University, Kutsukake-cho, Toyoake 470-1192, Japan
| | - Tomoyuki Shibata
- Department of Gastroenterology, Fujita Health University, Kutsukake-cho, Toyoake 470-1192, Japan
| | - Tomiyasu Arisawa
- Department of Gastroenterology, Kanazawa Medical University, Uchinada-machi, Ishikawa 920-0293, Japan
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14
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Valencia AM, Kadoch C. Chromatin regulatory mechanisms and therapeutic opportunities in cancer. Nat Cell Biol 2019; 21:152-161. [PMID: 30602726 DOI: 10.1038/s41556-018-0258-1] [Citation(s) in RCA: 123] [Impact Index Per Article: 24.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Accepted: 11/30/2018] [Indexed: 12/11/2022]
Abstract
Research over the past several decades has unmasked a major contribution of disrupted chromatin regulatory processes to human disease, particularly cancer. Advances in genome-wide technologies have highlighted frequent mutations in genes encoding chromatin-associated proteins, identified unexpected synthetic lethal opportunities and enabled increasingly comprehensive structural and functional dissection. Here, we review recent progress in our understanding of oncogenic mechanisms at each level of chromatin organization and regulation, and discuss new strategies towards therapeutic intervention.
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Affiliation(s)
- Alfredo M Valencia
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Chemical Biology Program, Harvard University, Cambridge, MA, USA
| | - Cigall Kadoch
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA. .,Broad Institute of MIT and Harvard, Cambridge, MA, USA.
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15
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Feng Y, Zhong M, Zeng S, Xiao D, Liu Y. Metachronous triple primary neoplasms with primary prostate cancer, lung cancer, and colon cancer: A case report. Medicine (Baltimore) 2018; 97:e11332. [PMID: 29953024 PMCID: PMC6039669 DOI: 10.1097/md.0000000000011332] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
RATIONALE Multiple primary neoplasms (MPNs) are rare. Most MPNs are double, and triple primary neoplasms are extremely rarer. Here, we describe a case of a 66-year-old man diagnosed with metachronous triple primary neoplasms with primary prostate cancer, lung cancer and colon cancer. PATIENT CONCERNS The patient complained of dysuria in January 2015, and he underwent transurethral resection of the prostate. The pathological results showed acinar adenocarcinoma of prostate with a Gleason score of 3+3. In January 2017, he complained of lower abdominal pain, then he took an enteroscopy examination, found a mass in the sigmoid colon, and positron emission tomography/computed tomography examination showed masses in the sigmoid colon and right upper lobe of the lung. Biopsy of the colon showed moderately differentiated adenocarcinoma with Kirsten rat sarcoma viral oncogene homolog exon 2 mutation, and biopsy of the lung showed moderately differentiated adenocarcinoma with epidermal rowth factor receptor exon 21 mutation. DIAGNOSES Metachronous triple primary neoplasms with primary prostate cancer, lung cancer and colon cancer. INTERVENTIONS The patient underwent surgical resection of the right upper lobe of the lung, postoperative stage was T1bN0M0 (stage IA). After 8 cycles of chemotherapy with modified FOLFOX6 regimen (oxaliplatin 85 mg/m, leucovorin 400 mg/m, 5-fluorouracil 400 mg/m on day 1, followed by 5-fluorouracil 2400 mg/m intravenous infusion over 46 hours every 2 weeks), the patient underwent radical resection of colon cancer, and he finished the remaining 4 cycles of modified FOLFOX6 regimen chemotherapy in November 2017. OUTCOMES The patient takes examination every three months, and the results show no recurrence. LESSONS When considering MPNs, thorough surveillance by new screening methods is required to detect a second or even third neoplasm at an early stage.
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Affiliation(s)
| | | | | | - Desheng Xiao
- Department of Pathology, Xiangya Hospital, Central South University, Changsha, Hunan Province, People's Republic of China
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16
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Szablewski V, Bret C, Kassambara A, Devin J, Cartron G, Costes-Martineau V, Moreaux J. An epigenetic regulator-related score (EpiScore) predicts survival in patients with diffuse large B cell lymphoma and identifies patients who may benefit from epigenetic therapy. Oncotarget 2018; 9:19079-19099. [PMID: 29721185 PMCID: PMC5922379 DOI: 10.18632/oncotarget.24901] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Accepted: 03/01/2018] [Indexed: 01/07/2023] Open
Abstract
Diffuse large B-cell lymphoma (DLBCL) is the most common form of lymphoma and shows considerable clinical and biological heterogeneity. Much research is currently focused on the identification of prognostic markers for more specific patients’ risk stratification and on the development of therapeutic approaches to improve the long-term outcome. Epigenetic alterations are involved in various cancers, including lymphoma. Interestingly, epigenetic alterations are reversible and drugs to target some of them have been developed. In this study, we demonstrated that the gene expression profile of epigenetic regulators has a prognostic value in DLBCL and identified pathways that could be involved in DLBCL poor outcome. We then designed a new risk score (EpiScore) based on the gene expression level of the epigenetic regulators DNMT3A, DOT1L, SETD8. EpiScore was predictive of overall survival in DLBCL and allowed splitting patients with DLBCL from two independent cohorts (n = 414 and n = 69) in three groups (high, intermediate and low risk). EpiScore was an independent predictor of survival when compared with previously described prognostic factors, such as the International Prognostic Index (IPI), germinal center B cell and activated B cell molecular subgroups, gene expression-based risk score (GERS) and DNA repair score. Immunohistochemistry analysis of DNMT3A in 31 DLBCL samples showed that DNMT3A overexpression (>42% of positive tumor cells) correlated with reduced overall and event-free survival. Finally, an HDAC gene signature was significantly enriched in the DLBCL samples included in the EpiScore high-risk group. We conclude that EpiScore identifies high-risk patients with DLBCL who could benefit from epigenetic therapy.
