1
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Duan C, Yan Z, Wu C, Zhou X, Bao W. DNA methylation characteristics associated with chemotherapy resistance in epithelial ovarian cancer. Heliyon 2024; 10:e27212. [PMID: 38468944 PMCID: PMC10926131 DOI: 10.1016/j.heliyon.2024.e27212] [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: 02/22/2024] [Accepted: 02/26/2024] [Indexed: 03/13/2024] Open
Abstract
Objective The high mortality rate of epithelial ovarian cancer (EOC) is often attributed to the frequent development of chemoresistance. DNA methylation is a predictive biomarker for chemoresistance. Methods This study utilized DNA methylation profiles and relevant information from GEO and TCGA to identify different methylated CpG sites (DMCs) between chemoresistant and chemosensitive patients. Subsequently, we constructed chemoresistance risk models with DMCs. The genes corresponding to candidate DMCs in chemoresistance risk models were further analyzed to identify different methylated gene symbols (DMGs) associated with chemoresistance. The DMGs that showed a strong correlation with the corresponding DMCs were analyzed through immunohistochemistry. Results Compared to chemosensitive EOC patients, chemoresistant patients showed 423 hypermethylated CpGs and 1445 hypomethylated CpGs. The chemoresistance risk models based on DMCs have shown the improved predictive ability for chemoresistance in EOC (AUC = 65.0-76.2%). The methylations of cg25510164, cg13154880, cg15362155 and cg08665359 were strongly associated with decreased risk of chemoresistance. Conversely, the methylation of cg08872590 and cg14739437 significantly increased the risk. We identified 13 DMGs, from 47 DMCs corresponding genes, between chemosensitive and chemoresistant samples. Among the DMGs, the expression levels of DDR2 and OPCML exhibited strong correlations with the corresponding DMCs. DDR2 and OPCML both showed enhanced expression in chemoresistant ovarian microarray tissue. Conclusions Hypomethylated CpGs may play a significant role in DNA methylation associated with chemoresistance in EOC. The epigenetic modification of DDR2 could have important implications for the development of chemoresistance. Our study provides valuable insights for future research on DNA methylation in the chemoresistance of EOC.
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Affiliation(s)
| | | | - Cailiang Wu
- Department of Obstetrics and Gynecology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, 200080, Shanghai, China
| | - Xuexin Zhou
- Department of Obstetrics and Gynecology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, 200080, Shanghai, China
| | - Wei Bao
- Department of Obstetrics and Gynecology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, 200080, Shanghai, China
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2
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Seem K, Kaur S, Kumar S, Mohapatra T. Epigenome editing for targeted DNA (de)methylation: a new perspective in modulating gene expression. Crit Rev Biochem Mol Biol 2024; 59:69-98. [PMID: 38440883 DOI: 10.1080/10409238.2024.2320659] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Accepted: 02/15/2024] [Indexed: 03/06/2024]
Abstract
Traditionally, it has been believed that inheritance is driven as phenotypic variations resulting from changes in DNA sequence. However, this paradigm has been challenged and redefined in the contemporary era of epigenetics. The changes in DNA methylation, histone modification, non-coding RNA biogenesis, and chromatin remodeling play crucial roles in genomic functions and regulation of gene expression. More importantly, some of these changes are inherited to the next generations as a part of epigenetic memory and play significant roles in gene expression. The sum total of all changes in DNA bases, histone proteins, and ncRNA biogenesis constitutes the epigenome. Continuous progress in deciphering epigenetic regulations and the existence of heritable epigenetic/epiallelic variations associated with trait of interest enables to deploy epigenome editing tools to modulate gene expression. DNA methylation marks can be utilized in epigenome editing for the manipulation of gene expression. Initially, genome/epigenome editing technologies relied on zinc-finger protein or transcriptional activator-like effector protein. However, the discovery of clustered regulatory interspaced short palindromic repeats CRISPR)/deadCRISPR-associated protein 9 (dCas9) enabled epigenome editing to be more specific/efficient for targeted DNA (de)methylation. One of the major concerns has been the off-target effects, wherein epigenome editing may unintentionally modify gene/regulatory element which may cause unintended change/harmful effects. Moreover, epigenome editing of germline cell raises several ethical/safety issues. This review focuses on the recent developments in epigenome editing tools/techniques, technological limitations, and future perspectives of this emerging technology in therapeutics for human diseases as well as plant improvement to achieve sustainable developmental goals.
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Affiliation(s)
- Karishma Seem
- Division of Biochemistry, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Simardeep Kaur
- Division of Biochemistry, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Suresh Kumar
- Division of Biochemistry, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Trilochan Mohapatra
- Protection of Plant Varieties and Farmers' Rights Authority, New Delhi, India
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3
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Yagci ZB, Kelkar GR, Johnson TJ, Sen D, Keung AJ. Designing Epigenome Editors: Considerations of Biochemical and Locus Specificities. Methods Mol Biol 2024; 2842:23-55. [PMID: 39012589 DOI: 10.1007/978-1-0716-4051-7_2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/17/2024]
Abstract
The advent of locus-specific protein recruitment technologies has enabled a new class of studies in chromatin biology. Epigenome editors (EEs) enable biochemical modifications of chromatin at almost any specific endogenous locus. Their locus-specificity unlocks unique information including the functional roles of distinct modifications at specific genomic loci. Given the growing interest in using these tools for biological and translational studies, there are many specific design considerations depending on the scientific question or clinical need. Here, we present and discuss important design considerations and challenges regarding the biochemical and locus specificities of epigenome editors. These include how to: account for the complex biochemical diversity of chromatin; control for potential interdependency of epigenome editors and their resultant modifications; avoid sequestration effects; quantify the locus specificity of epigenome editors; and improve locus-specificity by considering concentration, affinity, avidity, and sequestration effects.
