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Cheng T, Zhou C, Bian S, Sobeck K, Liu Y. Coordinated activation of DNMT3a and TET2 in cancer stem cell-like cells initiates and sustains drug resistance in hepatocellular carcinoma. Cancer Cell Int 2024; 24:110. [PMID: 38528605 DOI: 10.1186/s12935-024-03288-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Accepted: 02/29/2024] [Indexed: 03/27/2024] Open
Abstract
BACKGROUND Resistance to targeted therapies represents a significant hurdle to successfully treating hepatocellular carcinoma (HCC). While epigenetic abnormalities are critical determinants of HCC relapse and therapeutic resistance, the underlying mechanisms are poorly understood. We aimed to address whether and how dysregulated epigenetic regulators have regulatory and functional communications in establishing and maintaining drug resistance. METHODS HCC-resistant cells were characterized by CCK-8, IncuCyte Live-Cell analysis, flow cytometry and wound-healing assays. Target expression was assessed by qPCR and Western blotting. Global and promoter DNA methylation was measured by dotblotting, methylated-DNA immunoprecipitation and enzymatic digestion. Protein interaction and promoter binding of DNMT3a-TET2 were investigated by co-immunoprecipitation, ChIP-qPCR. The regulatory and functional roles of DNMT3a and TET2 were studied by lentivirus infection and puromycin selection. The association of DNMT and TET expression with drug response and survival of HCC patients was assessed by public datasets, spearman correlation coefficients and online tools. RESULTS We identified the coordination of DNMT3a and TET2 as an actionable mechanism of drug resistance in HCC. The faster growth and migration of resistant HCC cells were attributed to DNMT3a and TET2 upregulation followed by increased 5mC and 5hmC production. HCC patients with higher DNMT3a and TET2 had a shorter survival time with a less favorable response to sorafenib therapy than those with lower expression. Cancer stem cell-like cells (CSCs) displayed DNMT3a and TET2 overexpression, which were insensitive to sorafenib. Either genetic or pharmacological suppression of DNMT3a or/and TET2 impaired resistant cell growth and oncosphere formation, and restored sorafenib sensitivity. Mechanistically, DNMT3a did not establish a regulatory circuit with TET2, but formed a complex with TET2 and HDAC2. This complex bound the promoters of oncogenes (i.e., CDK1, CCNA2, RASEF), and upregulated them without involving promoter DNA methylation. In contrast, DNMT3a-TET2 crosstalk silences tumor suppressors (i.e., P15, SOCS2) through a corepressor complex with HDAC2 along with increased promoter DNA methylation. CONCLUSIONS We demonstrate that DNMT3a and TET2 act coordinately to regulate HCC cell fate in DNA methylation-dependent and -independent manners, representing strong predictors for drug resistance and poor prognosis, and thus are promising therapeutic targets for refractory HCC.
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Affiliation(s)
- Tao Cheng
- Department of Hepatobiliary and Pancreas Surgery, First Hospital of Jilin University, Changchun, Jilin, 130021, P.R. China
- The Hormel Institute, University of Minnesota, Austin, MN, 55912, USA
| | - Changli Zhou
- The Hormel Institute, University of Minnesota, Austin, MN, 55912, USA
- MetroHealth Research Institute, Case Western Reserve University, Cleveland, OH, 44109, USA
| | - Sicheng Bian
- MetroHealth Research Institute, Case Western Reserve University, Cleveland, OH, 44109, USA
| | - Kelsey Sobeck
- The Institute on the Biology of Aging and Metabolism, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Yahui Liu
- Department of Hepatobiliary and Pancreas Surgery, First Hospital of Jilin University, Changchun, Jilin, 130021, P.R. China.
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2
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Lopusna K, Nowialis P, Opavska J, Abraham A, Riva A, Opavsky R. Dnmt3b catalytic activity is critical for its tumour suppressor function in lymphomagenesis and is associated with c-Met oncogenic signalling. EBioMedicine 2021; 63:103191. [PMID: 33418509 PMCID: PMC7804970 DOI: 10.1016/j.ebiom.2020.103191] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Revised: 12/10/2020] [Accepted: 12/14/2020] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND DNA methylation regulates gene transcription in many physiological processes in mammals including development and haematopoiesis. It is catalysed by several DNA methyltransferases, including Dnmt3b that mediates both methylation-dependant and independent gene repression. Dnmt3b is critical for mouse embryogenesis and functions as a tumour suppressor in haematologic malignancies in mice. However, the extent to which Dnmt3b's catalytic activity (CA) is involved in development and cancer is unclear. METHODS We used a mouse model expressing catalytically inactive Dnmt3b (Dnmt3bCI) to study a role of Dnmt3b's CA in development and cancer. We utilized global approaches including Whole-genome Bisulfite sequencing and RNA-seq to analyse DNA methylation and gene expression to identify putative targets of Dnmt3b's CA. To analyse postnatal development and haematopoiesis, we used tissue staining, histological and FACS analysis. To determine potential involvement of selected genes in lymphomagenesis, we used overexpression and knock down approaches followed by in vitro growth assays. FINDINGS We show that mice expressing Dnmt3bCI only, survive postnatal development and develop ICF (the immunodeficiency-centromeric instability-facial anomalies) -like syndrome. The lack of Dnmt3b's CA promoted fibroblasts transformation in vitro, accelerated MLL-AF9 driven Acute Myeloid Leukaemia and MYC-induced T-cell lymphomagenesis in vivo. The elimination of Dnmt3b's CA resulted in decreased methylation of c-Met promoter and its upregulation, activated oncogenic Met signalling, Stat3 phosphorylation and up-regulation of Lin28b promoting lymphomagenesis. INTERPRETATION Our data demonstrates that Dnmt3b's CA is largely dispensable for mouse development but critical to prevent tumourigenesis by controlling events involved in cellular transformation. FUNDING This study was supported by Department of Anatomy and Cell Biology and Cancer Centre at the University of Florida start-up funds, NIH/NCI grant 1R01CA188561-01A1 (R.O.).
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Affiliation(s)
- Katarina Lopusna
- Department of Anatomy and Cell Biology, University of Florida College of Medicine, 2033 Mowry Rd, CGRC 258, Gainesville, FL 32610, United States
| | - Pawel Nowialis
- Department of Anatomy and Cell Biology, University of Florida College of Medicine, 2033 Mowry Rd, CGRC 258, Gainesville, FL 32610, United States
| | - Jana Opavska
- Department of Anatomy and Cell Biology, University of Florida College of Medicine, 2033 Mowry Rd, CGRC 258, Gainesville, FL 32610, United States
| | - Ajay Abraham
- Department of Anatomy and Cell Biology, University of Florida College of Medicine, 2033 Mowry Rd, CGRC 258, Gainesville, FL 32610, United States
| | - Alberto Riva
- ICBR Bioinformatics, Cancer and Genetics Research Complex, University of Florida, P.O. Box 103622. Gainesville, FL 32610, United States
| | - Rene Opavsky
- Department of Anatomy and Cell Biology, University of Florida College of Medicine, 2033 Mowry Rd, CGRC 258, Gainesville, FL 32610, United States.