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Affiliation(s)
- Vanessa Szablewski
- University of Montpellier, UFR de Médecine, Montpellier, France.,Department of Biopathology, CHU Montpellier, Montpellier, France
| | - Caroline Bret
- Department of Biological Hematology, CHU Montpellier, Montpellier, France.,Institute of Human Genetics, CNRS-UM UMR 9002, Montpellier, France.,University of Montpellier, UFR de Médecine, Montpellier, France
| | - Alboukadel Kassambara
- Department of Biological Hematology, CHU Montpellier, Montpellier, France.,Institute of Human Genetics, CNRS-UM UMR 9002, Montpellier, France
| | - Julie Devin
- Institute of Human Genetics, CNRS-UM UMR 9002, Montpellier, France
| | - Guillaume Cartron
- University of Montpellier, UFR de Médecine, Montpellier, France.,CHU Montpellier, Department of Clinical Hematology, Montpellier, France.,Montpellier University, UMR CNRS 5235, Montpellier, France
| | - Valérie Costes-Martineau
- University of Montpellier, UFR de Médecine, Montpellier, France.,Department of Biopathology, CHU Montpellier, Montpellier, France
| | - Jérôme Moreaux
- Department of Biological Hematology, CHU Montpellier, Montpellier, France.,Institute of Human Genetics, CNRS-UM UMR 9002, Montpellier, France.,University of Montpellier, UFR de Médecine, Montpellier, France
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17
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Abstract
RATIONALE Phyllodes tumors (PT) of the breast are rare neoplasm originating from fibroepithelial component. To our knowledge, our report is the first reported case of PT in 2 sisters. PATIENT CONCERNS We presented 2 cases of PT of the breast involving in 2 sisters. On physical examination of the younger sister, a firm mass measuring approximately 3 cm in diameter was identified in upper inner quadrant of the right breast. Physical examination of the elder sister revealed a 3 cm lump in upper outer quadrant of the left breast. DIAGNOSES Histopathology of the younger sister revealed a malignant PT. The elder sister was diagnosed with borderline PT. INTERVENTIONS The younger sister with malignant PT underwent right mastectomy. The elder sister with borderline PT was scheduled for wide resection of the mass in the left breast. OUTCOMES After a follow-up of 23 months, no local or distant recurrence was observed. LESSONS Our cases indicate that genetic factor may contribute to the risk of PT of the breast. Markers such as p53 and Ki-67 may have some correlation with PT malignancy.
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Affiliation(s)
| | | | | | | | - Xiaoqin Yang
- Department of Breast Surgery, West China Hospital, Sichuan University, Chengdu, Sichuan Province, China
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18
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19
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Wainwright EN, Scaffidi P. Epigenetics and Cancer Stem Cells: Unleashing, Hijacking, and Restricting Cellular Plasticity. Trends Cancer 2017; 3:372-386. [PMID: 28718414 PMCID: PMC5506260 DOI: 10.1016/j.trecan.2017.04.004] [Citation(s) in RCA: 220] [Impact Index Per Article: 31.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2017] [Revised: 03/30/2017] [Accepted: 04/10/2017] [Indexed: 02/07/2023]
Abstract
Epigenetic mechanisms have emerged as key players in cancer development which affect cellular states at multiple stages of the disease. During carcinogenesis, alterations in chromatin and DNA methylation resulting from genetic lesions unleash cellular plasticity and favor oncogenic cellular reprogramming. At later stages, during cancer growth and progression, additional epigenetic changes triggered by interaction with the microenvironment modulate cancer cell phenotypes and properties, and shape tumor architecture. We review here recent advances highlighting the interplay between epigenetics, genetics, and cell-to-cell signaling in cancer, with particular emphasis on mechanisms relevant for cancer stem cell formation (CSC) and function. Epigenetic regulators are one of the most commonly mutated classes of genes in cancer. During cancer initiation, mutated epigenetic regulators lead to oncogenic cellular reprogramming and promote the acquisition of uncontrolled self-renewal. The emergence of CSCs requires elaborate reorganization of the epigenome. During cancer growth, epigenetic mechanisms integrate the effect of cell-intrinsic (i.e., subclonal mutations) and cell-extrinsic (i.e., signaling from the microenvironment) changes and establish intratumoral heterogeneity, either promoting or inhibiting the CSC state. ‘Loose’ epigenetic constraints in cancer cells enhance cellular plasticity and allow reversible transitions between different phenotypic states. Enhanced cellular plasticity favors cancer cell adaptability and resistance to therapy. Modulation of epigenetic processes allows targeting of the most downstream determinants of the CSC state.
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Affiliation(s)
- Elanor N Wainwright
- Cancer Epigenetics Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Paola Scaffidi
- Cancer Epigenetics Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK; UCL Cancer Institute, University College London, London WC1E 6DD, UK.
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20
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Zeng XQ, Wang J, Chen SY. Methylation modification in gastric cancer and approaches to targeted epigenetic therapy (Review). Int J Oncol 2017; 50:1921-1933. [DOI: 10.3892/ijo.2017.3981] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2017] [Accepted: 03/22/2017] [Indexed: 11/06/2022] Open
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21
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Rinaldi L, Avgustinova A, Martín M, Datta D, Solanas G, Prats N, Benitah SA. Loss of Dnmt3a and Dnmt3b does not affect epidermal homeostasis but promotes squamous transformation through PPAR-γ. eLife 2017; 6:e21697. [PMID: 28425913 PMCID: PMC5429093 DOI: 10.7554/elife.21697] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2016] [Accepted: 04/13/2017] [Indexed: 12/12/2022] Open
Abstract
The DNA methyltransferase Dnmt3a suppresses tumorigenesis in models of leukemia and lung cancer. Conversely, deregulation of Dnmt3b is thought to generally promote tumorigenesis. However, the role of Dnmt3a and Dnmt3b in many types of cancer remains undefined. Here, we show that Dnmt3a and Dnmt3b are dispensable for homeostasis of the murine epidermis. However, loss of Dnmt3a-but not Dnmt3b-increases the number of carcinogen-induced squamous tumors, without affecting tumor progression. Only upon combined deletion of Dnmt3a and Dnmt3b, squamous carcinomas become more aggressive and metastatic. Mechanistically, Dnmt3a promotes the expression of epidermal differentiation genes by interacting with their enhancers and inhibits the expression of lipid metabolism genes, including PPAR-γ, by directly methylating their promoters. Importantly, inhibition of PPAR-γ partially prevents the increase in tumorigenesis upon deletion of Dnmt3a. Altogether, we demonstrate that Dnmt3a and Dnmt3b protect the epidermis from tumorigenesis and that squamous carcinomas are sensitive to inhibition of PPAR-γ.
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Affiliation(s)
- Lorenzo Rinaldi
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Centre for Genomic Regulation, The Barcelona Institute of Science and Technology, Barcelona, Spain
- Universitat Pompeu Fabra, Barcelona, Spain
| | - Alexandra Avgustinova
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Mercè Martín
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Debayan Datta
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Guiomar Solanas
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Neus Prats
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Salvador Aznar Benitah
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Catalan Institution for Research and Advanced Studies (ICREA), Barcelona, Spain
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22
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Abstract
In the past few years, it has become clear that mutations in epigenetic regulatory genes are common in human cancers. Therapeutic strategies are now being developed to target cancers with mutations in these genes using specific chemical inhibitors. In addition, a complementary approach based on the concept of synthetic lethality, which allows exploitation of loss-of-function mutations in cancers that are not targetable by conventional methods, has gained traction. Both of these approaches are now being tested in several clinical trials. In this Review, we present recent advances in epigenetic drug discovery and development, and suggest possible future avenues of investigation to drive progress in this area.