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Affiliation(s)
- Z Begum Yagci
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC, USA
| | - Gautami R Kelkar
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC, USA
| | - Tyler J Johnson
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC, USA
| | - Dilara Sen
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC, USA
| | - Albert J Keung
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC, USA.
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4
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Wang YJ, Tang L, Lu XH, Liu JT, Wang YY, Geng HX, Li XT, An Q. Efficacy of epi-1 modified epirubicin and curcumin encapsulated liposomes targeting-EpCAM in the inhibition of epithelial ovarian cancer cells. J Liposome Res 2022:1-17. [PMID: 36440599 DOI: 10.1080/08982104.2022.2153138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Treatment of epithelial ovarian cancer (EOC) is a challenge because it still leads to unsatisfactory clinical prognosis. This is due to the toxicity and poor targeting of chemotherapeutic agents, as well as metastasis of the tumor. In this study, we designed a targeted liposome with nanostructures to overcome these problems. In the liposomes, epirubicin and curcumin were encapsulated to achieve their synergistic antitumor efficacy, while Epi-1 was modified on the liposomal surface to target epithelial cell adhesion molecule (EpCAM). Epi-1, a macrocyclic peptide, exhibits active targeting for enhanced cellular uptake and potent cytotoxicity against tumor cells. The encapsulation of epirubicin and curcumin synergistically inhibited the formation of neovascularization and vasculogenic mimicry (VM) channels, thereby suppressing tumor metastasis on SKOV3 cells. The dual drug loaded Epi-1-liposomes also induced apoptosis and downregulated metastasis-related proteins for effective antitumor in vitro. In vivo studies showed that dual drug loaded Epi-1-liposomes prolonged circulation time in the blood and increased the selective accumulation of drug at the tumor site. H&E staining and immunohistochemistry with Ki-67 also showed that targeted liposomes elevated antitumor activity. Also, targeted liposomes downregulated angiogenesis-related proteins to inhibit angiogenesis and thus tumor metastasis. In conclusion, the production of dual drug loaded Epi-1-liposomes is an effective strategy for the treatment of EOC.
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Affiliation(s)
- Yu-Jia Wang
- School of Pharmacy, Liaoning University of Traditional Chinese Medicine, Dalian, China
| | - Ling Tang
- Department of Obstetrics and Gynecology, Affiliated Zhongshan Hospital of Dalian University, Dalian, China
| | - Xu-Hong Lu
- Department of Obstetrics and Gynecology, Affiliated Zhongshan Hospital of Dalian University, Dalian, China
| | - Ji-Tao Liu
- Technology Research and Development Centre, Yunnan Baiyao Group Health Products Co., Ltd, Kunming, China
| | - Yuan-Yuan Wang
- Department of Obstetrics and Gynecology, Affiliated Zhongshan Hospital of Dalian University, Dalian, China
| | - Hong-Xia Geng
- School of Pharmacy, Liaoning University of Traditional Chinese Medicine, Dalian, China
| | - Xue-Tao Li
- School of Pharmacy, Liaoning University of Traditional Chinese Medicine, Dalian, China
| | - Quan An
- Technology Research and Development Centre, Yunnan Baiyao Group Health Products Co., Ltd, Kunming, China
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5
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Chen B, Ying X, Bao L. MGMT gene promoter methylation in humoral tissue as biomarker for lung cancer diagnosis: An update meta-analysis. Thorac Cancer 2021; 12:3194-3200. [PMID: 34651448 PMCID: PMC8636218 DOI: 10.1111/1759-7714.14186] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Revised: 09/22/2021] [Accepted: 09/23/2021] [Indexed: 01/12/2023] Open
Abstract
Objective To investigate O‐6‐methylguanine‐DNA methyltransferase (MGMT) gene promoter methylation in humoral tissue as biomarker for lung cancer diagnosis by pooling relevant open published data. Methods Clinical studies relevant to MGMT gene promoter methylation and lung cancer were systematic electronic searched in the databases of Medline, EMBASE, Ovid, Web of Science, and CNKI. Data of true positive (tp), false positive (fp), false negative (fn), and true negative (tn) were extracted from the included studies and made combination. The diagnostic sensitivity, specificity, diagnostic odds ratio (DOR) and summary receiver operating characteristic (SROC) of MGMT gene methylation for lung cancer diagnosis were pooled. Results Twelve studies were included in the meta‐analysis. The diagnostic sensitivity, specificity, DOR were 0.39 (95% CI = 0.31–0.49) 0.92 (95% CI = 0.77–0.97), and 4.20 (95% CI = 2.09–8.44), respectively under random effect model. The SROC of MGMT gene methylation for lung cancer diagnosis was 0.58 (95% CI = 0.53–0.62). Conclusion MGMT methylation rate was higher in plasma and bronchoalveolar lavage fluid (BLAF) of lung cancer cases compared to controls. High diagnostic specificity indicated that MGMT methylation in plasma and BLAF can be applied as lung cancer confirmation test.