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3
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Lopusna K, Nowialis P, Opavska J, Abraham A, Riva A, Haney SL, Opavsky R. Decreases in different Dnmt3b activities drive distinct development of hematologic malignancies in mice. J Biol Chem 2021; 296:100285. [PMID: 33450231 PMCID: PMC7949038 DOI: 10.1016/j.jbc.2021.100285] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Revised: 01/04/2021] [Accepted: 01/11/2021] [Indexed: 12/20/2022] Open
Abstract
DNA methylation regulates gene transcription and is involved in various physiological processes in mammals, including development and hematopoiesis. It is catalyzed by DNA methyltransferases including Dnmt1, Dnmt3a, and Dnmt3b. For Dnmt3b, its effects on transcription can result from its own DNA methylase activity, the recruitment of other Dnmts to mediate methylation, or transcription repression in a methylation-independent manner. Low-frequency mutations in human DNMT3B are found in hematologic malignancies including cutaneous T-cell lymphomas, hairy cell leukemia, and diffuse large B-cell lymphomas. Moreover, Dnmt3b is a tumor suppressor in oncogene-driven lymphoid and myeloid malignancies in mice. However, it is poorly understood how the different Dnmt3b activities contribute to these outcomes. We modulated Dnmt3b activity in vivo by generating Dnmt3b+/- mice expressing one wild-type allele as well as Dnmt3b+/CI and Dnmt3bCI/CI mice where one or both alleles express catalytically inactive Dnmt3bCI. We show that 43% of Dnmt3b+/- mice developed T-cell lymphomas, chronic lymphocytic leukemia, and myeloproliferation over 18 months, thus resembling phenotypes previously observed in Dnmt3a+/- mice, possibly through regulation of shared target genes. Interestingly, Dnmt3b+/CI and Dnmt3bCI/CI mice survived postnatal development and were affected by B-cell rather than T-cell malignancies with decreased penetrance. Genome-wide hypomethylation, increased expression of oncogenes such as Jdp2, STAT1, and Trip13, and p53 downregulation were major events contributing to Dnmt3b+/- lymphoma development. We conclude that Dnmt3b catalytic activity is critical to prevent B-cell transformation in vivo, whereas accessory and methylation-independent repressive functions are important to prevent T-cell transformation.
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MESH Headings
- ATPases Associated with Diverse Cellular Activities/genetics
- ATPases Associated with Diverse Cellular Activities/metabolism
- Animals
- Cell Cycle Proteins/genetics
- Cell Cycle Proteins/metabolism
- DNA (Cytosine-5-)-Methyltransferases/deficiency
- DNA (Cytosine-5-)-Methyltransferases/genetics
- DNA Methylation
- DNA, Neoplasm/genetics
- DNA, Neoplasm/metabolism
- Female
- Gene Expression Regulation, Neoplastic
- Heterozygote
- Homozygote
- Humans
- Isoenzymes/genetics
- Isoenzymes/metabolism
- Leukemia, Lymphocytic, Chronic, B-Cell/enzymology
- Leukemia, Lymphocytic, Chronic, B-Cell/genetics
- Leukemia, Lymphocytic, Chronic, B-Cell/pathology
- Lymphoma, B-Cell/enzymology
- Lymphoma, B-Cell/genetics
- Lymphoma, B-Cell/pathology
- Lymphoma, T-Cell/enzymology
- Lymphoma, T-Cell/genetics
- Lymphoma, T-Cell/pathology
- Male
- Mice
- Mice, Knockout
- Myeloproliferative Disorders/enzymology
- Myeloproliferative Disorders/genetics
- Myeloproliferative Disorders/pathology
- Neoplasms, Experimental/enzymology
- Neoplasms, Experimental/genetics
- Neoplasms, Experimental/pathology
- Repressor Proteins/genetics
- Repressor Proteins/metabolism
- STAT1 Transcription Factor/genetics
- STAT1 Transcription Factor/metabolism
- Tumor Suppressor Protein p53/genetics
- Tumor Suppressor Protein p53/metabolism
- DNA Methyltransferase 3B
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Affiliation(s)
- Katarina Lopusna
- Department of Anatomy and Cell Biology, University of Florida College of Medicine, Gainesville, Florida, USA
| | - Pawel Nowialis
- Department of Anatomy and Cell Biology, University of Florida College of Medicine, Gainesville, Florida, USA
| | - Jana Opavska
- Department of Anatomy and Cell Biology, University of Florida College of Medicine, Gainesville, Florida, USA
| | - Ajay Abraham
- Department of Anatomy and Cell Biology, University of Florida College of Medicine, Gainesville, Florida, USA
| | - Alberto Riva
- ICBR Bioinformatics, Cancer and Genetics Research Complex, University of Florida, Gainesville, Florida, USA
| | - Staci L Haney
- Department of Internal Medicine, University of Nebraska Medical Center, 985950 Nebraska Medical Center, Omaha, Nebraska, USA
| | - Rene Opavsky
- Department of Anatomy and Cell Biology, University of Florida College of Medicine, Gainesville, Florida, USA.
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4
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Jia Y, Xie H, Zhang J, Ying H. Induction of TGF-β receptor I expression in a DNA methylation-independent manner mediated by DNMT3A downregulation is involved in early-onset severe preeclampsia. FASEB J 2020; 34:13224-13238. [PMID: 32794622 DOI: 10.1096/fj.202000253rr] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Revised: 07/09/2020] [Accepted: 07/09/2020] [Indexed: 02/06/2023]
Abstract
Preeclampsia, especially early-onset severe preeclampsia is one of the leading causes of maternal and fetal morbidity and mortality. Although it has been well known that the pathophysiology of early-onset severe preeclampsia begins with abnormal placentation and aberrant activation of TGF-β signaling inhibits trophoblast cell invasion, the mechanisms underlying dysregulation of TGF-β signaling in early-onset severe preeclampsia remain elusive to date. Here, we revealed that induction of TGFBR1/TGF-β signaling mediated by DNMT3A downregulation plays a critical role in early-onset severe preeclampsia. Our results show that DNMT3A downregulation elevates TGFBR1 expression in trophoblast cells. Moreover, inhibition of TGFBR1 and TGF-β/Smad signaling can rescue the deficiencies of trophoblast cell migration and invasion caused by DNMT3A knockdown. Mechanistically, DNMT3A suppresses the transcription of TGFBR1 through recruiting EZH2 to its promoter but not changing DNA methylation of TGFBR1 promoter. In human samples, we detected lowly expressed DNMT3A, highly expressed TGFBR1 and hyperactivation of TGF-β/Smad signaling in decidua-embedded extravillous trophoblasts in early-onset severe preeclampsia, which provides the clinical evidence for the correlation between DNMT3A and TGFBR1. Collectively, our findings demonstrate that DNA methylation-independent induction of TGFBR1 mediated by DNMT3A downregulation is relevant to the development of early-onset severe preeclampsia.