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23
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Neves M, Ribeiro J, Medeiros R, Sousa H. Genetic polymorphism in DNMTs and gastric cancer: A systematic review and meta-analysis. Porto Biomed J 2016; 1:164-172. [PMID: 32258570 DOI: 10.1016/j.pbj.2016.10.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2016] [Accepted: 10/24/2016] [Indexed: 02/07/2023] Open
Abstract
Highlights Single nucleotide polymorphisms (SNPs) in DNA methyltransferases (DNMTs) modulate protein expression and affect DNA methylation.Aberrant DNA methylation, have been associated with gastric carcinogenesis.DNMT2 rs11254413 is associated with protection for GC development.DNMT3A rs7560488, DNMT3A rs36012910 and, specially, DNMT1 rs16999593 are associated with increased susceptibility for GC development. Abstract Epigenetics alterations, including aberrant DNA methylation, have been associated with gastric carcinogenesis. Single nucleotide polymorphisms (SNPs) in DNA methyltransferases (DNMTs) may influence protein expression and therefore affect DNA regulation and susceptibility for Gastric Cancer (GC).We have performed a systematic review and meta-analysis involving 11 studies and a total of 24 SNPs in DNMTs were analyzed. According to literature, only 4 SNPs, DNMT1 rs16999593, DNMT2 rs11254413 and DNMT3A rs7560488 and DNMT3A rs36012910, were associated with GC. DNMT1 rs16999593 and DNMT3A rs7560488C allele and DNMT3A rs36012910 G allele showed an increased risk for GC. On the other hand, DNMT2 rs11254413 G allele presented a protective effect for GC. Additionally, the meta-analysis evaluated the SNPs analyzed in more than one study (n = 6). Results revealed that only DNMT1 rs16999593 had a statistically significant association with GC development (OR = 1.31; 95% CI = 1.08-1.60; p = 0.006 for TC + CC genotypes).Our study suggests that DNMT2 rs11254413, DNMT3A rs7560488, DNMT3A rs36012910 and, specially, DNMT1 rs16999593 may have an association with GC development. Nevertheless, further studies are need using different populations to clarify this association with GC risk.
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Affiliation(s)
- Marco Neves
- Molecular Oncology and Viral Pathology Group, Research Centre (CI-IPOP), Portuguese Oncology Institute of Porto (IPO-Porto), Porto, Portugal.,Faculty of Medicine of University of Porto, Alameda Prof. Hernâni Monteiro, Porto, Portugal
| | - Joana Ribeiro
- Molecular Oncology and Viral Pathology Group, Research Centre (CI-IPOP), Portuguese Oncology Institute of Porto (IPO-Porto), Porto, Portugal.,Faculty of Medicine of University of Porto, Alameda Prof. Hernâni Monteiro, Porto, Portugal.,Research Department, Portuguese League Against Cancer (LPCC-NRNorte), Porto, Portugal
| | - Rui Medeiros
- Molecular Oncology and Viral Pathology Group, Research Centre (CI-IPOP), Portuguese Oncology Institute of Porto (IPO-Porto), Porto, Portugal.,Faculty of Medicine of University of Porto, Alameda Prof. Hernâni Monteiro, Porto, Portugal.,Research Department, Portuguese League Against Cancer (LPCC-NRNorte), Porto, Portugal.,Abel Salazar Institute for the Biomedical Sciences (ICBAS), University of Porto, Porto, Portugal.,Virology Service, Portuguese Oncology Institute of Porto (IPO-Porto), Porto, Portugal
| | - Hugo Sousa
- Molecular Oncology and Viral Pathology Group, Research Centre (CI-IPOP), Portuguese Oncology Institute of Porto (IPO-Porto), Porto, Portugal.,Faculty of Medicine of University of Porto, Alameda Prof. Hernâni Monteiro, Porto, Portugal.,Virology Service, Portuguese Oncology Institute of Porto (IPO-Porto), Porto, Portugal
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24
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Yao X, Xing M, Ooi WF, Tan P, Teh BT. Epigenomic Consequences of Coding and Noncoding Driver Mutations. Trends Cancer 2016; 2:585-605. [PMID: 28741489 DOI: 10.1016/j.trecan.2016.09.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2016] [Revised: 08/30/2016] [Accepted: 09/02/2016] [Indexed: 12/27/2022]
Abstract
Chromatin alterations are integral to the pathogenic process of cancer, as demonstrated by recent discoveries of frequent mutations in chromatin-modifier genes and aberrant DNA methylation states in different cancer types. Progress is being made on elucidating how chromatin alterations, and how proteins catalyzing these alterations, mechanistically contribute to tissue-specific tumorigenesis. In parallel, technologies enabling the genome-wide profiling of histone modifications have revealed the existence of noncoding driver genetic alterations in cancer. In this review, we survey the current knowledge of coding and noncoding cancer drivers, and discuss their impact on the chromatin landscape. Translational implications of these findings for novel cancer therapies are also presented.
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Affiliation(s)
- Xiaosai Yao
- Cancer Therapeutics and Stratified Oncology, Genome Institute of Singapore, 60 Biopolis Street, Singapore 138672, Singapore
| | - Manjie Xing
- NUS Graduate School for Integrative Sciences and Engineering, National University of Singapore, 5 Lower Kent Ridge Road, Singapore 119074, Singapore; Cancer and Stem Cell Biology Program, Duke-NUS Medical School, 8 College Road, Singapore 169857, Singapore
| | - Wen Fong Ooi
- Cancer Therapeutics and Stratified Oncology, Genome Institute of Singapore, 60 Biopolis Street, Singapore 138672, Singapore
| | - Patrick Tan
- Cancer Therapeutics and Stratified Oncology, Genome Institute of Singapore, 60 Biopolis Street, Singapore 138672, Singapore; Cancer and Stem Cell Biology Program, Duke-NUS Medical School, 8 College Road, Singapore 169857, Singapore; National Cancer Centre, 11 Hospital Drive, Singapore 169610, Singapore; Cancer Science Institute of Singapore, National University of Singapore, 14 Medical Drive, #12-01, Singapore 117599, Singapore; SingHealth/Duke-NUS Precision Medicine Institute, Singapore 168752, Singapore.
| | - Bin Tean Teh
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, 8 College Road, Singapore 169857, Singapore; National Cancer Centre, 11 Hospital Drive, Singapore 169610, Singapore; Cancer Science Institute of Singapore, National University of Singapore, 14 Medical Drive, #12-01, Singapore 117599, Singapore; SingHealth/Duke-NUS Precision Medicine Institute, Singapore 168752, Singapore; Institute of Molecular and Cell Biology, 61 Biopolis Drive, Singapore 138673.