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Affiliation(s)
- Bizheng Chen
- Department of Radiotherapy, Lishui Central Hospital, Lishui, Zhejiang Province, China
| | - Xiaozhen Ying
- Department of Radiotherapy, Lishui Central Hospital, Lishui, Zhejiang Province, China
| | - Liming Bao
- Department of Radiotherapy, Lishui Central Hospital, Lishui, Zhejiang Province, China
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6
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Lowering DNA binding affinity of SssI DNA methyltransferase does not enhance the specificity of targeted DNA methylation in E. coli. Sci Rep 2021; 11:15226. [PMID: 34315949 PMCID: PMC8316445 DOI: 10.1038/s41598-021-94528-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Accepted: 07/12/2021] [Indexed: 11/09/2022] Open
Abstract
Targeted DNA methylation is a technique that aims to methylate cytosines in selected genomic loci. In the most widely used approach a CG-specific DNA methyltransferase (MTase) is fused to a sequence specific DNA binding protein, which binds in the vicinity of the targeted CG site(s). Although the technique has high potential for studying the role of DNA methylation in higher eukaryotes, its usefulness is hampered by insufficient methylation specificity. One of the approaches proposed to suppress methylation at unwanted sites is to use MTase variants with reduced DNA binding affinity. In this work we investigated how methylation specificity of chimeric MTases containing variants of the CG-specific prokaryotic MTase M.SssI fused to zinc finger or dCas9 targeting domains is influenced by mutations affecting catalytic activity and/or DNA binding affinity of the MTase domain. Specificity of targeted DNA methylation was assayed in E. coli harboring a plasmid with the target site. Digestions of the isolated plasmids with methylation sensitive restriction enzymes revealed that specificity of targeted DNA methylation was dependent on the activity but not on the DNA binding affinity of the MTase. These results have implications for the design of strategies of targeted DNA methylation.
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7
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Sin RWY, Foo DCC, Iyer DN, Fan MSY, Li X, Lo OSH, Law WL, Ng L. A Pilot Study Investigating the Expression Levels of Pluripotency-Associated Genes in Rectal Swab Samples for Colorectal Polyp and Cancer Diagnosis and Prognosis. Stem Cells Int 2021; 2021:4139528. [PMID: 34335790 PMCID: PMC8324395 DOI: 10.1155/2021/4139528] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Revised: 12/11/2020] [Accepted: 06/09/2021] [Indexed: 02/06/2023] Open
Abstract
Change in gene expression is inevitable in cancer development. With more studies demonstrating the contributions of cancer stem cells (CSCs) in colorectal cancer (CRC) development, this study is aimed at investigating whether rectal swab specimen serves as a tool for detection of dysregulation of CSC or stem cell (SC) markers and at evaluating its potential as a new promising screening method for high-risk patients. Expression levels of 15 pluripotency-associated genes were assessed by quantitative PCR in 53 rectal swab specimens referred for endoscopic screening. Dysregulated genes and joint panels based on such genes were examined for their diagnostic potentials for both polyp and CRC. Out of 15 genes, Oct4, CD26, c-MYC, and CXCR4 showed significantly differential expression among normal, polyp, and CRC patients. A panel of Oct4 and CD26 showed an AUC value of 0.80 (p = 0.003) in identifying CRC patients from polyp/normal subjects, with sensitivity and specificity of 84.6% and 69.2%. A panel of c-MYC and CXCR4 achieved CRC/polyp identification with an AUC value of 0.79 (p = 0.002), with a sensitivity of 82.8% and specificity of 80.0%. The sensitivity for polyp and CRC was 80.0% and 85.7%, respectively. Further analysis showed that higher c-MYC and CXCR4 level was detected in normal subjects who developed polyps after 5-6 years, in comparison with subjects with no lesion developed, and the AUC of the c-MYC and CXCR4 panel increased to 0.88 (p < 0.001), with sensitivity and specificity of 84.4% and 92.3%, respectively, when these patients were included in the polyp group. This study suggests that the Oct4 and CD26 panel is a promising biomarker for distinguishing CRC from normal and polyp patients, whereas the c-MYC and CXCR4 panel may identify polyp and CRC from normal individuals.
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Affiliation(s)
- Ryan Wai-Yan Sin
- Department of Surgery, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Dominic Chi-Chung Foo
- Department of Surgery, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Deepak Narayanan Iyer
- Department of Surgery, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - May Sau-Yee Fan
- Department of Surgery, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Xue Li
- Department of Surgery, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Oswens Siu-Hung Lo
- Department of Surgery, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Wai-Lun Law
- Department of Surgery, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Lui Ng
- Department of Surgery, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
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8
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Broche J, Kungulovski G, Bashtrykov P, Rathert P, Jeltsch A. Genome-wide investigation of the dynamic changes of epigenome modifications after global DNA methylation editing. Nucleic Acids Res 2021; 49:158-176. [PMID: 33300025 PMCID: PMC7797067 DOI: 10.1093/nar/gkaa1169] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Revised: 11/05/2020] [Accepted: 11/17/2020] [Indexed: 12/21/2022] Open
Abstract
Chromatin properties are regulated by complex networks of epigenome modifications. Currently, it is unclear how these modifications interact and if they control downstream effects such as gene expression. We employed promiscuous chromatin binding of a zinc finger fused catalytic domain of DNMT3A to introduce DNA methylation in HEK293 cells at many CpG islands (CGIs) and systematically investigated the dynamics of the introduced DNA methylation and the consequent changes of the epigenome network. We observed efficient methylation at thousands of CGIs, but it was unstable at about 90% of them, highlighting the power of genome-wide molecular processes that protect CGIs against DNA methylation. Partially stable methylation was observed at about 1000 CGIs, which showed enrichment in H3K27me3. Globally, the introduced DNA methylation strongly correlated with a decrease in gene expression indicating a direct effect. Similarly, global but transient reductions in H3K4me3 and H3K27ac were observed after DNA methylation but no changes were found for H3K9me3 and H3K36me3. Our data provide a global and time-resolved view on the network of epigenome modifications, their connections with DNA methylation and the responses triggered by artificial DNA methylation revealing a direct repressive effect of DNA methylation in CGIs on H3K4me3, histone acetylation, and gene expression.
