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The Contrasting Delayed Effects of Transient Exposure of Colorectal Cancer Cells to Decitabine or Azacitidine. Cancers (Basel) 2022; 14:cancers14061530. [PMID: 35326680 PMCID: PMC8945888 DOI: 10.3390/cancers14061530] [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: 12/01/2021] [Revised: 03/02/2022] [Accepted: 03/11/2022] [Indexed: 11/16/2022] Open
Abstract
Simple Summary Decitabine and azacitidine are cytosine analogs representing the class of drugs interfering with DNA methylation. Due to their molecular homology and similar clinical application these drugs are viewed as interchangeable. Despite their unique epigenetic mechanism of action, the studies of the prolonged activity of decitabine and azacitidine are rare. Our head-to-head comparison revealed profound differences in the activities of decitabine and azacitidine important in their anti-cancer potential and clinical application. We show that azacitidine, despite significant immediate toxicity, has negligible long-term effects. Contrary, decitabine, which does not exert initial toxicity, profoundly worsened the condition of the cancer cells over time. The effects of decitabine need a relatively long time to develop. This property is crucial for the proper design of studies or therapy involving decitabine. It undermines opinion about the similar therapeutic mechanism and interchangeability of decitabine and azacitidine. Abstract (1) Background: Decitabine and azacitidine are cytosine analogues representing the class of drugs interfering with DNA methylation. Due to their molecular homology and similar clinical application, both drugs are often regarded as interchangeable. Despite their unique mechanism of action the studies designed for observation and comparison of the prolonged activity of these drugs are rare. (2) Methods: The short-time (20–72 h) and long-term (up to 20 days) anti-cancer activity of decitabine and azacitidine has been studied in colorectal cancer cells. We observe the impact on cell culture’s viability, clonogenicity, proliferation, and expression of CDKN1A, CCND1, MDM2, MYC, CDKN2A, GLB1 genes, and activity of SA-β-galactosidase. (3) Results: Decitabine has much stronger anti-clonogenic activity than azacitidine. We show that azacitidine, despite significant immediate toxicity, has negligible long-term effects. Contrary, decitabine, which does not exert initial toxicity, profoundly worsened the condition of the cells over time. On the 13th day after treatment, the viability of cells was decreased and proliferation inhibited. These functional changes were accompanied by up-regulation of expression CDKN1A, CCND1, and CDKN2A genes and increased activation of SA-β-galactosidase, indicating cellular senescence. (4) Conclusions: Our head-to-head comparison revealed profound differences in the activities of decitabine and azacitidine important in their anti-cancer potential and clinical application. The effects of decitabine need relatively long time to develop. This property is crucial for proper design of studies and therapy concerning decitabine and undermines opinion about the similar therapeutic mechanism and interchangeability of these drugs.
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Xiao C, Fan T, Tian H, Zheng Y, Zhou Z, Li S, Li C, He J. H3K36 trimethylation-mediated biological functions in cancer. Clin Epigenetics 2021; 13:199. [PMID: 34715919 PMCID: PMC8555273 DOI: 10.1186/s13148-021-01187-2] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Accepted: 10/19/2021] [Indexed: 12/12/2022] Open
Abstract
Histone modification is an important form of epigenetic regulation. Thereinto, histone methylation is a critical determination of chromatin states, participating in multiple cellular processes. As a conserved histone methylation mark, histone 3 lysine 36 trimethylation (H3K36me3) can mediate multiple transcriptional-related events, such as the regulation of transcriptional activity, transcription elongation, pre-mRNA alternative splicing, and RNA m6A methylation. Additionally, H3K36me3 also contributes to DNA damage repair. Given the crucial function of H3K36me3 in genome regulation, the roles of H3K36me3 and its sole methyltransferase SETD2 in pathogenesis, especially malignancies, have been emphasized in many studies, and it is conceivable that disruption of histone methylation regulatory network composed of "writer", "eraser", "reader", and the mutation of H3K36me3 codes have the capacity of powerfully modulating cancer initiation and development. Here we review H3K36me3-mediated biological processes and summarize the latest findings regarding its role in cancers. We highlight the significance of epigenetic combination therapies in cancers.