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25
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Siraj AK, Masoodi T, Bu R, Beg S, Al-Sobhi SS, Al-Dayel F, Al-Dawish M, Alkuraya FS, Al-Kuraya KS. Genomic Profiling of Thyroid Cancer Reveals a Role for Thyroglobulin in Metastasis. Am J Hum Genet 2016; 98:1170-1180. [PMID: 27236916 DOI: 10.1016/j.ajhg.2016.04.014] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2016] [Accepted: 04/26/2016] [Indexed: 01/30/2023] Open
Abstract
Papillary thyroid carcinoma (PTC) has a wide geographic variation in incidence; it is most common in Saudi Arabia, where it is only second to breast cancer as the most common cancer among females. Genomic profiling of PTC from Saudi Arabia has not been attempted previously. We performed whole-exome sequencing of 101 PTC samples and the corresponding genomic DNA to identify genes with recurrent somatic mutations, then sequenced these genes by using a next-generation gene-panel approach in an additional 785 samples. In addition to BRAF, N-RAS, and H-RAS, which have previously been shown to be recurrently mutated in PTC, our analysis highlights additional genes, including thyroglobulin (TG), which harbored somatic mutations in 3% of the entire cohort. Surprisingly, although TG mutations were not exclusive to mutations in the RAS-MAP kinase pathway, their presence was associated with a significantly worse clinical outcome, which suggests a pathogenic role beyond driving initial oncogenesis. Analysis of metastatic PTC tissue revealed significant enrichment for TG mutations (p < 0.001), including events of apparent clonal expansion. Our results suggest a previously unknown role of TG somatic mutations in the pathogenesis of PTC and its malignant evolution.
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26
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Zhang W, Xu Y, Ma G, Qi W, Gu H, Jiang P. Genetic Polymorphism of DNA Methyltransferase 3A rs1550117 A>G and Risk of Cancer: A Meta-analysis. J INVEST SURG 2015. [DOI: 10.3109/08941939.2015.1010024] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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27
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Liu YN, Zhang N, Wu Y, Yang L, Ding XY, Zhou JF, Xiao M. DNMT3A mutation analysis in adult patients with acute lymphoblastic leukemia. ACTA ACUST UNITED AC 2015; 35:337-342. [PMID: 26072070 DOI: 10.1007/s11596-015-1434-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2014] [Revised: 04/25/2015] [Indexed: 01/03/2023]
Abstract
DNA methyl-transferase 3A (DNMT3A) mutation has recently been identified as an independent risk factor for patients with acute myeloid leukemia (AML). However, reports are scanty on its rate and subsequent impact on patients with acute lymphoblastic leukemia (ALL), especially in Chinese population. In this study, we investigated the incidence and prognostic implication of DNMT3A mutation in 57 Chinese adult ALL patients. A total of 3 (5.3%) T-ALL cases were found to have the DNMT3A R882H mutation, which was significantly greater than that found in B-ALL subtype (P=0.048). The patients aged between 40 and 60 years old had higher mutation rate than other age groups (P=0.042). Patients with DNMT3A mutation had shorter overall survival (OS) than their wild-type counterparts. Our study demonstrated that Chinese ALL patients might develop DNMT3A mutation, which exerts a negative impact on their prognosis. These findings might help in risk stratification and treatment choice for Chinese ALL patients.
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Affiliation(s)
- Ya-Nan Liu
- Department of Hematology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Na Zhang
- Department of Hematology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Ying Wu
- Department of Hematology, Hospital Affiliated to Medical College, Qingdao University, Qindao, 266003, China
| | - Li Yang
- Department of Hematology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Xiao-Yi Ding
- Department of Hematology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Jian-Feng Zhou
- Department of Hematology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Min Xiao
- Department of Hematology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China.
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Abstract
DNA methylation patterns are disrupted in various malignancies, suggesting a role in the development of cancer, but genetic aberrations directly linking the DNA methylation machinery to malignancies were rarely observed, so this association remained largely correlative. Recently, however, mutations in the gene encoding DNA methyltransferase 3A (DNMT3A) were reported in patients with acute myeloid leukaemia (AML), and subsequently in patients with various other haematological malignancies, pointing to DNMT3A as a critically important new tumour suppressor. Here, we review the clinical findings related to DNMT3A, tie these data to insights from basic science studies conducted over the past 20 years and present a roadmap for future research that should advance the agenda for new therapeutic strategies.
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Affiliation(s)
- Liubin Yang
- 1] Department of Molecular and Human Genetics, Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, Texas 77030, USA. [2]
| | - Rachel Rau
- 1] Department of Pediatrics, Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, Texas 77030, USA. [2]
| | - Margaret A Goodell
- 1] Department of Molecular and Human Genetics, Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, Texas 77030, USA. [2] Department of Pediatrics, Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, Texas 77030, USA
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Scourzic L, Mouly E, Bernard OA. TET proteins and the control of cytosine demethylation in cancer. Genome Med 2015; 7:9. [PMID: 25632305 PMCID: PMC4308928 DOI: 10.1186/s13073-015-0134-6] [Citation(s) in RCA: 155] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
The discovery that ten-eleven translocation (TET) proteins are α-ketoglutarate-dependent dioxygenases involved in the conversion of 5-methylcytosines (5-mC) to 5-hydroxymethylcytosine (5-hmC), 5-formylcytosine and 5-carboxycytosine has revealed new pathways in the cytosine methylation and demethylation process. The description of inactivating mutations in TET2 suggests that cellular transformation is in part caused by the deregulation of this 5-mC conversion. The direct and indirect deregulation of methylation control through mutations in DNA methyltransferase and isocitrate dehydrogenase (IDH) genes, respectively, along with the importance of cytosine methylation in the control of normal and malignant cellular differentiation have provided a conceptual framework for understanding the early steps in cancer development. Here, we review recent advances in our understanding of the cytosine methylation cycle and its implication in cellular transformation, with an emphasis on TET enzymes and 5-hmC. Ongoing clinical trials targeting the activity of mutated IDH enzymes provide a proof of principle that DNA methylation is targetable, and will trigger further therapeutic applications aimed at controlling both early and late stages of cancer development.