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Affiliation(s)
- Julian Broche
- Department of Biochemistry, Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, 70569 Stuttgart, Germany
| | - Goran Kungulovski
- Department of Biochemistry, Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, 70569 Stuttgart, Germany
| | - Pavel Bashtrykov
- Department of Biochemistry, Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, 70569 Stuttgart, Germany
| | - Philipp Rathert
- Department of Biochemistry, Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, 70569 Stuttgart, Germany
| | - Albert Jeltsch
- Department of Biochemistry, Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, 70569 Stuttgart, Germany
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9
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CRISPR-mediated promoter de/methylation technologies for gene regulation. Arch Pharm Res 2020; 43:705-713. [PMID: 32725389 DOI: 10.1007/s12272-020-01257-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2020] [Accepted: 07/24/2020] [Indexed: 01/10/2023]
Abstract
DNA methylation on cytosines of CpG dinucleotides is well established as a basis of epigenetic regulation in mammalian cells. Since aberrant regulation of DNA methylation in promoters of tumor suppressor genes or proto-oncogenes may contribute to the initiation and progression of various types of human cancer, sequence-specific methylation and demethylation technologies could have great clinical benefit. The CRISPR-Cas9 protein with a guide RNA can target DNA sequences regardless of the methylation status of the target site, making this system superb for precise methylation editing and gene regulation. Targeted methylation-editing technologies employing the dCas9 fusion proteins have been shown to be highly effective in gene regulation without altering the DNA sequence. In this review, we discuss epigenetic alterations in tumorigenesis as well as various dCas9 fusion technologies and their usages in site-specific methylation editing and gene regulation.
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10
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Sachdeva A, Gouge J, Kontovounisios C, Nikolaou S, Ashworth A, Lim K, Chong I. Klotho and the Treatment of Human Malignancies. Cancers (Basel) 2020; 12:cancers12061665. [PMID: 32585905 PMCID: PMC7352559 DOI: 10.3390/cancers12061665] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Accepted: 06/16/2020] [Indexed: 12/24/2022] Open
Abstract
Klotho was first discovered as an anti-ageing protein linked to a number of age-related disease processes, including cardiovascular, renal, musculoskeletal, and neurodegenerative conditions. Emerging research has also demonstrated a potential therapeutic role for Klotho in cancer biology, which is perhaps unsurprising given that cancer and ageing share similar molecular hallmarks. In addition to functioning as a tumour suppressor in numerous solid tumours and haematological malignancies, Klotho represents a candidate therapeutic target for patients with these diseases, the majority of whom have limited treatment options. Here, we examine contemporary evidence evaluating the anti-neoplastic effects of Klotho and describe the modulation of downstream oncogenic signalling pathways, including Wnt/β-catenin, FGF, IGF1, PIK3K/AKT, TGFβ, and the Unfolded Protein Response. We also discuss possible approaches to developing therapeutic Klotho and consider technological advances that may facilitate the delivery of Klotho through gene therapy.
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Affiliation(s)
- Aishani Sachdeva
- The Royal Marsden NHS Foundation Trust, London SW6 6JJ, UK; (A.S.); (C.K.)
- Department of Surgery and Cancer, Chelsea and Westminster Hospital, London SW10 9NH, UK;
| | - Jerome Gouge
- Institute of Structural and Molecular Biology, Birkbeck College, London WC1E 7HX, UK;
| | - Christos Kontovounisios
- The Royal Marsden NHS Foundation Trust, London SW6 6JJ, UK; (A.S.); (C.K.)
- Department of Surgery and Cancer, Chelsea and Westminster Hospital, London SW10 9NH, UK;
| | - Stella Nikolaou
- Department of Surgery and Cancer, Chelsea and Westminster Hospital, London SW10 9NH, UK;
| | - Alan Ashworth
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA 94158, USA;
| | - Kenneth Lim
- Division of Nephrology, Department of Medicine, Indiana University School of Medicine, Indianapolis, IN 46202-5181, USA;
| | - Irene Chong
- The Royal Marsden NHS Foundation Trust, London SW6 6JJ, UK; (A.S.); (C.K.)