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Affiliation(s)
- Yuanhui Jia
- Clinical and Translational Research Center, Shanghai First Maternity and Infant Hospital, Tongji University School of Medicine, Shanghai, China
| | - Han Xie
- Department of Obstetrics, Shanghai First Maternity and Infant Hospital, Tongji University School of Medicine, Shanghai, China
| | - Jiqin Zhang
- Shanghai Key Laboratory of Regulatory Biology, the Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, China
| | - Hao Ying
- Department of Obstetrics, Shanghai First Maternity and Infant Hospital, Tongji University School of Medicine, Shanghai, China
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5
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Zhang J, Yang C, Wu C, Cui W, Wang L. DNA Methyltransferases in Cancer: Biology, Paradox, Aberrations, and Targeted Therapy. Cancers (Basel) 2020; 12:cancers12082123. [PMID: 32751889 PMCID: PMC7465608 DOI: 10.3390/cancers12082123] [Citation(s) in RCA: 101] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Revised: 07/14/2020] [Accepted: 07/20/2020] [Indexed: 02/07/2023] Open
Abstract
DNA methyltransferases are an essential class of modifiers in epigenetics. In mammals, DNMT1, DNMT3A and DNMT3B participate in DNA methylation to regulate normal biological functions, such as embryo development, cell differentiation and gene transcription. Aberrant functions of DNMTs are frequently associated with tumorigenesis. DNMT aberrations usually affect tumor-related factors, such as hypermethylated suppressor genes and genomic instability, which increase the malignancy of tumors, worsen the prognosis for patients, and greatly increase the difficulty of cancer therapy. However, the impact of DNMTs on tumors is still controversial, and therapeutic approaches targeting DNMTs are still under exploration. Here, we summarize the biological functions and paradoxes associated with DNMTs and we discuss some emerging strategies for targeting DNMTs in tumors, which may provide novel ideas for cancer therapy.
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Affiliation(s)
- Jiayu Zhang
- Department of Pharmacology, Shenyang Pharmaceutical University, Shenyang 110016, China; (J.Z.); (C.Y.); (C.W.)
- Benxi Institute of Pharmaceutical Research, Shenyang Pharmaceutical University, Benxi 117004, China
| | - Cheng Yang
- Department of Pharmacology, Shenyang Pharmaceutical University, Shenyang 110016, China; (J.Z.); (C.Y.); (C.W.)
- Benxi Institute of Pharmaceutical Research, Shenyang Pharmaceutical University, Benxi 117004, China
| | - Chunfu Wu
- Department of Pharmacology, Shenyang Pharmaceutical University, Shenyang 110016, China; (J.Z.); (C.Y.); (C.W.)
- Benxi Institute of Pharmaceutical Research, Shenyang Pharmaceutical University, Benxi 117004, China
| | - Wei Cui
- Department of Pharmacology, Shenyang Pharmaceutical University, Shenyang 110016, China; (J.Z.); (C.Y.); (C.W.)
- Correspondence: (W.C.); (L.W.)
| | - Lihui Wang
- Department of Pharmacology, Shenyang Pharmaceutical University, Shenyang 110016, China; (J.Z.); (C.Y.); (C.W.)
- Benxi Institute of Pharmaceutical Research, Shenyang Pharmaceutical University, Benxi 117004, China
- Correspondence: (W.C.); (L.W.)
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6
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Liu SY, Shan NN. DNA methylation plays an important role in immune thrombocytopenia. Int Immunopharmacol 2020; 83:106390. [DOI: 10.1016/j.intimp.2020.106390] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2019] [Revised: 03/06/2020] [Accepted: 03/07/2020] [Indexed: 01/16/2023]
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7
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Nowialis P, Lopusna K, Opavska J, Haney SL, Abraham A, Sheng P, Riva A, Natarajan A, Guryanova O, Simpson M, Hlady R, Xie M, Opavsky R. Catalytically inactive Dnmt3b rescues mouse embryonic development by accessory and repressive functions. Nat Commun 2019; 10:4374. [PMID: 31558711 PMCID: PMC6763448 DOI: 10.1038/s41467-019-12355-7] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Accepted: 09/04/2019] [Indexed: 01/19/2023] Open
Abstract
DNA methylation regulates gene expression in a variety of processes, including mouse embryonic development. Four catalytically active enzymes function in mice as DNA methyltransferases (Dnmts) and as transcriptional regulators. Inactivation of Dnmt3b results in mouse embryonic lethality, but which activities are involved is unclear. Here we show that catalytically inactive Dnmt3b restores a majority of methylation and expression changes deregulated in the absence of Dnmt3b, and as a result, mice survive embryonic development. Thus, Dnmt3b functions as an accessory cofactor supporting catalytic activities performed by other Dnmts. We further demonstrate that Dnmt3b is linked to a control of major developmental pathways, including Wnt and hedgehog signaling. Dnmt3b directly represses Wnt9b whose aberrant up-regulation contributes to embryonic lethality of Dnmt3b knockout embryos. Our results highlight that Dnmt3b is a multifaceted protein that serves as an enzyme, an accessory factor for other methyltransferases, and as a transcriptional repressor in mouse embryogenesis.
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Affiliation(s)
- Pawel Nowialis
- Department of Anatomy and Cell Biology, University of Florida College of Medicine, 2033 Mowry Rd, CGRC 258, Gainesville, FL, 32610, USA
- UF Health Cancer Center, University of Florida, Gainesville, FL, 32610, USA
| | - Katarina Lopusna
- Department of Anatomy and Cell Biology, University of Florida College of Medicine, 2033 Mowry Rd, CGRC 258, Gainesville, FL, 32610, USA
- UF Health Cancer Center, University of Florida, Gainesville, FL, 32610, USA
| | - Jana Opavska
- Department of Anatomy and Cell Biology, University of Florida College of Medicine, 2033 Mowry Rd, CGRC 258, Gainesville, FL, 32610, USA
- UF Health Cancer Center, University of Florida, Gainesville, FL, 32610, USA
| | - Staci L Haney
- Department of Internal Medicine, University of Nebraska Medical Center, 985950 Nebraska Medical Center, Omaha, NE, 68198, USA
| | - Ajay Abraham
- Department of Anatomy and Cell Biology, University of Florida College of Medicine, 2033 Mowry Rd, CGRC 258, Gainesville, FL, 32610, USA
- UF Health Cancer Center, University of Florida, Gainesville, FL, 32610, USA
| | - Peike Sheng
- Department of Biochemistry and Molecular Biology, University of Florida College of Medicine, 2033 Mowry Rd, CGRC 263, Gainesville, FL, 32610, USA
| | - Alberto Riva
- ICBR Bioinformatics, Cancer and Genetics Research Complex, University of Florida, P.O. Box 103622, Gainesville, FL, 32610, USA
| | - Amarnath Natarajan
- University of Nebraska Medical Center, The Eppley Institute for Research in Cancer and Allied Diseases, Fred & Pamela Buffett Cancer Center, 986805 Nebraska Medical Center, Omaha, NE, 68198, USA
| | - Olga Guryanova
- Department of Pharmacology and Therapeutics, University of Florida College of Medicine, 2033 Mowry Rd, CGRC 260, Gainesville, FL, 32610, USA
| | - Melanie Simpson
- Molecular and Structural Biochemistry, NC State University, Raleigh, NC, 27695, USA
| | - Ryan Hlady
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN, 55901, USA
| | - Mingyi Xie
- UF Health Cancer Center, University of Florida, Gainesville, FL, 32610, USA
- Department of Biochemistry and Molecular Biology, University of Florida College of Medicine, 2033 Mowry Rd, CGRC 263, Gainesville, FL, 32610, USA
| | - Rene Opavsky
- Department of Anatomy and Cell Biology, University of Florida College of Medicine, 2033 Mowry Rd, CGRC 258, Gainesville, FL, 32610, USA.
