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Kumar R, Paul AM, Rameshwar P, Pillai MR. Epigenetic Dysregulation at the Crossroad of Women's Cancer. Cancers (Basel) 2019; 11:cancers11081193. [PMID: 31426393 PMCID: PMC6721458 DOI: 10.3390/cancers11081193] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2019] [Revised: 08/07/2019] [Accepted: 08/08/2019] [Indexed: 02/07/2023] Open
Abstract
An increasingly number of women of all age groups are affected by cancer, despite substantial progress in our understanding of cancer pathobiology, the underlying genomic alterations and signaling cascades, and cellular-environmental interactions. Though our understanding of women’s cancer is far more complete than ever before, there is no comprehensive model to explain the reasons behind the increased incidents of certain reproductive cancer among older as well as younger women. It is generally suspected that environmental and life-style factors affecting hormonal and growth control pathways might help account for the rise of women’s cancers in younger age, as well, via epigenetic mechanisms. Epigenetic regulators play an important role in orchestrating an orderly coordination of cellular signals in gene activity in response to upstream signaling and/or epigenetic modifiers present in a dynamic extracellular milieu. Here we will discuss the broad principles of epigenetic regulation of DNA methylation and demethylation, histone acetylation and deacetylation, and RNA methylation in women’s cancers in the context of gene expression, hormonal action, and the EGFR family of cell surface receptor tyrosine kinases. We anticipate that a better understanding of the epigenetics of women’s cancers may provide new regulatory leads and further fuel the development of new epigenetic biomarkers and therapeutic approaches.
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Affiliation(s)
- Rakesh Kumar
- Cancer Biology Program, Rajiv Gandhi Centre for Biotechnology, Trivandrum, Kerala 695014, India.
- Department of Medicine, Division of Hematology-Oncology, Rutgers New Jersey Medical School, Newark, NJ 07103, USA.
- Department of Human and Molecular Genetics, Virginia Commonwealth University School of Medicine, Richmond, VA 23298, USA.
| | - Aswathy Mary Paul
- Cancer Biology Program, Rajiv Gandhi Centre for Biotechnology, Trivandrum, Kerala 695014, India
- Graduate Degree Program, Manipal Academy of Higher Education, Manipal, Karnataka 576104, India
| | - Pranela Rameshwar
- Department of Medicine, Division of Hematology-Oncology, Rutgers New Jersey Medical School, Newark, NJ 07103, USA
| | - M Radhakrishna Pillai
- Cancer Biology Program, Rajiv Gandhi Centre for Biotechnology, Trivandrum, Kerala 695014, India
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CRISPR/Cas9 therapeutics: a cure for cancer and other genetic diseases. Oncotarget 2018; 7:52541-52552. [PMID: 27250031 PMCID: PMC5239572 DOI: 10.18632/oncotarget.9646] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2016] [Accepted: 05/19/2016] [Indexed: 12/21/2022] Open
Abstract
Cancer is caused by a series of alterations in genome and epigenome mostly resulting in activation of oncogenes or inactivation of cancer suppressor genes. Genetic engineering has become pivotal in the treatment of cancer and other genetic diseases, especially the formerly-niche use of clustered regularly interspaced short palindromic repeats (CRISPR) associated with Cas9. In defining its superior use, we have followed the recent advances that have been made in producing CRISPR/Cas9 as a therapy of choice. We also provide important genetic mutations where CRISPRs can be repurposed to create adaptive immunity to fight carcinomas and edit genetic mutations causing it. Meanwhile, challenges to CRISPR technology are also discussed with emphasis on ability of pathogens to evolve against CRISPRs. We follow the recent developments on the function of CRISPRs with different carriers which can efficiently deliver it to target cells; furthermore, analogous technologies are also discussed along CRISPRs, including zinc-finger nuclease (ZFN) and transcription activator-like effector nucleases (TALENs). Moreover, progress in clinical applications of CRISPR therapeutics is reviewed; in effect, patients can have lower morbidity and/or mortality from the therapeutic method with least possible side-effects.