- The Institute of Cancer Research, London SW3 6JB, UK
- Correspondence:
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11
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Harnessing targeted DNA methylation and demethylation using dCas9. Essays Biochem 2020; 63:813-825. [PMID: 31724704 DOI: 10.1042/ebc20190029] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Revised: 10/23/2019] [Accepted: 10/24/2019] [Indexed: 12/15/2022]
Abstract
DNA methylation is an essential DNA modification that plays a crucial role in genome regulation during differentiation and development, and is disrupted in a range of disease states. The recent development of CRISPR/catalytically dead CRISPR/Cas9 (dCas9)-based targeted DNA methylation editing tools has enabled new insights into the roles and functional relevance of this modification, including its importance at regulatory regions and the role of aberrant methylation in various diseases. However, while these tools are advancing our ability to understand and manipulate this regulatory layer of the genome, they still possess a variety of limitations in efficacy, implementation, and targeting specificity. Effective targeted DNA methylation editing will continue to advance our fundamental understanding of the role of this modification in different genomic and cellular contexts, and further improvements may enable more accurate disease modeling and possible future treatments. In this review, we discuss strategies, considerations, and future directions for targeted DNA methylation editing.
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12
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Hofacker D, Broche J, Laistner L, Adam S, Bashtrykov P, Jeltsch A. Engineering of Effector Domains for Targeted DNA Methylation with Reduced Off-Target Effects. Int J Mol Sci 2020; 21:ijms21020502. [PMID: 31941101 PMCID: PMC7013458 DOI: 10.3390/ijms21020502] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Revised: 01/07/2020] [Accepted: 01/08/2020] [Indexed: 12/22/2022] Open
Abstract
Epigenome editing is a promising technology, potentially allowing the stable reprogramming of gene expression profiles without alteration of the DNA sequence. Targeted DNA methylation has been successfully documented by many groups for silencing selected genes, but recent publications have raised concerns regarding its specificity. In the current work, we developed new EpiEditors for programmable DNA methylation in cells with a high efficiency and improved specificity. First, we demonstrated that the catalytically deactivated Cas9 protein (dCas9)-SunTag scaffold, which has been used earlier for signal amplification, can be combined with the DNMT3A-DNMT3L single-chain effector domain, allowing for a strong methylation at the target genomic locus. We demonstrated that off-target activity of this system is mainly due to untargeted freely diffusing DNMT3A-DNMT3L subunits. Therefore, we generated several DNMT3A-DNMT3L variants containing mutations in the DNMT3A part, which reduced their endogenous DNA binding. We analyzed the genome-wide DNA methylation of selected variants and confirmed a striking reduction of untargeted methylation, most pronounced for the R887E mutant. For all potential applications of targeted DNA methylation, the efficiency and specificity of the treatment are the key factors. By developing highly active targeted methylation systems with strongly improved specificity, our work contributes to future applications of this approach.
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Affiliation(s)
| | | | | | | | - Pavel Bashtrykov
- Correspondence: or (P.B.); or (A.J.); Tel.: +49-711-685-64363 (P.B.); +49-711-685-64390 (A.J.); Fax: +49-711-685-64392 (P.B. & A.J.)
| | - Albert Jeltsch
- Correspondence: or (P.B.); or (A.J.); Tel.: +49-711-685-64363 (P.B.); +49-711-685-64390 (A.J.); Fax: +49-711-685-64392 (P.B. & A.J.)
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13
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Taghbalout A, Du M, Jillette N, Rosikiewicz W, Rath A, Heinen CD, Li S, Cheng AW. Enhanced CRISPR-based DNA demethylation by Casilio-ME-mediated RNA-guided coupling of methylcytosine oxidation and DNA repair pathways. Nat Commun 2019; 10:4296. [PMID: 31541098 PMCID: PMC6754513 DOI: 10.1038/s41467-019-12339-7] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Accepted: 09/04/2019] [Indexed: 12/11/2022] Open
Abstract
Here we develop a methylation editing toolbox, Casilio-ME, that enables not only RNA-guided methylcytosine editing by targeting TET1 to genomic sites, but also by co-delivering TET1 and protein factors that couple methylcytosine oxidation to DNA repair activities, and/or promote TET1 to achieve enhanced activation of methylation-silenced genes. Delivery of TET1 activity by Casilio-ME1 robustly alters the CpG methylation landscape of promoter regions and activates methylation-silenced genes. We augment Casilio-ME1 to simultaneously deliver the TET1-catalytic domain and GADD45A (Casilio-ME2) or NEIL2 (Casilio-ME3) to streamline removal of oxidized cytosine intermediates to enhance activation of targeted genes. Using two-in-one effectors or modular effectors, Casilio-ME2 and Casilio-ME3 remarkably boost gene activation and methylcytosine demethylation of targeted loci. We expand the toolbox to enable a stable and expression-inducible system for broader application of the Casilio-ME platforms. This work establishes a platform for editing DNA methylation to enable research investigations interrogating DNA methylomes.
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Affiliation(s)
- Aziz Taghbalout
- The Jackson Laboratory for Genomic Medicine, 10 Discovery Drive, Farmington, CT, 06032, USA
| | - Menghan Du
- The Jackson Laboratory for Genomic Medicine, 10 Discovery Drive, Farmington, CT, 06032, USA
| | - Nathaniel Jillette
- The Jackson Laboratory for Genomic Medicine, 10 Discovery Drive, Farmington, CT, 06032, USA
| | - Wojciech Rosikiewicz
- The Jackson Laboratory for Genomic Medicine, 10 Discovery Drive, Farmington, CT, 06032, USA
| | - Abhijit Rath
- Center for Molecular Oncology, University of Connecticut Health, 263 Farmington Avenue, Farmington, CT, 06030, USA
| | - Christopher D Heinen
- Center for Molecular Oncology, University of Connecticut Health, 263 Farmington Avenue, Farmington, CT, 06030, USA
| | - Sheng Li
- The Jackson Laboratory for Genomic Medicine, 10 Discovery Drive, Farmington, CT, 06032, USA
| | - Albert W Cheng
- The Jackson Laboratory for Genomic Medicine, 10 Discovery Drive, Farmington, CT, 06032, USA.