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Affiliation(s)
- Laurianne Scourzic
- Institut National de la Santé et de la Recherche Médicale (INSERM), Unité 1170, équipe labellisée Ligue Contre le Cancer, 94805 Villejuif, France ; Institut Gustave Roussy, 94805 Villejuif, France ; University Paris 11 Sud, 91405 Orsay, France
| | - Enguerran Mouly
- Institut National de la Santé et de la Recherche Médicale (INSERM), Unité 1170, équipe labellisée Ligue Contre le Cancer, 94805 Villejuif, France ; Institut Gustave Roussy, 94805 Villejuif, France ; University Paris 11 Sud, 91405 Orsay, France
| | - Olivier A Bernard
- Institut National de la Santé et de la Recherche Médicale (INSERM), Unité 1170, équipe labellisée Ligue Contre le Cancer, 94805 Villejuif, France ; Institut Gustave Roussy, 94805 Villejuif, France ; University Paris 11 Sud, 91405 Orsay, France
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Incidence and prognostic impact of DNMT3A mutations in Korean normal karyotype acute myeloid leukemia patients. BIOMED RESEARCH INTERNATIONAL 2015; 2015:723682. [PMID: 25650308 PMCID: PMC4306257 DOI: 10.1155/2015/723682] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/10/2014] [Revised: 12/22/2014] [Accepted: 12/22/2014] [Indexed: 11/28/2022]
Abstract
Background. DNA methyltransferase 3A (DNMT3A) mutation was recently introduced as a prognostic indicator in normal karyotype (NK) AML and we evaluated the incidence and prognostic impact of DNMT3A mutations in Korean NK AML patients. Methods. Total 67 NK AML patients diagnosed during the recent 10 years were enrolled. DNMT3A mutations were analyzed by direct sequencing and categorized into nonsynonymous variations (NSV), deleterious mutations (DM), and R882 mutation based on in silico analysis results. Clinical features and prognosis were compared with respect to DNMT3A mutation status. Results. Three novel (I158M, K219V, and E177V) and two known (R736H and R882H) NSVs were identified and the latter three were predicted as DMs. DNMT3A NSVs, DMs, and R882 mutation were identified in 14.9%–17.9%, 10.3%–10.4%, and 7.5% of patients, respectively. DNMT3A mutations were frequently detected in FLT3 ITD mutated patients (P = 0.054, 0.071, and 0.071 in NSV, DMs, and R882 mutation, resp.) but did not affect clinical features and prognosis significantly. Conclusions. Incidences of DNMT3A NSVs, DMs, and R882 mutation are 14.9%–17.9%, 10.3%–10.4%, and 7.5%, respectively, in Korean NK AML patients. DNMT3A mutations are associated with FLT3 ITD mutations but do not affect clinical outcome significantly in Korean NK AML patients.
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Savio AJ, Bapat B. Beyond the island: epigenetic biomarkers of colorectal and prostate cancer. Methods Mol Biol 2015; 1238:103-24. [PMID: 25421657 DOI: 10.1007/978-1-4939-1804-1_6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Epigenetic dysregulation is a common feature across all cancer types. Epigenetic mechanisms, from DNA methylation to histone modifications, allow for a vast number of cellular phenotypes to be created from the same genetic material. Just as certain genetic changes play a key role in tumor initiation and progression, epigenetic changes may also set the course of tumor development and be required for malignant transformation. The most frequently studied epigenetic changes investigated thus far are global genomic DNA hypomethylation along with specific hypermethylation, predominantly at promoter CpG islands of tumor suppressor genes. In addition to DNA methylation changes at CpG islands, there is an abundance of other epigenetic alterations occurring within cancer cells including DNA methylation alterations outside of CpG islands, non-CpG methylation, changes in cytosine oxidative species (hydroxymethylcytosine, formylcytosine, carboxylcytosine) levels, and histone modifications. This chapter examines epigenetic alterations beyond the island, and summarizes recent findings in DNA-based epigenetic regulation of the two most commonly diagnosed cancers in the Western world: colorectal cancer and prostate cancer.
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Affiliation(s)
- Andrea J Savio
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
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Li W, Gao C, Cui L, Liu S, Zhao X, Zhang R, Wu M, Zheng H, Deng G, Li Z, Zhang Q. DNMT3A mutations and prognostic significance in childhood acute lymphoblastic leukemia. Leuk Lymphoma 2014; 56:1066-71. [PMID: 25242092 DOI: 10.3109/10428194.2014.947607] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Little is known about DNMT3A mutations in childhood acute lymphoblastic leukemia (ALL). We screened for DNMT3A mutations in exon 23 and its adjacent intron regions in diagnostic samples of 201 children with ALL. The cDNA samples from 82 patients were also sequenced to identify other mutations in the entire coding region. DNMT3A mutations were detected in exon 23 and its adjacent intron regions only in five patients (2.5%). There was only one mutation in exon 23 in two patients, respectively. In the other three patients, five intronic mutations were found. None of the mutations was found in the five corresponding complete remission samples. DNMT3A mutations were correlated with higher minimal residual disease at the end of remission induction (p = 0.078). Treatment outcome was obviously worse in patients with DNMT3A mutations than in other patients (p < 0.05). Thus, DNMT3A mutations can be found in a few children with ALL, and may have an adverse impact on prognosis.
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Affiliation(s)
- Weijing Li
- Beijing Key Laboratory of Pediatric Hematology Oncology; National Key Discipline of Pediatrics, Ministry of Education; Key Laboratory of Major Diseases in Children, Ministry of Education; Hematology Oncology Center, Beijing Children's Hospital, Capital Medical University , Beijing , China
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Zou Y, Huang MZ, Liu FY, Yang BC, Wang LQ, Wang F, Yu XH, Wan L, Wan XDI, Xu XY, Li W, Huang OP, He M. Absence of DICER1, CTCF, RPL22, DNMT3A, TRRAP, IDH1 and IDH2 hotspot mutations in patients with various subtypes of ovarian carcinomas. Biomed Rep 2014; 3:33-37. [PMID: 25469243 DOI: 10.3892/br.2014.378] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2014] [Accepted: 10/24/2014] [Indexed: 12/12/2022] Open
Abstract
Cancer is caused by multiple genetic alterations within cells. Recently, large-scale sequencing has identified frequent ribonuclease type III (DICER1), CCCTC-binding factor (CTCF), ribosomal protein L22 (RPL22), DNA (cytosine-5-)-methyltransferase 3α (DNMT3A), transformation/transcription domain-associated protein (TRRAP), isocitrate dehydrogenase (IDH)1 and IDH2 hotspot mutations in diverse types of cancer. However, it remains largely unknown whether these mutations also exist in ovarian carcinomas. In the present study, a collection of 251 patients with distinct subtypes of ovarian carcinomas were recruited and sequenced for the presence of these hotspot mutations. However, no mutations in the seven genes were detected in the samples. These negative results, together with certain recent reports, indicate that the hotspot mutations in the CTCF, RPL22, DNMT3A, TRRAP, IDH1 and IDH2 genes may not be actively involved in the carcinogenesis of ovarian carcinoma. Of note, the DICER1 mutation frequency in Sertoli-Leydig cell tumor in the present study was significantly lower compared to prior observation, and therefore, it is speculated that this discrepancy may be mainly due to the small sample size analyzed in the study. In addition, among these samples, frequent polymerase (DNA directed) ε, catalytic subunit (POLE1) and ring finger protein 43 (RNF43) mutations were identified in endometrioid and mucinous ovarian carcinomas, respectively; thus DICER1, CTCF, RPL22, DNMT3A, TRRAP, IDH1 and IDH2 hotspot mutations may not play synergistic roles with POLE1 or RNF43 mutations in the carcinogenesis of endometrioid or mucinous ovarian carcinomas.