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Affiliation(s)
- Chu Xiao
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Tao Fan
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - He Tian
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Yujia Zheng
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Zheng Zhou
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Shuofeng Li
- Department of Colorectal Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Chunxiang Li
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China.
| | - Jie He
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China.
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Carmel M, Michaelovsky E, Weinberger R, Frisch A, Mekori-Domachevsky E, Gothelf D, Weizman A. Differential methylation of imprinting genes and MHC locus in 22q11.2 deletion syndrome-related schizophrenia spectrum disorders. World J Biol Psychiatry 2021; 22:46-57. [PMID: 32212948 DOI: 10.1080/15622975.2020.1747113] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
OBJECTIVES 22q11.2 deletion syndrome (DS) is the strongest known genetic risk for schizophrenia. Methylome screening was conducted to elucidate possible involvement of epigenetic alterations in the emergence of schizophrenia spectrum disorders (SZ-SD) in 22q11.2DS. METHODS Sixteen adult men with/without SZ-SD were recruited from a 22q11.2DS cohort and underwent genome-wide DNA methylation profile analysis. Differentially methylated probes (DMPs) and regions (DMRs) were analysed using the ChAMP software. RESULTS The DMPs (p-value <10-6) and DMRs (p-valueArea <0.01) were enriched in two gene sets, 'imprinting genes' and 'chr6p21', a region overlapping the MHC locus. Most of the identified imprinting genes are involved in neurodevelopment and located in clusters under imprinting control region (ICR) regulation, including PEG10, SGCE (7q21.3), GNAS, GNAS-AS1 (20q13.32) and SNHG14, SNURF-SNRPN, SNORD115 (15q11.2). The differentially methylated genes from the MHC locus included immune HLA-genes and non-immune genes, RNF39, PPP1R18 and NOTCH4, implicated in neurodevelopment and synaptic plasticity. The most significant DMR is located in MHC locus and covered the transcription regulator ZFP57 that is required for control and maintenance of gene imprinting at multiple ICRs. CONCLUSIONS The differential methylation in imprinting genes and in chr6p21-22 indicate the neurodevelopmental nature of 22q11.2DS-related SZ and the major role of MHC locus in the risk to develop SZ.
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Affiliation(s)
- Miri Carmel
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.,Felsenstein Medical Research Center, Petach Tikva, Israel
| | - Elena Michaelovsky
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.,Felsenstein Medical Research Center, Petach Tikva, Israel
| | - Ronnie Weinberger
- The Behavioral Neurogenetics Center and Child Psychiatry Division, Sheba Medical Center, Ramat Gan, Israel
| | - Amos Frisch
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.,Felsenstein Medical Research Center, Petach Tikva, Israel
| | - Ehud Mekori-Domachevsky
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.,The Behavioral Neurogenetics Center and Child Psychiatry Division, Sheba Medical Center, Ramat Gan, Israel
| | - Doron Gothelf
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.,The Behavioral Neurogenetics Center and Child Psychiatry Division, Sheba Medical Center, Ramat Gan, Israel.,Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel
| | - Abraham Weizman
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.,Felsenstein Medical Research Center, Petach Tikva, Israel.,Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel.,Geha Mental Health Center, Petach Tikva, Israel
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Morales-Ruiz T, García-Ortiz MV, Devesa-Guerra I, Raya-Ruiz L, Tejedor JR, Bayón GF, Sierra MI, Fraga MF, Ariza RR, Roldán-Arjona T. DNA methylation reprogramming of human cancer cells by expression of a plant 5-methylcytosine DNA glycosylase. Epigenetics 2018; 13:95-107. [PMID: 29235922 PMCID: PMC5836972 DOI: 10.1080/15592294.2017.1414128] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2017] [Revised: 11/24/2017] [Accepted: 11/29/2017] [Indexed: 12/18/2022] Open
Abstract
Patterns of DNA methylation, an important epigenetic modification involved in gene silencing and development, are disrupted in cancer cells. Understanding the functional significance of aberrant methylation in tumors remains challenging, due in part to the lack of suitable tools to actively modify methylation patterns. DNA demethylation caused by mammalian DNA methyltransferase inhibitors is transient and replication-dependent, whereas that induced by TET enzymes involves oxidized 5mC derivatives that perform poorly understood regulatory functions. Unlike animals, plants possess enzymes that directly excise unoxidized 5mC from DNA, allowing restoration of unmethylated C through base excision repair. Here, we show that expression of Arabidopsis 5mC DNA glycosylase DEMETER (DME) in colon cancer cells demethylates and reactivates hypermethylated silenced loci. Interestingly, DME expression causes genome-wide changes that include both DNA methylation losses and gains, and partially restores the methylation pattern observed in normal tissue. Furthermore, such methylome reprogramming is accompanied by altered cell cycle responses and increased sensibility to anti-tumor drugs, decreased ability to form colonospheres, and tumor growth impairment in vivo. Our study shows that it is possible to reprogram a human cancer DNA methylome by expression of a plant DNA demethylase.