- Department of Genetics and Genome Sciences, University of Connecticut Health, 400 Farmington Avenue, Farmington, CT, 06030, USA.
- Institute for Systems Genomics, UConn Health Science Center, 400 Farmington Avenue, Farmington, CT, 06030, USA.
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14
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Abstract
The advent of locus-specific protein recruitment technologies has enabled a new class of studies in chromatin biology. Epigenome editors enable biochemical modifications of chromatin at almost any specific endogenous locus. Their locus specificity unlocks unique information including the functional roles of distinct modifications at specific genomic loci. Given the growing interest in using these tools for biological and translational studies, there are many specific design considerations depending on the scientific question or clinical need. Here we present and discuss important design considerations and challenges regarding the biochemical and locus specificities of epigenome editors. These include how to account for the complex biochemical diversity of chromatin; control for potential interdependency of epigenome editors and their resultant modifications; avoid sequestration effects; quantify the locus specificity of epigenome editors; and improve locus specificity by considering concentration, affinity, avidity, and sequestration effects.
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15
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Yahyazadeh Mashhadi SM, Kazemimanesh M, Arashkia A, Azadmanesh K, Meshkat Z, Golichenari B, Sahebkar A. Shedding light on the EpCAM: An overview. J Cell Physiol 2019; 234:12569-12580. [DOI: 10.1002/jcp.28132] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Accepted: 11/30/2018] [Indexed: 12/13/2022]
Affiliation(s)
- Seyed Muhammad Yahyazadeh Mashhadi
- Department of Virology Pasteur Institute of Iran Tehran Iran
- Antimicrobial Resistance Research Center, Mashhad University of Medical Sciences Mashhad Iran
- Production Expert at Samandaroo 8 (Biotech Pharmaceutical) Co. Mashhad Iran
| | | | - Arash Arashkia
- Department of Virology Pasteur Institute of Iran Tehran Iran
| | | | - Zahra Meshkat
- Antimicrobial Resistance Research Center, Mashhad University of Medical Sciences Mashhad Iran
| | - Behrouz Golichenari
- Biotechnology Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences Mashhad Iran
| | - Amirhosein Sahebkar
- Biotechnology Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences Mashhad Iran
- Neurogenic inflammation Research Center, Mashhad University of Medical Sciences Mashhad Iran
- School of Pharmacy, Mashhad University of Medical Sciences Mashhad Iran
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16
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Abstract
DNA methylation plays important roles in determining cellular identity, disease, and environmental responses, but little is known about the mechanisms that drive methylation changes during cellular differentiation and tumorigenesis. Meanwhile, the causal relationship between DNA methylation and transcription remains incompletely understood. Recently developed targeted DNA methylation manipulation tools can address these gaps in knowledge, leading to new insights into how methylation governs gene expression. Here, we summarize technological developments in the DNA methylation editing field and discuss the remaining challenges facing current tools, as well as potential future directions.
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Affiliation(s)
- Yong Lei
- Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, TX, 77030, USA.,Center for Cell and Gene Therapy, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Yung-Hsin Huang
- Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, TX, 77030, USA.,Center for Cell and Gene Therapy, Baylor College of Medicine, Houston, TX, 77030, USA.,Program in Developmental Biology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Margaret A Goodell
- Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, TX, 77030, USA. .,Center for Cell and Gene Therapy, Baylor College of Medicine, Houston, TX, 77030, USA. .,Program in Developmental Biology, Baylor College of Medicine, Houston, TX, 77030, USA. .,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA.
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17
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Pflueger C, Tan D, Swain T, Nguyen T, Pflueger J, Nefzger C, Polo JM, Ford E, Lister R. A modular dCas9-SunTag DNMT3A epigenome editing system overcomes pervasive off-target activity of direct fusion dCas9-DNMT3A constructs. Genome Res 2018; 28:1193-1206. [PMID: 29907613 PMCID: PMC6071642 DOI: 10.1101/gr.233049.117] [Citation(s) in RCA: 106] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Accepted: 06/06/2018] [Indexed: 12/15/2022]
Abstract
Detection of DNA methylation in the genome has been possible for decades; however, the ability to deliberately and specifically manipulate local DNA methylation states in the genome has been extremely limited. Consequently, this has impeded our understanding of the direct effect of DNA methylation on transcriptional regulation and transcription factor binding in the native chromatin context. Thus, highly specific targeted epigenome editing tools are needed to address this. Recent adaptations of genome editing technologies, including fusion of the DNMT3A DNA methyltransferase catalytic domain to catalytically inactive Cas9 (dC9-D3A), have aimed to alter DNA methylation at desired loci. Here, we show that these tools exhibit consistent off-target DNA methylation deposition in the genome, limiting their capabilities to unambiguously assess the functional consequences of DNA methylation. To address this, we developed a modular dCas9-SunTag (dC9Sun-D3A) system that can recruit multiple DNMT3A catalytic domains to a target site for editing DNA methylation. dC9Sun-D3A is tunable, specific, and exhibits much higher induction of DNA methylation at target sites than the dC9-D3A direct fusion protein. Importantly, genome-wide characterization of dC9Sun-D3A binding sites and DNA methylation revealed minimal off-target protein binding and induction of DNA methylation with dC9Sun-D3A, compared to pervasive off-target methylation by dC9-D3A. Furthermore, we used dC9Sun-D3A to demonstrate the binding sensitivity to DNA methylation for CTCF and NRF1 in situ. Overall, this modular dC9Sun-D3A system enables precise DNA methylation deposition with the lowest off-target DNA methylation levels reported to date, allowing accurate functional determination of the role of DNA methylation at single loci.