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Affiliation(s)
- Yang Zou
- Key Laboratory of Women's Reproductive Health of Jiangxi Province, P.R. China ; Central Laboratory, Jiangxi Provincial Maternal and Child Health Hospital, Nanchang, Jiangxi 330006, P.R. China
| | - Mei-Zhen Huang
- Key Laboratory of Women's Reproductive Health of Jiangxi Province, P.R. China ; Central Laboratory, Jiangxi Provincial Maternal and Child Health Hospital, Nanchang, Jiangxi 330006, P.R. China ; Graduate School of Nanchang University, Nanchang, Jiangxi 330031, P.R. China
| | - Fa-Ying Liu
- Key Laboratory of Women's Reproductive Health of Jiangxi Province, P.R. China ; Central Laboratory, Jiangxi Provincial Maternal and Child Health Hospital, Nanchang, Jiangxi 330006, P.R. China
| | - Bi-Cheng Yang
- Key Laboratory of Women's Reproductive Health of Jiangxi Province, P.R. China
| | - Li-Qun Wang
- Key Laboratory of Women's Reproductive Health of Jiangxi Province, P.R. China
| | - Feng Wang
- Key Laboratory of Women's Reproductive Health of Jiangxi Province, P.R. China ; Central Laboratory, Jiangxi Provincial Maternal and Child Health Hospital, Nanchang, Jiangxi 330006, P.R. China
| | - Xiao-Hong Yu
- Department of Pathology, Jiangxi Provincial Maternal and Child Health Hospital, P.R. China
| | - Lei Wan
- Key Laboratory of Women's Reproductive Health of Jiangxi Province, P.R. China
| | - Xi-DI Wan
- Key Laboratory of Women's Reproductive Health of Jiangxi Province, P.R. China
| | - Xiao-Yun Xu
- Key Laboratory of Women's Reproductive Health of Jiangxi Province, P.R. China ; Central Laboratory, Jiangxi Provincial Maternal and Child Health Hospital, Nanchang, Jiangxi 330006, P.R. China ; Graduate School of Nanchang University, Nanchang, Jiangxi 330031, P.R. China
| | - Wei Li
- Key Laboratory of Women's Reproductive Health of Jiangxi Province, P.R. China ; Central Laboratory, Jiangxi Provincial Maternal and Child Health Hospital, Nanchang, Jiangxi 330006, P.R. China ; Graduate School of Nanchang University, Nanchang, Jiangxi 330031, P.R. China
| | - Ou-Ping Huang
- Key Laboratory of Women's Reproductive Health of Jiangxi Province, P.R. China ; Central Laboratory, Jiangxi Provincial Maternal and Child Health Hospital, Nanchang, Jiangxi 330006, P.R. China
| | - Ming He
- Department of Pharmacology and Molecular Therapeutics, Nanchang University School of Pharmaceutical Science, Nanchang, Jiangxi 330006, P.R. China
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Shaknovich R, De S, Michor F. Epigenetic diversity in hematopoietic neoplasms. Biochim Biophys Acta Rev Cancer 2014; 1846:477-84. [PMID: 25240947 DOI: 10.1016/j.bbcan.2014.09.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2014] [Revised: 09/09/2014] [Accepted: 09/11/2014] [Indexed: 12/31/2022]
Abstract
Tumor cell populations display a remarkable extent of variability in non-genetic characteristics such as DNA methylation, histone modification patterns, and differentiation levels of individual cells. It remains to be elucidated whether non-genetic heterogeneity is simply a byproduct of tumor evolution or instead a manifestation of a higher-order tissue organization that is maintained within the neoplasm to establish a differentiation hierarchy, a favorable microenvironment, or a buffer against changing selection pressures during tumorigenesis. Here, we review recent findings on epigenetic diversity, particularly heterogeneity in DNA methylation patterns in hematologic malignancies. We also address the implications of epigenetic heterogeneity for the clonal evolution of tumors and discuss its effects on gene expression and other genome functions in cancer.
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Affiliation(s)
- Rita Shaknovich
- Division of Hematology/Oncology, Department of Medicine, Weill Cornell Medical College, New York, NY 10021, USA; Division of Immunopathology, Department of Pathology, Weill Cornell Medical College, New York, NY 10021, USA
| | - Subhajyoti De
- Department of Medicine, University of Colorado School of Medicine, Aurora, CO 80045, USA; University of Colorado Cancer Center, Aurora, CO 80045, USA
| | - Franziska Michor
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Harvard School of Public Health, Boston, MA 02215, USA; Department of Biostatistics, Harvard School of Public Health, Boston, MA 02215, USA.
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Martinez-Chacin RC, Keniry M, Dearth RK. Analysis of high fat diet induced genes during mammary gland development: identifying role players in poor prognosis of breast cancer. BMC Res Notes 2014; 7:543. [PMID: 25134718 PMCID: PMC4153917 DOI: 10.1186/1756-0500-7-543] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2014] [Accepted: 08/07/2014] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Epidemiological studies have shown that consumption of a high-fat diet (HFD) increases the risk of developing breast cancer (BC). Studies in rodents have shown HFD causes changes in the genetic programming of the maturing mammary gland (MG) increasing the susceptibility of developing the disease. Less is known about how HFD induced genes impact BC development. HFD exposure two weeks before conception to six weeks of age was previously shown to dramatically change MG gene expression in 10 week old mice. Therefore, we investigated these differentially expressed HFD-induced genes for their expression in BC using the NKI 295 breast tumor dataset. RESULTS To examine the potential role of HFD induced genes in BC, we first investigated whether these HFD-induced genes in mouse MGs were differentially expressed in different types of human BC. Of the 28 HFD induced genes that were differentially expressed between BC subtypes in the NKI set, 79% were significantly higher in basal-like BC. Next, we analyzed whether HFD induced genes were associated with BC prognosis utilizing gene expression and survival data for each HFD induced gene from the NKI data and constructed Kaplan Meier survival plots. Significantly, 93% of the prognosis associated genes (13/14) were associated with poor prognosis (P = 0.002). Kaplan Meier analysis with 249 non-basal-like BC found that all but one of the genes examined were still significantly associated with poor prognosis. Furthermore, gene set enrichment analysis (GSEA) with HFD microarray data revealed that invasive BC genes where enriched in HFD samples that also had lost expression of luminal genes. CONCLUSIONS HFD exposed mouse MGs maintain differential expression of genes that are found highly expressed in basal-like breast cancer. These HFD-induced genes associate with poor survival in numerous BC subtypes, making them more likely to directly impact prognosis. Furthermore, HFD exposure leads to a loss in the expression of luminal genes and a gain in expression of mesenchymal and BC invasion genes in MGs. Collectively, our study suggests that HFD exposure during development induces genes associated with poor prognosis, thus identifying how HFD diet may regulate BC development.
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Affiliation(s)
| | | | - Robert K Dearth
- Department of Biology, University of Texas-Pan American, 1201 West University Drive, Edinburg, TX 78539, USA.