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Rewriting DNA Methylation Signatures at Will: The Curable Genome Within Reach? ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 945:475-490. [DOI: 10.1007/978-3-319-43624-1_17] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/09/2023]
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Falahi F, Sgro A, Blancafort P. Epigenome engineering in cancer: fairytale or a realistic path to the clinic? Front Oncol 2015; 5:22. [PMID: 25705610 PMCID: PMC4319383 DOI: 10.3389/fonc.2015.00022] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2014] [Accepted: 01/19/2015] [Indexed: 01/15/2023] Open
Abstract
Epigenetic modifications such as histone post-transcriptional modifications, DNA methylation, and non-protein-coding RNAs organize the DNA in the nucleus of eukaryotic cells and are critical for the spatio-temporal regulation of gene expression. These epigenetic modifications are reversible and precisely regulated by epigenetic enzymes. In addition to genetic mutations, epigenetic modifications are highly disrupted in cancer relative to normal tissues. Many epigenetic alterations (epi-mutations) are associated with aberrations in the expression and/or activity of epigenetic enzymes. Thus, epigenetic regulators have emerged as prime targets for cancer therapy. Currently, several inhibitors of epigenetic enzymes (epi-drugs) have been approved for use in the clinic to treat cancer patients with hematological malignancies. However, one potential disadvantage of epi-drugs is their lack of locus-selective specificity, which may result in the over-expression of undesirable parts of the genome. The emerging and rapidly growing field of epigenome engineering has opened new grounds for improving epigenetic therapy in view of reducing the genome-wide “off-target” effects of the treatment. In the current review, we will first describe the language of epigenetic modifications and their involvement in cancer. Next, we will overview the current strategies for engineering of artificial DNA-binding domains in order to manipulate and ultimately normalize the aberrant landscape of the cancer epigenome (epigenome engineering). Lastly, the potential clinical applications of these emerging genome-engineering approaches will be discussed.
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Affiliation(s)
- Fahimeh Falahi
- Cancer Epigenetics Group, Harry Perkins Institute of Medical Research, School of Anatomy, Physiology and Human Biology, The University of Western Australia , Perth, WA , Australia
| | - Agustin Sgro
- Cancer Epigenetics Group, Harry Perkins Institute of Medical Research, School of Anatomy, Physiology and Human Biology, The University of Western Australia , Perth, WA , Australia
| | - Pilar Blancafort
- Cancer Epigenetics Group, Harry Perkins Institute of Medical Research, School of Anatomy, Physiology and Human Biology, The University of Western Australia , Perth, WA , Australia
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van der Wijst MGP, Venkiteswaran M, Chen H, Xu GL, Plösch T, Rots MG. Local chromatin microenvironment determines DNMT activity: from DNA methyltransferase to DNA demethylase or DNA dehydroxymethylase. Epigenetics 2015; 10:671-6. [PMID: 26098813 PMCID: PMC4622917 DOI: 10.1080/15592294.2015.1062204] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2015] [Revised: 06/03/2015] [Accepted: 06/09/2015] [Indexed: 12/22/2022] Open
Abstract
Insights on active DNA demethylation disproved the original assumption that DNA methylation is a stable epigenetic modification. Interestingly, mammalian DNA methyltransferases 3A and 3B (DNMT-3A and -3B) have also been reported to induce active DNA demethylation, in addition to their well-known function in catalyzing methylation. In situations of extremely low levels of S-adenosyl methionine (SAM), DNMT-3A and -3B might demethylate C-5 methyl cytosine (5mC) via deamination to thymine, which is subsequently replaced by an unmodified cytosine through the base excision repair (BER) pathway. Alternatively, 5mC when converted to 5- hydroxymethylcytosine (5hmC) by TET enzymes, might be further modified to an unmodified cytosine by DNMT-3A and -3B under oxidized redox conditions, although exact pathways are yet to be elucidated. Interestingly, even direct conversion of 5mC to cytosine might be catalyzed by DNMTs. Here, we summarize the evidence on the DNA dehydroxymethylase and demethylase activity of DNMT-3A and -3B. Although physiological relevance needs to be demonstrated, the current indications on the 5mC- and 5hmC-modifying activities of de novo DNA C-5 methyltransferases shed a new light on these enzymes. Despite the extreme circumstances required for such unexpected reactions to occur, we here put forward that the chromatin microenvironment can be locally exposed to extreme conditions, and hypothesize that such waves of extremes allow enzymes to act in differential ways.