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Affiliation(s)
- Christian Pflueger
- Australian Research Council Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Crawley, Western Australia 6009, Australia.,Harry Perkins Institute of Medical Research, Nedlands, Western Australia 6009, Australia
| | - Dennis Tan
- Australian Research Council Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Crawley, Western Australia 6009, Australia
| | - Tessa Swain
- Australian Research Council Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Crawley, Western Australia 6009, Australia.,Harry Perkins Institute of Medical Research, Nedlands, Western Australia 6009, Australia
| | - Trung Nguyen
- Australian Research Council Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Crawley, Western Australia 6009, Australia.,Harry Perkins Institute of Medical Research, Nedlands, Western Australia 6009, Australia
| | - Jahnvi Pflueger
- Australian Research Council Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Crawley, Western Australia 6009, Australia.,Harry Perkins Institute of Medical Research, Nedlands, Western Australia 6009, Australia
| | - Christian Nefzger
- Department of Anatomy and Developmental Biology, Monash University, Clayton, Victoria 3800, Australia.,Development and Stem Cells Program, Monash Biomedicine Discovery Institute, Clayton, Victoria 3800, Australia.,Australian Regenerative Medicine Institute, Monash University, Clayton, Victoria 3800, Australia
| | - Jose M Polo
- Department of Anatomy and Developmental Biology, Monash University, Clayton, Victoria 3800, Australia.,Development and Stem Cells Program, Monash Biomedicine Discovery Institute, Clayton, Victoria 3800, Australia.,Australian Regenerative Medicine Institute, Monash University, Clayton, Victoria 3800, Australia
| | - Ethan Ford
- Australian Research Council Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Crawley, Western Australia 6009, Australia
| | - Ryan Lister
- Australian Research Council Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Crawley, Western Australia 6009, Australia.,Harry Perkins Institute of Medical Research, Nedlands, Western Australia 6009, Australia
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18
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Gyparaki MT, Papavassiliou AG. Epigenetic Pathways Offer Targets for Ovarian Cancer Treatment. Clin Breast Cancer 2018; 18:189-191. [DOI: 10.1016/j.clbc.2017.09.009] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2015] [Accepted: 05/02/2015] [Indexed: 11/26/2022]
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19
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Herreros-Pomares A, Aguilar-Gallardo C, Calabuig-Fariñas S, Sirera R, Jantus-Lewintre E, Camps C. EpCAM duality becomes this molecule in a new Dr. Jekyll and Mr. Hyde tale. Crit Rev Oncol Hematol 2018; 126:52-63. [DOI: 10.1016/j.critrevonc.2018.03.006] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Revised: 03/16/2018] [Accepted: 03/17/2018] [Indexed: 02/08/2023] Open
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20
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Jeffries MA. Epigenetic editing: How cutting-edge targeted epigenetic modification might provide novel avenues for autoimmune disease therapy. Clin Immunol 2018; 196:49-58. [PMID: 29421443 DOI: 10.1016/j.clim.2018.02.001] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2018] [Revised: 02/01/2018] [Accepted: 02/01/2018] [Indexed: 12/19/2022]
Abstract
Autoimmune diseases are enigmatic and complex, and most been associated with epigenetic changes. Epigenetics describes changes in gene expression related to environmental influences mediated by a variety of effectors that alter the three-dimensional structure of chromatin and facilitate transcription factor or repressor binding. Recent years have witnessed a dramatic change and acceleration in epigenetic editing approaches, spurred on by the discovery and later development of the CRISPR/Cas9 system as a highly modular and efficient site-specific DNA binding domain. The purpose of this article is to offer a review of epigenetic editing approaches to date, with a focus on alterations of DNA methylation, and to describe a few prominent published examples of epigenetic editing. We will also offer as an example work done by our laboratory demonstrating epigenetic editing of the FOXP3 gene in human T cells. Finally, we discuss briefly the future of epigenetic editing in autoimmune disease.
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Affiliation(s)
- Matlock A Jeffries
- University of Oklahoma Health Sciences Center, Department of Internal Medicine, Division of Rheumatology, Immunology, and Allergy, Oklahoma City, OK, United States; Oklahoma Medical Research Foundation, Arthritis & Clinical Immunology Program, Oklahoma City, OK, United States.