- UF Health Cancer Center, University of Florida, Gainesville, FL, 32610, USA.
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8
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Poole CJ, Zheng W, Lodh A, Yevtodiyenko A, Liefwalker D, Li H, Felsher DW, van Riggelen J. DNMT3B overexpression contributes to aberrant DNA methylation and MYC-driven tumor maintenance in T-ALL and Burkitt's lymphoma. Oncotarget 2017; 8:76898-76920. [PMID: 29100357 PMCID: PMC5652751 DOI: 10.18632/oncotarget.20176] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2017] [Accepted: 07/18/2017] [Indexed: 12/26/2022] Open
Abstract
Aberrant DNA methylation is a hallmark of cancer. However, our understanding of how tumor cell-specific DNA methylation patterns are established and maintained is limited. Here, we report that in T-cell acute lymphoblastic leukemia (T-ALL) and Burkitt's lymphoma the MYC oncogene causes overexpression of DNA methyltransferase (DNMT) 1 and 3B, which contributes to tumor maintenance. By utilizing a tetracycline-regulated MYC transgene in a mouse T-ALL (EμSRα-tTA;tet-o-MYC) and human Burkitt's lymphoma (P493-6) model, we demonstrated that DNMT1 and DNMT3B expression depend on high MYC levels, and that their transcription decreased upon MYC-inactivation. Chromatin immunoprecipitation indicated that MYC binds to the DNMT1 and DNMT3B promoters, implicating a direct transcriptional regulation. Hence, shRNA-mediated knock-down of endogenous MYC in human T-ALL and Burkitt's lymphoma cell lines downregulated DNMT3B expression. Knock-down and pharmacologic inhibition of DNMT3B in T-ALL reduced cell proliferation associated with genome-wide changes in DNA methylation, indicating a tumor promoter function during tumor maintenance. We provide novel evidence that MYC directly deregulates the expression of both de novo and maintenance DNMTs, showing that MYC controls DNA methylation in a genome-wide fashion. Our finding that a coordinated interplay between the components of the DNA methylating machinery contributes to MYC-driven tumor maintenance highlights the potential of specific DNMTs for targeted therapies.
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Affiliation(s)
- Candace J. Poole
- Augusta University, Department of Biochemistry and Molecular Biology, Augusta, GA 30912, USA
| | - Wenli Zheng
- Augusta University, Department of Biochemistry and Molecular Biology, Augusta, GA 30912, USA
| | - Atul Lodh
- Augusta University, Department of Biochemistry and Molecular Biology, Augusta, GA 30912, USA
| | - Aleksey Yevtodiyenko
- Stanford University School of Medicine, Division of Oncology, Departments of Medicine and Pathology, Stanford, CA 94305, USA
| | - Daniel Liefwalker
- Stanford University School of Medicine, Division of Oncology, Departments of Medicine and Pathology, Stanford, CA 94305, USA
| | - Honglin Li
- Augusta University, Department of Biochemistry and Molecular Biology, Augusta, GA 30912, USA
| | - Dean W. Felsher
- Stanford University School of Medicine, Division of Oncology, Departments of Medicine and Pathology, Stanford, CA 94305, USA
| | - Jan van Riggelen
- Augusta University, Department of Biochemistry and Molecular Biology, Augusta, GA 30912, USA
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Kelly AD, Issa JPJ. The promise of epigenetic therapy: reprogramming the cancer epigenome. Curr Opin Genet Dev 2017; 42:68-77. [PMID: 28412585 DOI: 10.1016/j.gde.2017.03.015] [Citation(s) in RCA: 105] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Accepted: 03/27/2017] [Indexed: 02/07/2023]
Abstract
Epigenetics refers to heritable molecular determinants of phenotype independent of DNA sequence. Epigenetic features include DNA methylation, histone modifications, non-coding RNAs, and chromatin structure. The epigenetic status of cells plays a crucial role in determining their differentiation state and proper function within multicellular organisms. Disruption of these processes is now understood to be a major contributor to cancer development and progression, and recent efforts have attempted to pharmacologically reverse such altered epigenetics. In this mini-review we introduce the concept of epigenetic drivers of cancer and discuss how aberrant DNA methylation, histone modifications, and chromatin states are being targeted using drugs either in preclinical, or clinical development, and how they fit in the context of existing therapies.
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Affiliation(s)
- Andrew D Kelly
- Fels Institute for Cancer Research and Molecular Biology, Lewis Katz School of Medicine at Temple University, Philadelphia, PA 19140, USA
| | - Jean-Pierre J Issa
- Fels Institute for Cancer Research and Molecular Biology, Lewis Katz School of Medicine at Temple University, Philadelphia, PA 19140, USA.
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10
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Peralta-Arrieta I, Hernández-Sotelo D, Castro-Coronel Y, Leyva-Vázquez MA, Illades-Aguiar B. DNMT3B modulates the expression of cancer-related genes and downregulates the expression of the gene VAV3 via methylation. Am J Cancer Res 2017; 7:77-87. [PMID: 28123849 PMCID: PMC5250682] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2016] [Accepted: 09/02/2016] [Indexed: 06/06/2023] Open
Abstract
Altered promoter DNA methylation is one of the most important epigenetic abnormalities in human cancer. DNMT3B, de novo methyltransferase, is clearly related to abnormal methylation of tumour suppressor genes, DNA repair genes and its overexpression contributes to oncogenic processes and tumorigenesis in vivo. The purpose of this study was to assess the effect of the overexpression of DNMT3B in HaCaT cells on global gene expression and on the methylation of selected genes to the identification of genes that can be target of DNMT3B. We found that the overexpression of DNMT3B in HaCaT cells, modulate the expression of genes related to cancer, downregulated the expression of 151 genes with CpG islands and downregulated the expression of the VAV3 gene via methylation of its promoter. These results highlight the importance of DNMT3B in gene expression and human cancer.