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Key Words
- 5caC, 5-carboxylcytosine
- 5fC, 5-formylcytosine
- 5hmC, 5 hydroxymethylcytosine
- 5mC, 5-methylcytosine
- AID, activation-induced cytidine deaminase
- APOBEC, apolipoprotein B mRNA editing enzyme catalytic polypeptide-like
- BER, base excision and repair
- C, cytosine
- CGI, CpG islands
- DNA dehydroxymethylation
- DNA demethylation
- DNMT, DNA methyltransferase
- DNMTs
- GADD45, growth arrest and DNA-damage-inducible protein 45
- RARE, retinoic acid response element
- S-adenosyl methionine (SAM)
- SAM, S-adenosyl methionine
- TDG, thymine DNA glycosylase
- TET, ten-eleven translocation.
- chromatin microenvironment
- oxidizing redox state
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Affiliation(s)
- Monique G P van der Wijst
- Epigenetic Editing; Department of Pathology and Medical Biology; University Medical Center Groningen; University of Groningen; Groningen, The Netherlands
| | - Muralidhar Venkiteswaran
- Epigenetic Editing; Department of Pathology and Medical Biology; University Medical Center Groningen; University of Groningen; Groningen, The Netherlands
| | - Hui Chen
- Epigenetic Editing; Department of Pathology and Medical Biology; University Medical Center Groningen; University of Groningen; Groningen, The Netherlands
- Group of DNA Metabolism; The State Key Laboratory of Molecular Biology; Institute of Biochemistry and Cell Biology; Shanghai Institutes for Biological Sciences; Chinese Academy of Sciences; Shanghai, China
| | - Guo-Liang Xu
- Group of DNA Metabolism; The State Key Laboratory of Molecular Biology; Institute of Biochemistry and Cell Biology; Shanghai Institutes for Biological Sciences; Chinese Academy of Sciences; Shanghai, China
| | - Torsten Plösch
- Department of Obstetrics and Gynecology; University Medical Center Groningen; University of Groningen; Groningen, The Netherlands
| | - Marianne G Rots
- Epigenetic Editing; Department of Pathology and Medical Biology; University Medical Center Groningen; University of Groningen; Groningen, The Netherlands
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Chen H, Kazemier HG, de Groote ML, Ruiters MHJ, Xu GL, Rots MG. Induced DNA demethylation by targeting Ten-Eleven Translocation 2 to the human ICAM-1 promoter. Nucleic Acids Res 2013; 42:1563-74. [PMID: 24194590 PMCID: PMC3919596 DOI: 10.1093/nar/gkt1019] [Citation(s) in RCA: 110] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Increasing evidence indicates that active DNA demethylation is involved in several processes in mammals, resulting in developmental stage-specificity and cell lineage-specificity. The recently discovered Ten-Eleven Translocation (TET) dioxygenases are accepted to be involved in DNA demethylation by initiating 5-mC oxidation. Aberrant DNA methylation profiles are associated with many diseases. For example in cancer, hypermethylation results in silencing of tumor suppressor genes. Such silenced genes can be re-expressed by epigenetic drugs, but this approach has genome-wide effects. In this study, fusions of designer DNA binding domains to TET dioxygenase family members (TET1, -2 or -3) were engineered to target epigenetically silenced genes (ICAM-1, EpCAM). The effects on targeted CpGs’ methylation and on expression levels of the target genes were assessed. The results indicated demethylation of targeted CpG sites in both promoters for targeted TET2 and to a lesser extent for TET1, but not for TET3. Interestingly, we observed re-activation of transcription of ICAM-1. Thus, our work suggests that we provided a mechanism to induce targeted DNA demethylation, which facilitates re-activation of expression of the target genes. Furthermore, this Epigenetic Editing approach is a powerful tool to investigate functions of epigenetic writers and erasers and to elucidate consequences of epigenetic marks.
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Affiliation(s)
- Hui Chen
- Epigenetic Editing, Department of Pathology and Medical Biology, University Medical Center Groningen, University of Groningen, Hanzeplein1, 9713 GZ Groningen, The Netherlands, The State Key Laboratory of Molecular Biology, Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200031, China and Synvolux Therapeutics Inc., LJ. Zielstraweg 1, 9713 GX Groningen, The Netherlands
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