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Li WL, Xiao MS, Zhang DF, Yu D, Yang RX, Li XY, Yao YG. Mutation and expression analysis of the IDH1, IDH2, DNMT3A, and MYD88 genes in colorectal cancer. Gene 2014; 546:263-70. [PMID: 24887488 DOI: 10.1016/j.gene.2014.05.070] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2013] [Revised: 05/12/2014] [Accepted: 05/29/2014] [Indexed: 12/13/2022]
Abstract
Colorectal cancer (CRC) is one of the leading causes of death around the world. Its genetic mechanism was intensively investigated in the past decades with findings of a number of canonical oncogenes and tumor-suppressor genes such as APC, KRAS, and TP53. Recent genome-wide association and sequencing studies have identified a series of promising oncogenes including IDH1, IDH2, DNMT3A, and MYD88 in hematologic malignancies. However, whether these genes are involved in CRC remains unknown. In this study, we screened the hotspot mutations of these four genes in 305 CRC samples from Han Chinese by direct sequencing. mRNA expression levels of these genes were quantified by quantitative real-time PCR (RT-qPCR) in paired cancerous and paracancerous tissues. Association analyses between mRNA expression levels and different cancerous stages were performed. Except for one patient harboring IDH1 mutation p.I99M, we identified no previously reported hotspot mutations in colorectal cancer tissues. mRNA expression levels of IDH1, DNMT3A, and MYD88, but not IDH2, were significantly decreased in the cancerous tissues comparing with the paired paracancerous normal tissues. Taken together, the hotspot mutations of IDH1, IDH2, DNMT3A, and MYD88 gene were absent in CRC. Aberrant mRNA expression of IDH1, DNMT3A, and MYD88 gene might be actively involved in the development of CRC.
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Affiliation(s)
- Wen-Liang Li
- Department of Oncology, The First Affiliated Hospital of Kunming Medical University, Kunming, Yunnan 650032, China.
| | - Mei-Sheng Xiao
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Kunming, Yunnan 650223, China
| | - Deng-Feng Zhang
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Kunming, Yunnan 650223, China; Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan 650204, China
| | - Dandan Yu
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Kunming, Yunnan 650223, China
| | - Run-Xiang Yang
- Chemotherapy Research Center, Yunnan Provincial Tumor Hospital, Kunming Medical University, Kunming, China
| | - Xiao-Yan Li
- Department of Gastroenterology, The First Affiliated Hospital of Kunming Medical University, Kunming, Yunnan 650032, China
| | - Yong-Gang Yao
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Kunming, Yunnan 650223, China; Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan 650204, China.
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DNMT3a epigenetic program regulates the HIF-2α oxygen-sensing pathway and the cellular response to hypoxia. Proc Natl Acad Sci U S A 2014; 111:7783-8. [PMID: 24817692 DOI: 10.1073/pnas.1322909111] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Epigenetic regulation of gene expression by DNA methylation plays a central role in the maintenance of cellular homeostasis. Here we present evidence implicating the DNA methylation program in the regulation of hypoxia-inducible factor (HIF) oxygen-sensing machinery and hypoxic cell metabolism. We show that DNA methyltransferase 3a (DNMT3a) methylates and silences the HIF-2α gene (EPAS1) in differentiated cells. Epigenetic silencing of EPAS1 prevents activation of the HIF-2α gene program associated with hypoxic cell growth, thereby limiting the proliferative capacity of adult cells under low oxygen tension. Naturally occurring defects in DNMT3a, observed in primary tumors and malignant cells, cause the unscheduled activation of EPAS1 in early dysplastic foci. This enables incipient cancer cells to exploit the HIF-2α pathway in the hypoxic tumor microenvironment necessary for the formation of cellular masses larger than the oxygen diffusion limit. Reintroduction of DNMT3a in DNMT3a-defective cells restores EPAS1 epigenetic silencing, prevents hypoxic cell growth, and suppresses tumorigenesis. These data support a tumor-suppressive role for DNMT3a as an epigenetic regulator of the HIF-2α oxygen-sensing pathway and the cellular response to hypoxia.
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Peters SL, Hlady RA, Opavska J, Klinkebiel D, Pirruccello SJ, Talmon GA, Sharp JG, Wu L, Jaenisch R, Simpson MA, Karpf AR, Opavsky R. Tumor suppressor functions of Dnmt3a and Dnmt3b in the prevention of malignant mouse lymphopoiesis. Leukemia 2014; 28:1138-42. [PMID: 24292811 DOI: 10.1038/leu.2013.364] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Affiliation(s)
- S L Peters
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE, USA
| | - R A Hlady
- Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, NE, USA
| | - J Opavska
- Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, NE, USA
| | - D Klinkebiel
- Department of Biochemistry and Molecular Biology, College of Medicine, University of Nebraska Medical Center, Omaha, NE, USA
| | - S J Pirruccello
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, NE, USA
| | - G A Talmon
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, NE, USA
| | - J G Sharp
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE, USA
| | - L Wu
- Department of Microbiology and Molecular Genetics, Rutgers New Jersey Medical School, Cancer Center, Newark, NJ, USA
| | - R Jaenisch
- Whitehead Institute, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - M A Simpson
- Department of Biochemistry, University of Nebraska, Lincoln, NE, USA
| | - A R Karpf
- Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, NE, USA
| | - R Opavsky
- 1] Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE, USA [2] Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, NE, USA [3] Center for Lymphoma and Leukemia Research, University of Nebraska Medical Center, Omaha, NE, USA
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Seritrakul P, Gross JM. Expression of the de novo DNA methyltransferases (dnmt3 - dnmt8) during zebrafish lens development. Dev Dyn 2013; 243:350-6. [PMID: 24123478 DOI: 10.1002/dvdy.24077] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2013] [Revised: 09/10/2013] [Accepted: 10/03/2013] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND De novo DNA methylation is thought to be critical for cellular reprogramming during tissue differentiation and development. Little is known about the roles of de novo DNA methylation during eye development, and particularly during lens development. The lens is composed of lens epithelial (LE) and lens fiber (LF) cells, with proliferative LE cells giving rise to differentiated LFs at the "transition zone." Given the unique architecture and developmental program of the lens, and the involvement of de novo DNA methylation during differentiation events in other tissues, we sought to identify de novo DNA methyltransferases expressed in the zebrafish lens. RESULTS Zebrafish possess six de novo DNA methyltransferase genes, dnmt3 - dnmt8. At 24 hr postfertilization (hpf), all six are expressed ubiquitously throughout the eye. By 72 hpf, dnmt3 and dnmt5 become restricted to cells of the retinal ciliary marginal zone (CMZ), dnmt4 and dnmt7 to cells of the CMZ and LE, and dnmt6 and dnmt8 to ganglion cells and cells of the inner nuclear layer of the retina. CONCLUSIONS These data identify regions of the eye where de novo methyltransferases could mediate DNA methylation events during development. Overlapping expression domains also suggest functional redundancy within this gene family in the eye.