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Affiliation(s)
- Irlanda Peralta-Arrieta
- Laboratorio de Biomedicina Molecular, Facultad de Ciencias Químico Biológicas, Universidad Autónoma de GuerreroChilpancingo, Guerrero, México
| | - Daniel Hernández-Sotelo
- Laboratorio de Epigenética del Cáncer, Facultad de Ciencias Químico Biológicas, Universidad Autónoma de GuerreroChilpancingo, Guerrero, México
| | - Yaneth Castro-Coronel
- Laboratorio de Investigación en Citopatología e Histoquímica, Facultad de Ciencias Químico Biológicas, Universidad Autónoma de GuerreroChilpancingo, Guerrero, México
| | - Marco Antonio Leyva-Vázquez
- Laboratorio de Biomedicina Molecular, Facultad de Ciencias Químico Biológicas, Universidad Autónoma de GuerreroChilpancingo, Guerrero, México
| | - Berenice Illades-Aguiar
- Laboratorio de Biomedicina Molecular, Facultad de Ciencias Químico Biológicas, Universidad Autónoma de GuerreroChilpancingo, Guerrero, México
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11
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Megiorni F, Camero S, Ceccarelli S, McDowell HP, Mannarino O, Marampon F, Pizer B, Shukla R, Pizzuti A, Marchese C, Clerico A, Dominici C. DNMT3B in vitro knocking-down is able to reverse embryonal rhabdomyosarcoma cell phenotype through inhibition of proliferation and induction of myogenic differentiation. Oncotarget 2016; 7:79342-79356. [PMID: 27764816 PMCID: PMC5346718 DOI: 10.18632/oncotarget.12688] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2016] [Accepted: 09/29/2016] [Indexed: 01/08/2023] Open
Abstract
Aberrant DNA methylation has been frequently observed in many human cancers, including rhabdomyosarcoma (RMS), the most common soft tissue sarcoma in children. To date, the expression and function of the de novo DNA methyltransferase (DNMT) 3B in RMS have not yet been investigated. Our study show for the first time a significant up-regulation of DNMT3B levels in 14 RMS tumour samples and 4 RMS cell lines in comparison to normal skeletal muscle. Transfection of RD and TE671 cells, two in vitro models of embryonal RMS (ERMS), with a synthetic DNMT3B siRNA decreased cell proliferation by arresting cell cycle at G1 phase, as demonstrated by the reduced expression of Cyclin B1, Cyclin D1 and Cyclin E2, and by the concomitant up-regulation of the checkpoint regulators p21 and p27. DNMT3B depletion also impaired RB phosphorylation status and decreased migratory capacity and clonogenic potential. Interestingly, DNMT3B knock-down was able to commit ERMS cells towards myogenic terminal differentiation, as confirmed by the acquisition of a myogenic-like phenotype and by the increased expression of the myogenic markers MYOD1, Myogenin and MyHC. Finally, inhibition of MEK/ERK signalling by U0126 resulted in a reduction of DNMT3B protein, giving evidence that DNMT3B is a down-stream molecule of this oncogenic pathway.Taken together, our data indicate that altered expression of DNMT3B plays a key role in ERMS development since its silencing is able to reverse cell cancer phenotype by rescuing myogenic program. Epigenetic therapy, by targeting the DNA methylation machinery, may represent a novel therapeutic strategy against RMS.
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Affiliation(s)
- Francesca Megiorni
- Department of Paediatrics and Infantile Neuropsychiatry, Sapienza University of Rome, Rome, Italy
| | - Simona Camero
- Department of Paediatrics and Infantile Neuropsychiatry, Sapienza University of Rome, Rome, Italy
| | - Simona Ceccarelli
- Department of Experimental Medicine, Sapienza University of Rome, Rome, Italy
| | - Heather P. McDowell
- Department of Paediatrics and Infantile Neuropsychiatry, Sapienza University of Rome, Rome, Italy
- Department of Oncology, Alder Hey Children's NHS Foundation Trust, Liverpool, United Kingdom
| | - Olga Mannarino
- Department of Paediatrics and Infantile Neuropsychiatry, Sapienza University of Rome, Rome, Italy
| | - Francesco Marampon
- Department of Biotechnological and Applied Clinical Sciences, University of L'Aquila, L'Aquila, Italy
| | - Barry Pizer
- Department of Oncology, Alder Hey Children's NHS Foundation Trust, Liverpool, United Kingdom
| | - Rajeev Shukla
- Department of Perinatal and Paediatric Pathology, Alder Hey Children's NHS Foundation Trust, Liverpool, United Kingdom
| | - Antonio Pizzuti
- Department of Experimental Medicine, Sapienza University of Rome, Rome, Italy
| | - Cinzia Marchese
- Department of Experimental Medicine, Sapienza University of Rome, Rome, Italy
| | - Anna Clerico
- Department of Paediatrics and Infantile Neuropsychiatry, Sapienza University of Rome, Rome, Italy
| | - Carlo Dominici
- Department of Paediatrics and Infantile Neuropsychiatry, Sapienza University of Rome, Rome, Italy
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12
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Kramer A, Challen GA. The epigenetic basis of hematopoietic stem cell aging. Semin Hematol 2016; 54:19-24. [PMID: 28088983 DOI: 10.1053/j.seminhematol.2016.10.006] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Revised: 10/19/2016] [Accepted: 10/19/2016] [Indexed: 12/12/2022]
Abstract
Highly proliferative tissues such as the gut, skin, and bone marrow lose millions of cells each day to normal attrition and challenge from different biological adversities. To achieve a lifespan beyond the longevity of individual cell types, tissue-specific stem cells sustain these tissues throughout the life of a human. For example, the lifespan of erythrocytes is about 100 days and adults make about two million new erythrocytes every second. A small pool of hematopoietic stem cells (HSCs) in the bone marrow is responsible for the lifetime maintenance of these populations. However, there are changes that occur within the HSC pool during aging. Biologically, these changes manifest as blunted immune responses, decreased bone marrow cellularity, and increased risk of myeloid diseases. Understanding the molecular mechanisms underlying dysfunction of aging HSCs is an important focus of biomedical research. With advances in modern health care, the average age of the general population is ever increasing. If molecular or pharmacological interventions could be discovered that rejuvenate aging HSCs, it could reduce the burden of age related immune system compromise as well as open up new opportunities for treatment of hematological disorders with regenerative therapy.
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Affiliation(s)
- Ashley Kramer
- Section of Stem Cell Biology, Division of Oncology, Department of Medicine, Washington University in St. Louis School of Medicine, St. Louis, MO
| | - Grant A Challen
- Section of Stem Cell Biology, Division of Oncology, Department of Medicine, Washington University in St. Louis School of Medicine, St. Louis, MO; Developmental, Regenerative and Stem Cell Biology Program, Division of Biology and Biomedical Sciences, Washington University in St. Louis School of Medicine, St. Louis, MO.
