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Bowler EH, Bell J, Divecha N, Skipp P, Ewing RM. Proteomic Analysis of Azacitidine-Induced Degradation Profiles Identifies Multiple Chromatin and Epigenetic Regulators Including Uhrf1 and Dnmt1 as Sensitive to Azacitidine. J Proteome Res 2019; 18:1032-1042. [PMID: 30672294 DOI: 10.1021/acs.jproteome.8b00745] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
DNA methylation is a critical epigenetic modification that is established and maintained across the genome by DNA methyltransferase enzymes (Dnmts). Altered patterns of DNA methylation are a frequent occurrence in many tumor genomes, and inhibitors of Dnmts have become important epigenetic drugs. Azacitidine is a cytidine analog that is incorporated into DNA and induces the specific inhibition and proteasomal-mediated degradation of Dnmts. The downstream effects of azacitidine on CpG methylation and on gene transcription have been widely studied in many systems, but how azacitidine impacts the proteome is not well-understood. In addition, with its specific ability to induce the rapid degradation of Dnmts (in particular, the primary maintenance DNA methyltransferase, Dnmt1), it may be employed as a specific chemical knockdown for investigating the Dnmt1-associated functional or physical interactome. In this study, we use quantitative proteomics to analyze the degradation profile of proteins in the nuclear proteome of cells treated with azacitidine. We identify specific proteins as well as multiple pathways and processes that are impacted by azacitidine. The Dnmt1 interaction partner, Uhrf1, exhibits significant azacitidine-induced degradation, and this azacitidine-induced degradation is independent of the levels of Dnmt1 protein. We identify multiple other chromatin- and epigenetic-associated factors, including the bromodomain-containing transcriptional regulator, Brd2. We show that azacitidine induces highly specific perturbations of the Dnmt1-associated proteome, and while interaction partners such as Uhrf1 are sensitive to azacitidine, others such as the Dnmt1 interaction partner and stability regulator, Usp7, are not. In summary, we have conducted the first comprehensive proteomic analysis of the azacitidine-sensitive nuclear proteome, and we show how 5-azacitidine can be used as a specific probe to explore Dnmt- and chromatin-related protein networks.
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Affiliation(s)
- Emily H Bowler
- School of Biological Sciences , University of Southampton , Southampton SO17 1BJ , United Kingdom
| | - Joseph Bell
- School of Biological Sciences , University of Southampton , Southampton SO17 1BJ , United Kingdom
| | - Nullin Divecha
- School of Biological Sciences , University of Southampton , Southampton SO17 1BJ , United Kingdom
| | - Paul Skipp
- School of Biological Sciences , University of Southampton , Southampton SO17 1BJ , United Kingdom
| | - Rob M Ewing
- School of Biological Sciences , University of Southampton , Southampton SO17 1BJ , United Kingdom
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Zahnow C, Topper M, Stone M, Murray-Stewart T, Li H, Baylin S, Casero R. Inhibitors of DNA Methylation, Histone Deacetylation, and Histone Demethylation: A Perfect Combination for Cancer Therapy. Adv Cancer Res 2016; 130:55-111. [PMID: 27037751 DOI: 10.1016/bs.acr.2016.01.007] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Epigenetic silencing and inappropriate activation of gene expression are frequent events during the initiation and progression of cancer. These events involve a complex interplay between the hypermethylation of CpG dinucleotides within gene promoter and enhancer regions, the recruitment of transcriptional corepressors and the deacetylation and/or methylation of histone tails. These epigenetic regulators act in concert to block transcription or interfere with the maintenance of chromatin boundary regions. However, DNA/histone methylation and histone acetylation states are reversible, enzyme-mediated processes and as such, have emerged as promising targets for cancer therapy. This review will focus on the potential benefits and synergistic/additive effects of combining DNA-demethylating agents and histone deacetylase inhibitors or lysine-specific demethylase inhibitors together in epigenetic therapy for solid tumors and will highlight what is known regarding the mechanisms of action that contribute to the antitumor response.
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BORTHAKUR GAUTAM, HUANG XUELIN, KANTARJIAN HAGOP, FADERL STEFAN, RAVANDI FARHAD, FERRAJOLI ALESSANDRA, TORMA RITVA, MORRIS GAIL, BERRY DONALD, ISSA JEANPIERRE. Report of a phase 1/2 study of a combination of azacitidine and cytarabine in acute myelogenous leukemia and high-risk myelodysplastic syndromes. Leuk Lymphoma 2010; 51:73-8. [PMID: 20017599 PMCID: PMC2876330 DOI: 10.3109/10428190903318329] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Cytarabine resistance characterizes relapsed and refractory acute myelogenous leukemia (AML). Restoration of cytarabine sensitivity can potentially improve treatment outcome in this setting. Acquired hypermethylation of gene promoters and associated silencing of gene expression has been implicated in chemo resistance, and drug-induced hypomethylation can improve sensitivity to cytarabine in vitro. We conducted an adaptively randomized study of a combination of azacitidine, a hypomethylating agent, and cytarabine in 34 patients with AML. The combination administered in a concomitant fashion is safe at full doses of azacitidine and cytarabine, without unexpected toxicities. However, in this advanced AML population, it was difficult to deliver more than one cycle of therapy, and minimal anti-leukemia activity was seen in patients with relapsed/refractory disease. Complete remission was achieved in 2 of 6 minimally pre-treated patients. We conclude that the combination of azacitidine and cytarabine is feasible but has limited activity in relapsed/refractory AML.