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Affiliation(s)
- Pawat Seritrakul
- Department of Molecular Biosciences, Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, Texas
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Li L, Lorzadeh A, Hirst M. Regulatory variation: an emerging vantage point for cancer biology. WILEY INTERDISCIPLINARY REVIEWS-SYSTEMS BIOLOGY AND MEDICINE 2013; 6:37-59. [DOI: 10.1002/wsbm.1250] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Luolan Li
- Centre for High-Throughput Biology, Department of Microbiology & Immunology; University of British Columbia; Vancouver, British Columbia Canada
| | - Alireza Lorzadeh
- Centre for High-Throughput Biology, Department of Microbiology & Immunology; University of British Columbia; Vancouver, British Columbia Canada
| | - Martin Hirst
- Centre for High-Throughput Biology, Department of Microbiology & Immunology; University of British Columbia; Vancouver, British Columbia Canada
- Canada's Michael Smith Genome Sciences Centre; BC Cancer Agency; Vancouver, British Columbia Canada
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Cao XY, Jia ZF, Cao DH, Kong F, Jin MS, Suo J, Jiang J. DNMT3a rs1550117 Polymorphism Association with Increased Risk of Helicobacter pylori Infection. Asian Pac J Cancer Prev 2013; 14:5713-8. [DOI: 10.7314/apjcp.2013.14.10.5713] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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Vendetti FP, Rudin CM. Epigenetic therapy in non-small-cell lung cancer: targeting DNA methyltransferases and histone deacetylases. Expert Opin Biol Ther 2013; 13:1273-85. [PMID: 23859704 DOI: 10.1517/14712598.2013.819337] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
INTRODUCTION Epigenetics refers to heritable modifications of DNA and associated chromatin components that influence gene expression without altering DNA coding sequence. Epigenetic dysregulation is a central contributor to oncogenesis and is increasingly a focus of interest in cancer therapeutic research. Two key levels of aberrant epigenetic control are DNA methylation and histone acetylation. Primary regulators of these epigenetic changes include DNA methyltransferases (DNMTs) and histone deacetylases (HDACs). AREAS COVERED This review focuses on epigenetic changes in non-small-cell lung cancer and recent preclinical and clinical studies targeting these changes. DNMT inhibitors were previously explored at or near maximally tolerated doses, levels at which these agents are cytotoxic but have suboptimal effects on DNA methylation. Use of these inhibitors at substantially lower doses, in combination with HDAC inhibitors, can promote re-expression of silenced tumor suppressor genes, can result in major clinical responses and may alter tumor responsiveness to subsequent cytotoxic therapies. EXPERT OPINION Combinatorial epigenetic therapy has demonstrated encouraging clinical activity, but many relevant questions remain. Global strategies influencing the epigenome may have both positive and potential negative long-term effects on cancer progression. Further clinical investigation of this approach, including exploratory studies to define predictive biomarkers, is warranted.
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Affiliation(s)
- Frank P Vendetti
- Johns Hopkins University, The Sidney Kimmel Comprehensive Cancer Center, David H. Koch Cancer Research Building 2, Room 562, 1550 Orleans Street, Baltimore, MD 21231, USA
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Huang X, Ma D, Dong W, Li P, Lu T, He N, Tian T, Liu N, DU Y, Ji C. Gene expression profiling of the DNMT3A R882 mutation in acute leukemia. Oncol Lett 2013; 6:268-274. [PMID: 23946816 PMCID: PMC3742503 DOI: 10.3892/ol.2013.1347] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2012] [Accepted: 04/30/2013] [Indexed: 11/06/2022] Open
Abstract
DNA methyltransferase 3A (DNMT3A) is one of two human de novo DNA methyltransferases essential for the regulation of gene expression. DNMT3A mutations and deletions have been previously observed in acute myeloid leukemia (AML), myelodysplastic sydromes and myeloproliferative neoplasms. However, the involvement of DNMT3A in acute lymphoblastic leukemia (ALL) has rarely been reported. In the present study, PCR and direct sequencing was performed to analyze mutations of DNMT3A amino acid residue 882 in 99 acute leukemia patients, including 57 AML patients, 41 ALL patients and a single biphenotypic acute leukemia (BAL) patient. DNMT3A expression was detected in mono-nuclear cells of the bone marrow in these patients and in normal individuals using real-time quantitative polymerase chain reaction, and 17.5% (10/57) of AML patients were found to exhibit DNMT3A mutations. Four missense mutations were observed in the DNMT3A-mutated AML patients, including R882 mutations and a novel single nucleotide polymorphism resulting in the M880V amino acid substitution. However, the ALL and BAL patients were not found to exhibit DNMT3A mutations. The DNMT3A expression levels in the AML patients were significantly higher compared with those of the ALL patients or normal controls. The reduced expression levels of DNMT3A were associated with a significantly lower complete remission rate in the AML patients. However, in the ALL patients, no statistical significance was identified. The results of the present study indicate that DNMT3A may play varying roles in the regulation of DNA methylation in AML and ALL.
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Affiliation(s)
- Xiangnan Huang
- Department of Hematology, Qilu Hospital of Shandong University, Jinan, Shandong 250012, P.R. China
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Gonzalez-Perez A, Jene-Sanz A, Lopez-Bigas N. The mutational landscape of chromatin regulatory factors across 4,623 tumor samples. Genome Biol 2013; 14:r106. [PMID: 24063517 PMCID: PMC4054018 DOI: 10.1186/gb-2013-14-9-r106] [Citation(s) in RCA: 88] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2013] [Accepted: 09/24/2013] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Chromatin regulatory factors are emerging as important genes in cancer development and are regarded as interesting candidates for novel targets for cancer treatment. However, we lack a comprehensive understanding of the role of this group of genes in different cancer types. RESULTS We have analyzed 4,623 tumor samples from thirteen anatomical sites to determine which chromatin regulatory factors are candidate drivers in these different sites. We identify 34 chromatin regulatory factors that are likely drivers in tumors from at least one site, all with relatively low mutational frequency. We also analyze the relative importance of mutations in this group of genes for the development of tumorigenesis in each site, and indifferent tumor types from the same site. CONCLUSIONS We find that, although tumors from all thirteen sites show mutations in likely driver chromatin regulatory factors, these are more prevalent in tumors arising from certain tissues. With the exception of hematopoietic, liver and kidney tumors, as a median, the mutated factors are less than one fifth of all mutated drivers across all sites analyzed. We also show that mutations in two of these genes, MLL and EP300, correlate with broad expression changes across cancer cell lines, thus presenting at least one mechanism through which these mutations could contribute to tumorigenesis in cells of the corresponding tissues.
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Affiliation(s)
- Abel Gonzalez-Perez
- Research Unit on Biomedical Informatics, Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Dr. Aiguader 88, Barcelona, Spain
| | - Alba Jene-Sanz
- Research Unit on Biomedical Informatics, Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Dr. Aiguader 88, Barcelona, Spain
| | - Nuria Lopez-Bigas
- Research Unit on Biomedical Informatics, Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Dr. Aiguader 88, Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
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