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Affiliation(s)
- Teresa Morales-Ruiz
- Maimónides Biomedical Research Institute of Córdoba (IMIBIC), Córdoba, Spain
- Department of Genetics, University of Córdoba, Córdoba, Spain
- Reina Sofia University Hospital, Córdoba, Spain
| | - María Victoria García-Ortiz
- Maimónides Biomedical Research Institute of Córdoba (IMIBIC), Córdoba, Spain
- Department of Genetics, University of Córdoba, Córdoba, Spain
- Reina Sofia University Hospital, Córdoba, Spain
| | - Iván Devesa-Guerra
- Maimónides Biomedical Research Institute of Córdoba (IMIBIC), Córdoba, Spain
- Department of Genetics, University of Córdoba, Córdoba, Spain
- Reina Sofia University Hospital, Córdoba, Spain
| | - Laura Raya-Ruiz
- Maimónides Biomedical Research Institute of Córdoba (IMIBIC), Córdoba, Spain
- Department of Genetics, University of Córdoba, Córdoba, Spain
- Reina Sofia University Hospital, Córdoba, Spain
| | - Juan R. Tejedor
- Cancer Epigenetics Laboratory, Institute of Oncology of Asturias (IUOPA), HUCA, Universidad de Oviedo, Oviedo, Spain
| | - Gustavo F. Bayón
- Cancer Epigenetics Laboratory, Institute of Oncology of Asturias (IUOPA), HUCA, Universidad de Oviedo, Oviedo, Spain
| | - Marta I. Sierra
- Cancer Epigenetics Laboratory, Institute of Oncology of Asturias (IUOPA), HUCA, Universidad de Oviedo, Oviedo, Spain
| | - Mario F. Fraga
- Cancer Epigenetics Laboratory, Institute of Oncology of Asturias (IUOPA), HUCA, Universidad de Oviedo, Oviedo, Spain
- Nanomaterials and Nanotechnology Research Center (CINN-CSIC)-Universidad de Oviedo-Principado de Asturias, Spain
| | - Rafael R. Ariza
- Maimónides Biomedical Research Institute of Córdoba (IMIBIC), Córdoba, Spain
- Department of Genetics, University of Córdoba, Córdoba, Spain
- Reina Sofia University Hospital, Córdoba, Spain
| | - Teresa Roldán-Arjona
- Maimónides Biomedical Research Institute of Córdoba (IMIBIC), Córdoba, Spain
- Department of Genetics, University of Córdoba, Córdoba, Spain
- Reina Sofia University Hospital, Córdoba, Spain
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Abstract
CpG islands (CGI) are critical genomic regulatory elements that support transcriptional initiation and are associated with the promoters of most human genes. CGI are distinguished from the bulk genome by their high CpG density, lack of DNA methylation, and euchromatic features. While CGI are canonically known as strong promoters, thousands of 'orphan' CGI lie far from any known transcript, leaving their function an open question. We undertook a comprehensive analysis of the epigenetic state of orphan CGI across over 100 cell types. Here we show that most orphan CGI display the chromatin features of active enhancers (H3K4me1, H3K27Ac) in at least one cell type. Relative to classical enhancers, these enhancer CGI (ECGI) are stronger, as gauged by chromatin state and in functional assays, are more broadly expressed, and are more highly conserved. Likewise, ECGI engage in more genomic contacts and are enriched for transcription factor binding relative to classical enhancers. In human cancers, these epigenetic differences between ECGI vs. classical enhancers manifest in distinct alterations in DNA methylation. Thus, ECGI define a class of highly active enhancers, strengthened by the broad transcriptional activity, CpG density, hypomethylation, and chromatin features they share with promoter CGI. In addition to indicating a role for thousands of orphan CGI, these findings suggests that enhancer activity may be an intrinsic function of CGI in general and provides new insights into the evolution of enhancers and their epigenetic regulation during development and tumorigenesis.