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Affiliation(s)
- GAUTAM BORTHAKUR
- Department of Leukemia, University of Texas M. D. Anderson Cancer Center, Houston, TX, USA
| | - XUELIN HUANG
- Division of Quantitative Science, University of Texas M. D. Anderson Cancer Center, Houston, TX, USA
| | - HAGOP KANTARJIAN
- Department of Leukemia, University of Texas M. D. Anderson Cancer Center, Houston, TX, USA
| | - STEFAN FADERL
- Department of Leukemia, University of Texas M. D. Anderson Cancer Center, Houston, TX, USA
| | - FARHAD RAVANDI
- Department of Leukemia, University of Texas M. D. Anderson Cancer Center, Houston, TX, USA
| | - ALESSANDRA FERRAJOLI
- Department of Leukemia, University of Texas M. D. Anderson Cancer Center, Houston, TX, USA
| | - RITVA TORMA
- Department of Leukemia, University of Texas M. D. Anderson Cancer Center, Houston, TX, USA
| | - GAIL MORRIS
- Department of Leukemia, University of Texas M. D. Anderson Cancer Center, Houston, TX, USA
| | - DONALD BERRY
- Division of Quantitative Science, University of Texas M. D. Anderson Cancer Center, Houston, TX, USA
| | - JEAN-PIERRE ISSA
- Department of Leukemia, University of Texas M. D. Anderson Cancer Center, Houston, TX, USA
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Grosso LE, Pitot HC. Alterations in the maturation and structure of ribosomal precursor RNA in Novikoff hepatoma cells induced by 5-fluorocytidine. Biochemistry 2002; 23:2651-6. [PMID: 6565495 DOI: 10.1021/bi00307a017] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The effects of 5-fluorocytidine on ribosomal RNA maturation and structure in Novikoff hepatoma cells were investigated. Like other nucleic acid base analogues that are incorporated into RNA, this compound inhibits maturation of the 45S ribosomal RNA precursor. The 45S RNA precursor produced in the presence of 5-fluorocytidine has an abnormal electrophoretic mobility compared with that of the control precursor under nondenaturing conditions, but the two have identical mobilities under denaturing conditions. Under the conditions of these experiments, 5-fluorocytidine inhibited cellular protein synthesis only slightly, whereas equimolar concentrations of 5-azacytidine resulted in nearly 75% inhibition of this process. Despite this difference in the effects of the two analogues as well as the greater chemical lability of the 5-azacytidine, their effects on ribosomal RNA maturation are identical.
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Demethylation enhances removal of pyrimidine dimers from the overall genome and from specific DNA sequences in Chinese hamster ovary cells. Mol Cell Biol 1989. [PMID: 2725518 DOI: 10.1128/mcb.9.4.1594] [Citation(s) in RCA: 25] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We have examined the effects of changes in cytosine methylation on DNA repair in UV-irradiated Chinese hamster ovary (CHO) cells. A hypomethylated derivative of the CHO K1B11 line, B11aza, was established by passaging B11 cells over several months in increasing concentrations of 5-azacytidine; greater than 60% demethylation was consistently demonstrated in these conditioned cells. Following a UV dose of 10 J/m2, the amount of repair replication performed within 24 h was approximately twofold higher in B11aza cells than in control B11 cells. Removal of T4 endonuclease V-sensitive sites (ESS) from specific restriction fragments within and around the dihydrofolate reductase (DHFR) gene was then examined in B11aza cells and compared with that in B11 cells. Although demethylation had little or no effect on repair in the 5' half of the DHFR gene, within a nontranscribed sequence immediately downstream from the gene, or within an extragenic region further downstream from the DHFR gene, significant increases in repair were observed at the 3' end of the DHFR gene and within an extragenic region upstream of the DHFR gene. However, the increases in DNA repair were not accompanied by any changes in overall cellular resistance to UV when colony-forming ability was assayed. We suggest that the level of DNA methylation may play an indirect role in the regulation of DNA repair, perhaps through an effect on chromatin structure or transcriptional activity.