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13
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Haney SL, Upchurch GM, Opavska J, Klinkebiel D, Hlady RA, Roy S, Dutta S, Datta K, Opavsky R. Dnmt3a Is a Haploinsufficient Tumor Suppressor in CD8+ Peripheral T Cell Lymphoma. PLoS Genet 2016; 12:e1006334. [PMID: 27690235 PMCID: PMC5045215 DOI: 10.1371/journal.pgen.1006334] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2016] [Accepted: 08/31/2016] [Indexed: 12/29/2022] Open
Abstract
DNA methyltransferase 3A (DNMT3A) is an enzyme involved in DNA methylation that is frequently mutated in human hematologic malignancies. We have previously shown that inactivation of Dnmt3a in hematopoietic cells results in chronic lymphocytic leukemia in mice. Here we show that 12% of Dnmt3a-deficient mice develop CD8+ mature peripheral T cell lymphomas (PTCL) and 29% of mice are affected by both diseases. 10% of Dnmt3a+/- mice develop lymphomas, suggesting that Dnmt3a is a haploinsufficient tumor suppressor in PTCL. DNA methylation was deregulated genome-wide with 10-fold more hypo- than hypermethylated promoters and enhancers, demonstrating that hypomethylation is a major event in the development of PTCL. Hypomethylated promoters were enriched for binding sites of transcription factors AML1, NF-κB and OCT1, implying the transcription factors potential involvement in Dnmt3a-associated methylation. Whereas 71 hypomethylated genes showed an increased expression in PTCL, only 3 hypermethylated genes were silenced, suggesting that cancer-specific hypomethylation has broader effects on the transcriptome of cancer cells than hypermethylation. Interestingly, transcriptomes of Dnmt3a+/- and Dnmt3aΔ/Δ lymphomas were largely conserved and significantly overlapped with those of human tumors. Importantly, we observed downregulation of tumor suppressor p53 in Dnmt3a+/- and Dnmt3aΔ/Δ lymphomas as well as in pre-tumor thymocytes from 9 months old but not 6 weeks old Dnmt3a+/- tumor-free mice, suggesting that p53 downregulation is chronologically an intermediate event in tumorigenesis. Decrease in p53 is likely an important event in tumorigenesis because its overexpression inhibited proliferation in mouse PTCL cell lines, suggesting that low levels of p53 are important for tumor maintenance. Altogether, our data link the haploinsufficient tumor suppressor function of Dnmt3a in the prevention of mouse mature CD8+ PTCL indirectly to a bona fide tumor suppressor of T cell malignancies p53. Global deregulation of cytosine methylation is an epigenetic hallmark of hematologic malignancies that may promote tumorigenesis by silencing tumor suppressor genes, upregulating oncogenes, and inducing genomic instability. DNA methyltransferase 3a (DNMT3A) is one of the three catalytically active enzymes responsible for cytosine methylation and one of the most frequently mutated genes in myeloid and T cell malignancies. Its role in malignant hematopoiesis, however, remains poorly understood. Here we show that Dnmt3a is a haploinsufficient tumor suppressor in the prevention of peripheral T cell lymphomas in mice. Our molecular studies identified a large number of genes deregulated in the absence of Dnmt3a that may be putative drivers of oncogenesis. We also show that downregulation of the tumor suppressor p53 is an important event in the development of mouse T cell lymphomas. Thus, this study establishes a novel mouse model to elucidate how epigenetic deregulation of transcription contributes to the pathogenesis of T cell lymphomas.
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Affiliation(s)
- Staci L. Haney
- Department of Genetics, Cell Biology, and Anatomy, University of Nebraska Medical Center, Omaha, Nebraska, United States of America
| | - G. Michael Upchurch
- Eppley Institute for Research in Cancer and Allied Diseases, Fred and Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, Nebraska, United States of America
| | - Jana Opavska
- Eppley Institute for Research in Cancer and Allied Diseases, Fred and Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, Nebraska, United States of America
| | - David Klinkebiel
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, Nebraska, United States of America
| | - Ryan A. Hlady
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, Minnesota, United States of America
| | - Sohini Roy
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, Nebraska, United States of America
| | - Samikshan Dutta
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, Nebraska, United States of America
| | - Kaustubh Datta
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, Nebraska, United States of America
| | - Rene Opavsky
- Department of Genetics, Cell Biology, and Anatomy, University of Nebraska Medical Center, Omaha, Nebraska, United States of America
- Eppley Institute for Research in Cancer and Allied Diseases, Fred and Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, Nebraska, United States of America
- Center for Leukemia and Lymphoma Research, University of Nebraska Medical Center, Omaha, Nebraska, United States of America
- * E-mail:
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14
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Haney SL, Upchurch GM, Opavska J, Klinkebiel D, Appiah AK, Smith LM, Heavican TB, Iqbal J, Joshi S, Opavsky R. Loss of Dnmt3a induces CLL and PTCL with distinct methylomes and transcriptomes in mice. Sci Rep 2016; 6:34222. [PMID: 27677595 PMCID: PMC5039761 DOI: 10.1038/srep34222] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2016] [Accepted: 09/07/2016] [Indexed: 01/09/2023] Open
Abstract
Cytosine methylation of DNA is an epigenetic modification involved in the repression of genes that affect biological processes including hematopoiesis. It is catalyzed by DNA methyltransferases, one of which -DNMT3A- is frequently mutated in human hematologic malignancies. We have previously reported that Dnmt3a inactivation in hematopoietic stem cells results in chronic lymphocytic leukemia (CLL) and CD8-positive peripheral T cell lymphomas (PTCL) in EμSRα-tTA;Teto-Cre;Dnmt3afl/fl; Rosa26LOXPEGFP/EGFP (Dnmt3aΔ/Δ) mice. The extent to which molecular changes overlap between these diseases is not clear. Using high resolution global methylation and expression analysis we show that whereas patterns of methylation and transcription in normal B-1a cells and CD8-positive T cells are similar, methylomes and transcriptomes in malignant B-1a and CD8+ T cells are remarkably distinct, suggesting a cell-type specific function for Dnmt3a in cellular transformation. Promoter hypomethylation in tumors was 10 times more frequent than hypermethylation, three times more frequent in CLL than PTCL and correlated better with gene expression than hypermethylation. Cross-species molecular comparison of mouse and human CLL and PTCL reveals significant overlaps and identifies putative oncogenic drivers of disease. Thus, Dnmt3aΔ/Δ mice can serve as a new mouse model to study CLL and PTCL in relevant physiological settings.