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Affiliation(s)
- Joshua S K Bell
- a Department of Radiation Oncology , Emory University School of Medicine , Atlanta , GA , USA.,b Winship Cancer Institute of Emory University , Atlanta , GA , USA.,c Graduate Program in Genetics & Molecular Biology , Emory University , Atlanta , GA, USA
| | - Paula M Vertino
- a Department of Radiation Oncology , Emory University School of Medicine , Atlanta , GA , USA.,b Winship Cancer Institute of Emory University , Atlanta , GA , USA
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Ariazi EA, Taylor JC, Black MA, Nicolas E, Slifker MJ, Azzam DJ, Boyd J. A New Role for ERα: Silencing via DNA Methylation of Basal, Stem Cell, and EMT Genes. Mol Cancer Res 2016; 15:152-164. [PMID: 28108626 DOI: 10.1158/1541-7786.mcr-16-0283] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2016] [Revised: 10/10/2016] [Accepted: 10/18/2016] [Indexed: 12/30/2022]
Abstract
Resistance to hormonal therapies is a major clinical problem in the treatment of estrogen receptor α-positive (ERα+) breast cancers. Epigenetic marks, namely DNA methylation of cytosine at specific CpG sites (5mCpG), are frequently associated with ERα+ status in human breast cancers. Therefore, ERα may regulate gene expression in part via DNA methylation. This hypothesis was evaluated using a panel of breast cancer cell line models of antiestrogen resistance. Microarray gene expression profiling was used to identify genes normally silenced in ERα+ cells but derepressed upon exposure to the demethylating agent decitabine, derepressed upon long-term loss of ERα expression, and resuppressed by gain of ERα activity/expression. ERα-dependent DNA methylation targets (n = 39) were enriched for ERα-binding sites, basal-up/luminal-down markers, cancer stem cell, epithelial-mesenchymal transition, and inflammatory and tumor suppressor genes. Kaplan-Meier survival curve and Cox proportional hazards regression analyses indicated that these targets predicted poor distant metastasis-free survival among a large cohort of breast cancer patients. The basal breast cancer subtype markers LCN2 and IFI27 showed the greatest inverse relationship with ERα expression/activity and contain ERα-binding sites. Thus, genes that are methylated in an ERα-dependent manner may serve as predictive biomarkers in breast cancer. IMPLICATIONS ERα directs DNA methylation-mediated silencing of specific genes that have biomarker potential in breast cancer subtypes. Mol Cancer Res; 15(2); 152-64. ©2016 AACR.
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Affiliation(s)
- Eric A Ariazi
- Fox Chase Cancer Center, Temple University Health System, Philadelphia, Pennsylvania.
| | - John C Taylor
- Fox Chase Cancer Center, Temple University Health System, Philadelphia, Pennsylvania
| | - Michael A Black
- Department of Biochemistry, University of Otago, Dunedin, New Zealand
| | - Emmanuelle Nicolas
- Fox Chase Cancer Center, Temple University Health System, Philadelphia, Pennsylvania
| | - Michael J Slifker
- Fox Chase Cancer Center, Temple University Health System, Philadelphia, Pennsylvania
| | - Diana J Azzam
- Department of Human and Molecular Genetics, Herbert Wertheim College of Medicine, Florida International University, Miami, Florida
| | - Jeff Boyd
- Fox Chase Cancer Center, Temple University Health System, Philadelphia, Pennsylvania.
- Department of Human and Molecular Genetics, Herbert Wertheim College of Medicine, Florida International University, Miami, Florida
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