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Ho L, Bohr VA, Hanawalt PC. Demethylation enhances removal of pyrimidine dimers from the overall genome and from specific DNA sequences in Chinese hamster ovary cells. Mol Cell Biol 1989; 9:1594-603. [PMID: 2725518 PMCID: PMC362576 DOI: 10.1128/mcb.9.4.1594-1603.1989] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
We have examined the effects of changes in cytosine methylation on DNA repair in UV-irradiated Chinese hamster ovary (CHO) cells. A hypomethylated derivative of the CHO K1B11 line, B11aza, was established by passaging B11 cells over several months in increasing concentrations of 5-azacytidine; greater than 60% demethylation was consistently demonstrated in these conditioned cells. Following a UV dose of 10 J/m2, the amount of repair replication performed within 24 h was approximately twofold higher in B11aza cells than in control B11 cells. Removal of T4 endonuclease V-sensitive sites (ESS) from specific restriction fragments within and around the dihydrofolate reductase (DHFR) gene was then examined in B11aza cells and compared with that in B11 cells. Although demethylation had little or no effect on repair in the 5' half of the DHFR gene, within a nontranscribed sequence immediately downstream from the gene, or within an extragenic region further downstream from the DHFR gene, significant increases in repair were observed at the 3' end of the DHFR gene and within an extragenic region upstream of the DHFR gene. However, the increases in DNA repair were not accompanied by any changes in overall cellular resistance to UV when colony-forming ability was assayed. We suggest that the level of DNA methylation may play an indirect role in the regulation of DNA repair, perhaps through an effect on chromatin structure or transcriptional activity.
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Affiliation(s)
- L Ho
- Department of Biological Sciences, Stanford University, California 94305-5020
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Acute effect of 5-fluorouracil on cytoplasmic and nuclear dihydrofolate reductase messenger RNA metabolism. J Biol Chem 1986. [DOI: 10.1016/s0021-9258(17)38400-4] [Citation(s) in RCA: 32] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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8
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Jones PA. Effects of 5-azacytidine and its 2'-deoxyderivative on cell differentiation and DNA methylation. Pharmacol Ther 1985; 28:17-27. [PMID: 2414786 DOI: 10.1016/0163-7258(85)90080-4] [Citation(s) in RCA: 88] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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9
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Abstract
The modified base 5-methylcytidine has been found in the DNA of a number of different eukaryotic cells where it occurs principally in the dinucleotide sequence -CmpG- which is present as a palindrome in double-strand nucleic acid molecules. There is considerable evidence to indicate and suggest that 5-methylcytosine serves as a regulatory signal in eukaryotic gene expression. Replication of DNA containing -CmpG- gives rise to daughter DNA molecules containing new -CpG- dinucleotide sequences in which the cytidine residues are not methylated. Methylation of these residues is carried out by a methylase enzyme using S-adenosyl-L-methionine as a specific methyl group donor. The model discussed in the present communication tries to explain in chemical and biological terms the mechanism of the methylation reaction. The first reactions of the scheme are well known through the work of other investigators. However, we introduce a new concept into our reaction mechanism by postulating the direct involvement of S-adenosyl-L-methionine in the reaction through its covalent attachment to the cytosine ring followed by a specific ring closure and methylation involving transfer of a hydride ion. The model also gives a possible explanation of mechanism of interaction of dimethyl sulphoxide with the enzyme systems of certain eukaryotic cells, which are altered or changed in the regulation of gene expression by this chemical reagent.
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Armstrong RD, Vera R, Snyder P, Cadman E. Enhancement of 6-thioguanine cytotoxic activity with methotrexate. Biochem Biophys Res Commun 1982; 109:595-601. [PMID: 7181934 DOI: 10.1016/0006-291x(82)91763-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
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12
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Johnson-Thompson M, Rosenthal LJ. Inhibition of SV40 replication by 5-azacytidine: effect on DNA synthesis and conformation. Virology 1979; 93:605-8. [PMID: 88126 DOI: 10.1016/0042-6822(79)90266-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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13
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McGuire W, Grotzinger K, Young R. Alterations in [3H]thymidine incorporation into DNA and [3H]uridine incorporation into RNA induced by 5-azacytidine in vivo. Biochem Pharmacol 1978; 27:745-50. [PMID: 77668 DOI: 10.1016/0006-2952(78)90514-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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14
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Veselý J, Čihák A. 5-Azacytidine: Mechanism of action and biological effects in mammalian cells. ACTA ACUST UNITED AC 1978. [DOI: 10.1016/0362-5478(78)90016-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Torelli U. An overlooked aspect of the mechanism of action of most antineoplastic drugs: the inhibition of macromolecular RNA metabolism. Eur J Cancer 1977; 13:1363-7. [PMID: 340234 DOI: 10.1016/0014-2964(77)90148-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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17
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Lu LW, Chiang GH, Medina D, Randerath K. Drug effects on nucleic acid modification. I. A specific effect of 5-azacytidine on mammalian transfer RNA methylation in vivo. Biochem Biophys Res Commun 1976; 68:1094-101. [PMID: 57778 DOI: 10.1016/0006-291x(76)90308-9] [Citation(s) in RCA: 47] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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18
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Fuska J, Proksa B. Cytotoxic and antitumor antibiotics produced by microorganisms. ADVANCES IN APPLIED MICROBIOLOGY 1976; 20:259-370. [PMID: 998366 DOI: 10.1016/s0065-2164(08)70114-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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