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Affiliation(s)
- Staci L Haney
- Department of Genetics, Cell Biology, and Anatomy, University of Nebraska Medical Center, Omaha, Nebraska, 68198, USA
| | - Garland M Upchurch
- Eppley Institute for Research in Cancer and Allied Diseases, Fred and Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, Nebraska, 68198, USA
| | - Jana Opavska
- Eppley Institute for Research in Cancer and Allied Diseases, Fred and Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, Nebraska, 68198, USA
| | - David Klinkebiel
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, Nebraska, 68198, USA
| | | | | | - Tayla B Heavican
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, Nebraska, 68198, USA
| | - Javeed Iqbal
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, Nebraska, 68198, USA.,Center for Leukemia and Lymphoma Research, University of Nebraska Medical Center, Omaha, Nebraska, 68198, USA
| | - Shantaram Joshi
- Department of Genetics, Cell Biology, and Anatomy, University of Nebraska Medical Center, Omaha, Nebraska, 68198, USA.,Center for Leukemia and Lymphoma Research, University of Nebraska Medical Center, Omaha, Nebraska, 68198, USA
| | - Rene Opavsky
- Department of Genetics, Cell Biology, and Anatomy, University of Nebraska Medical Center, Omaha, Nebraska, 68198, USA.,Eppley Institute for Research in Cancer and Allied Diseases, Fred and Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, Nebraska, 68198, USA.,Center for Leukemia and Lymphoma Research, University of Nebraska Medical Center, Omaha, Nebraska, 68198, USA
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15
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Brenner C, Luciani J, Bizet M, Ndlovu M, Josseaux E, Dedeurwaerder S, Calonne E, Putmans P, Cartron PF, Defrance M, Fuks F, Deplus R. The interplay between the lysine demethylase KDM1A and DNA methyltransferases in cancer cells is cell cycle dependent. Oncotarget 2016; 7:58939-58952. [PMID: 27449289 PMCID: PMC5312287 DOI: 10.18632/oncotarget.10624] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2016] [Accepted: 07/06/2016] [Indexed: 12/12/2022] Open
Abstract
DNA methylation and histone modifications are key epigenetic regulators of gene expression, and tight connections are known between the two. DNA methyltransferases are upregulated in several tumors and aberrant DNA methylation profiles are a cancer hallmark. On the other hand, histone demethylases are upregulated in cancer cells. Previous work on ES cells has shown that the lysine demethylase KDM1A binds to DNMT1, thereby affecting DNA methylation. In cancer cells, the occurrence of this interaction has not been explored. Here we demonstrate in several tumor cell lines an interaction between KDM1A and both DNMT1 and DNMT3B. Intriguingly and in contrast to what is observed in ES cells, KDM1A depletion in cancer cells was found not to trigger any reduction in the DNMT1 or DNMT3B protein level or any change in DNA methylation. In the S-phase, furthermore, KDM1A and DNMT1 were found, to co-localize within the heterochromatin. Using P-LISA, we revealed substantially increased binding of KDM1A to DNMT1 during the S-phase. Together, our findings propose a mechanistic link between KDM1A and DNA methyltransferases in cancer cells and suggest that the KDM1A/DNMT1 interaction may play a role during replication. Our work also strengthens the idea that DNMTs can exert functions unrelated to act on DNA methylation.
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Affiliation(s)
- Carmen Brenner
- Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB-Cancer Research Centre (U-CRC), Université Libre de Bruxelles, 1070 Brussels, Belgium
| | - Judith Luciani
- Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB-Cancer Research Centre (U-CRC), Université Libre de Bruxelles, 1070 Brussels, Belgium
| | - Martin Bizet
- Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB-Cancer Research Centre (U-CRC), Université Libre de Bruxelles, 1070 Brussels, Belgium
| | - Matladi Ndlovu
- Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB-Cancer Research Centre (U-CRC), Université Libre de Bruxelles, 1070 Brussels, Belgium
| | - Eleonore Josseaux
- Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB-Cancer Research Centre (U-CRC), Université Libre de Bruxelles, 1070 Brussels, Belgium
| | - Sarah Dedeurwaerder
- Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB-Cancer Research Centre (U-CRC), Université Libre de Bruxelles, 1070 Brussels, Belgium
| | - Emilie Calonne
- Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB-Cancer Research Centre (U-CRC), Université Libre de Bruxelles, 1070 Brussels, Belgium
| | - Pascale Putmans
- Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB-Cancer Research Centre (U-CRC), Université Libre de Bruxelles, 1070 Brussels, Belgium
| | - Pierre-Francois Cartron
- Centre de Recherche en Cancérologie Nantes-Angers, INSERM, U892, Equipe Apoptose et Progression Tumorale, BP7021, 44007 Nantes, France
- Département de Recherche en Cancérologie, Faculté de Médecine, Université de Nantes, IFR26, F-4400, Nantes, France
- LaBCT, Institut de Cancérologie de l'Ouest, 44805 Nantes, Saint Herblain Cedex, France
| | - Matthieu Defrance
- Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB-Cancer Research Centre (U-CRC), Université Libre de Bruxelles, 1070 Brussels, Belgium
| | - François Fuks
- Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB-Cancer Research Centre (U-CRC), Université Libre de Bruxelles, 1070 Brussels, Belgium
| | - Rachel Deplus
- Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB-Cancer Research Centre (U-CRC), Université Libre de Bruxelles, 1070 Brussels, Belgium
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16
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Cree SL, Fredericks R, Miller A, Pearce FG, Filichev V, Fee C, Kennedy MA. DNA G-quadruplexes show strong interaction with DNA methyltransferases in vitro. FEBS Lett 2016; 590:2870-83. [PMID: 27468168 DOI: 10.1002/1873-3468.12331] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2016] [Revised: 07/07/2016] [Accepted: 07/21/2016] [Indexed: 12/16/2022]
Abstract
The DNA methyltransferase enzymes (DNMTs) catalyzing cytosine methylation do so at specific locations of the genome, although with some level of redundancy. The de novo methyltransferases DNMT3A and 3B play a vital role in methylating the genome of the developing embryo in regions devoid of methylation marks. The ability of DNMTs to colocalize at sites of DNA damage is suggestive that recognition of mispaired bases and unusual structures is inherent to the function of these proteins. We provide evidence for G-quadruplex formation within imprinted gene promoters, and report high-affinity binding of recombinant human DNMTs to such DNA G-quadruplexes in vitro. These observations suggest a potential interaction of G-quadruplexes with the DNA methylation machinery, which may be of epigenetic and biological significance.
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Affiliation(s)
- Simone L Cree
- Department of Pathology, University of Otago, Christchurch, New Zealand
| | - Rayleen Fredericks
- Department of Chemical and Process Engineering, University of Canterbury, Christchurch, New Zealand
- Biomolecular Interaction Centre, University of Canterbury, Christchurch, New Zealand
| | - Allison Miller
- Department of Pathology, University of Otago, Christchurch, New Zealand
| | - F Grant Pearce
- Biomolecular Interaction Centre, University of Canterbury, Christchurch, New Zealand
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - Vyacheslav Filichev
- Institute of Fundamental Sciences, Massey University, Palmerston North, New Zealand
| | - Conan Fee
- Department of Chemical and Process Engineering, University of Canterbury, Christchurch, New Zealand
- Biomolecular Interaction Centre, University of Canterbury, Christchurch, New Zealand
| | - Martin A Kennedy
- Department of Pathology, University of Otago, Christchurch, New Zealand
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17
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Upchurch GM, Haney SL, Opavsky R. Aberrant Promoter Hypomethylation in CLL: Does It Matter for Disease Development? Front Oncol 2016; 6:182. [PMID: 27563627 PMCID: PMC4980682 DOI: 10.3389/fonc.2016.00182] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2016] [Accepted: 07/27/2016] [Indexed: 12/11/2022] Open
Abstract
Over the last 30 years, studies of aberrant DNA methylation in hematologic malignancies have been dominated by the primary focus of understanding promoter hypermethylation. These efforts not only resulted in a better understanding of the basis of epigenetic silencing of tumor suppressor genes but also resulted in approval of hypomethylating agents for the treatment of several malignancies, such as myelodysplastic syndrome and acute myeloid leukemia. Recent advances in global methylation profiling coupled with the use of mouse models suggest that aberrant promoter hypomethylation is also a frequent event in hematologic malignancies, particularly in chronic lymphocytic leukemia (CLL). Promoter hypomethylation affects gene expression and, therefore, may play an important role in disease pathogenesis. Here, we review recent findings and discuss the potential involvement of aberrant promoter hypomethylation in CLL.
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Affiliation(s)
- Garland Michael Upchurch
- Fred and Pamela Buffett Cancer Center, Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center , Omaha, NE , USA
| | - Staci L Haney
- Department of Genetics, Cell Biology, and Anatomy, University of Nebraska Medical Center , Omaha, NE , USA
| | - Rene Opavsky
- Fred and Pamela Buffett Cancer Center, Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, NE, USA; Department of Genetics, Cell Biology, and Anatomy, University of Nebraska Medical Center, Omaha, NE, USA; Center for Leukemia and Lymphoma Research, University of Nebraska Medical Center, Omaha, NE, USA
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18
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Haney SL, Upchurch GM, Opavska J, Klinkebiel D, Hlady RA, Suresh A, Pirruccello SJ, Shukla V, Lu R, Costinean S, Rizzino A, Karpf AR, Joshi S, Swanson P, Opavsky R. Promoter Hypomethylation and Expression Is Conserved in Mouse Chronic Lymphocytic Leukemia Induced by Decreased or Inactivated Dnmt3a. Cell Rep 2016; 15:1190-201. [PMID: 27134162 DOI: 10.1016/j.celrep.2016.04.004] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2015] [Revised: 02/18/2016] [Accepted: 03/28/2016] [Indexed: 01/06/2023] Open
Abstract
DNA methyltransferase 3a (DNMT3A) catalyzes the formation of 5-methyl-cytosine in mammalian genomic DNA, and it is frequently mutated in human hematologic malignancies. Bi-allelic loss of Dnmt3a in mice results in leukemia and lymphoma, including chronic lymphocytic leukemia (CLL). Here, we investigate whether mono-allelic loss of Dnmt3a is sufficient to induce disease. We show that, by 16 months of age, 65% of Dnmt3a(+/-) mice develop a CLL-like disease, and 15% of mice develop non-malignant myeloproliferation. Genome-wide methylation analysis reveals that reduced Dnmt3a levels induce promoter hypomethylation at similar loci in Dnmt3a(+/-) and Dnmt3a(Δ/Δ) CLL, suggesting that promoters are particularly sensitive to Dnmt3a levels. Gene expression analysis identified 26 hypomethylated and overexpressed genes common to both Dnmt3a(+/-) and Dnmt3a(Δ/Δ) CLL as putative oncogenic drivers. Our data provide evidence that Dnmt3a is a haplo-insufficient tumor suppressor in CLL and highlights the importance of deregulated molecular events in disease pathogenesis.
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Affiliation(s)
- Staci L Haney
- Department of Genetics, Cell Biology, and Anatomy, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - G Michael Upchurch
- Eppley Institute for Research in Cancer and Allied Diseases, Fred and Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Jana Opavska
- Eppley Institute for Research in Cancer and Allied Diseases, Fred and Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - David Klinkebiel
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Ryan A Hlady
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN 55905, USA
| | - Abhinav Suresh
- Eppley Institute for Research in Cancer and Allied Diseases, Fred and Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Samuel J Pirruccello
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, NE 68198, USA; Center for Leukemia and Lymphoma Research, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Vipul Shukla
- Department of Genetics, Cell Biology, and Anatomy, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Runqing Lu
- Department of Genetics, Cell Biology, and Anatomy, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Stefan Costinean
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Angie Rizzino
- Eppley Institute for Research in Cancer and Allied Diseases, Fred and Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE 68198, USA; Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE 68198, USA; Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Adam R Karpf
- Eppley Institute for Research in Cancer and Allied Diseases, Fred and Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Shantaram Joshi
- Department of Genetics, Cell Biology, and Anatomy, University of Nebraska Medical Center, Omaha, NE 68198, USA; Center for Leukemia and Lymphoma Research, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Patrick Swanson
- Department of Medical Microbiology and Immunology, Creighton University, Omaha, NE 68102, USA
| | - Rene Opavsky
- Department of Genetics, Cell Biology, and Anatomy, University of Nebraska Medical Center, Omaha, NE 68198, USA; Eppley Institute for Research in Cancer and Allied Diseases, Fred and Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE 68198, USA; Center for Leukemia and Lymphoma Research, University of Nebraska Medical Center, Omaha, NE 68198, USA.
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19
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Rowles DL, Tsai YC, Greco TM, Lin AE, Li M, Yeh J, Cristea IM. DNA methyltransferase DNMT3A associates with viral proteins and impacts HSV-1 infection. Proteomics 2015; 15:1968-82. [PMID: 25758154 DOI: 10.1002/pmic.201500035] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2015] [Revised: 02/17/2015] [Accepted: 03/07/2015] [Indexed: 01/21/2023]
Abstract
Viral infections can alter the cellular epigenetic landscape, through modulation of either DNA methylation profiles or chromatin remodeling enzymes and histone modifications. These changes can act to promote viral replication or host defense. Herpes simplex virus type 1 (HSV-1) is a prominent human pathogen, which relies on interactions with host factors for efficient replication and spread. Nevertheless, the knowledge regarding its modulation of epigenetic factors remains limited. Here, we used fluorescently-labeled viruses in conjunction with immunoaffinity purification and MS to study virus-virus and virus-host protein interactions during HSV-1 infection in primary human fibroblasts. We identified interactions among viral capsid and tegument proteins, detecting phosphorylation of the capsid protein VP26 at sites within its UL37-binding domain, and an acetylation within the major capsid protein VP5. Interestingly, we found a nuclear association between viral capsid proteins and the de novo DNA methyltransferase DNA (cytosine-5)-methyltransferase 3A (DNMT3A), which we confirmed by reciprocal isolations and microscopy. We show that drug-induced inhibition of DNA methyltransferase activity, as well as siRNA- and shRNA-mediated DNMT3A knockdowns trigger reductions in virus titers. Altogether, our results highlight a functional association of viral proteins with the mammalian DNA methyltransferase machinery, pointing to DNMT3A as a host factor required for effective HSV-1 infection.
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Affiliation(s)
- Daniell L Rowles
- Lewis Thomas Laboratory, Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Yuan-Chin Tsai
- Lewis Thomas Laboratory, Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Todd M Greco
- Lewis Thomas Laboratory, Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Aaron E Lin
- Lewis Thomas Laboratory, Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Minghao Li
- Lewis Thomas Laboratory, Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Justin Yeh
- Lewis Thomas Laboratory, Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Ileana M Cristea
- Lewis Thomas Laboratory, Department of Molecular Biology, Princeton University, Princeton, NJ, USA
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