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21
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Waryah CB, Moses C, Arooj M, Blancafort P. Zinc Fingers, TALEs, and CRISPR Systems: A Comparison of Tools for Epigenome Editing. Methods Mol Biol 2018. [PMID: 29524128 DOI: 10.1007/978-1-4939-7774-1_2] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The completion of genome, epigenome, and transcriptome mapping in multiple cell types has created a demand for precision biomolecular tools that allow researchers to functionally manipulate DNA, reconfigure chromatin structure, and ultimately reshape gene expression patterns. Epigenetic editing tools provide the ability to interrogate the relationship between epigenetic modifications and gene expression. Importantly, this information can be exploited to reprogram cell fate for both basic research and therapeutic applications. Three different molecular platforms for epigenetic editing have been developed: zinc finger proteins (ZFs), transcription activator-like effectors (TALEs), and the system of Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) and CRISPR-associated (Cas) proteins. These platforms serve as custom DNA-binding domains (DBDs), which are fused to epigenetic modifying domains to manipulate epigenetic marks at specific sites in the genome. The addition and/or removal of epigenetic modifications reconfigures local chromatin structure, with the potential to provoke long-lasting changes in gene transcription. Here we summarize the molecular structure and mechanism of action of ZF, TALE, and CRISPR platforms and describe their applications for the locus-specific manipulation of the epigenome. The advantages and disadvantages of each platform will be discussed with regard to genomic specificity, potency in regulating gene expression, and reprogramming cell phenotypes, as well as ease of design, construction, and delivery. Finally, we outline potential applications for these tools in molecular biology and biomedicine and identify possible barriers to their future clinical implementation.
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Affiliation(s)
- Charlene Babra Waryah
- Cancer Epigenetics Group, The Harry Perkins Institute of Medical Research, Nedlands, Perth, WA, Australia
| | - Colette Moses
- Cancer Epigenetics Group, The Harry Perkins Institute of Medical Research, Nedlands, Perth, WA, Australia
- School of Human Sciences, The University of Western Australia, Perth, WA, Australia
| | - Mahira Arooj
- Cancer Epigenetics Group, The Harry Perkins Institute of Medical Research, Nedlands, Perth, WA, Australia
- School of Biomedical Sciences, Curtin Health Innovation Research Institute, Curtin University, Perth, WA, Australia
| | - Pilar Blancafort
- Cancer Epigenetics Group, The Harry Perkins Institute of Medical Research, Nedlands, Perth, WA, Australia.
- School of Human Sciences, The University of Western Australia, Perth, WA, Australia.
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22
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Abstract
The discovery and adaptation of the CRISPR/Cas system for epigenome editing has allowed for a straightforward design of targeting modules which can direct epigenetic editors to virtually any genomic site. This advancement in DNA-targeting technology brings allele-specific epigenome editing into reach, a "super-specific" variation of epigenome editing whose goal is an alteration of chromatin marks at only one selected allele of the target genomic locus. This technology would be useful for the treatment of diseases caused by a mutant allele with a dominant effect, because allele-specific epigenome editing allows the specific silencing of the mutated allele leaving the healthy counterpart expressed. Moreover, it may allow the direct correction of aberrant imprints in imprinting disorders where editing of DNA methylation is needed in one allele only. Here, we describe some principal setups of allele-specific epigenome editing systems and present exemplary data illustrating the feasibility of the concept.
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Affiliation(s)
- Pavel Bashtrykov
- Department of Biochemistry, Institute of Biochemistry and Technical Biochemistry, Stuttgart University, Stuttgart, Germany.
| | - Albert Jeltsch
- Department of Biochemistry, Institute of Biochemistry and Technical Biochemistry, Stuttgart, Germany.
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23
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Kroll C, Rathert P. Stable Expression of Epigenome Editors via Viral Delivery and Genomic Integration. Methods Mol Biol 2018. [PMID: 29524137 DOI: 10.1007/978-1-4939-7774-1_11] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
The advent of precise genomic targeting systems has revolutionized epigenome editing through fusion of epigenetic effector proteins with engineered DNA-binding proteins. However, the delivery of plasmid DNA to express these fusion proteins via conventional transient transfection has certain consequences which need to be considered during the experimental design. Transient transfection achieves peak gene expression between 24 and 96 h post-transfection after which the foreign gene is lost through cell division and degradation. The use of cell lines stably expressing the effector fusion protein of interest provides several advantages compared to standard transfection methods, and the most suitable means for creating these cell lines was found to be viral delivery followed by stable integration of the transgenes into the host genome. Here we describe a practical protocol to generate murine cell lines stably expressing fusion proteins of chromatin regulators and DNA-binding proteins using a retroviral murine stem cell virus (MSCV)-based vector system.
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Affiliation(s)
- Carolin Kroll
- Department of Biochemistry, Institute of Biochemistry and Technical Biochemistry, Stuttgart University, Stuttgart, Germany
| | - Philipp Rathert
- Department of Biochemistry, Institute of Biochemistry and Technical Biochemistry, Stuttgart University, Stuttgart, Germany.
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24
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Henri JL, Macdonald J, Strom M, Duan W, Shigdar S. Aptamers as potential therapeutic agents for ovarian cancer. Biochimie 2017; 145:34-44. [PMID: 29224849 DOI: 10.1016/j.biochi.2017.12.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2017] [Accepted: 12/05/2017] [Indexed: 12/30/2022]
Abstract
Current therapy for ovarian cancer typically involves indiscriminate chemotherapies that can have severe off target effects on healthy tissue and are still plagued by aggressive recurrence. Recent shifts towards targeted therapies offer the possibility of circumventing the obstacles experienced by these traditional treatments. While antibodies are the pioneering agents in targeted therapies, clinical experience has demonstrated that their antitumor efficacy is limited due to their high immunogenicity, large molecular size, and costly and laborious production. In contrast, nucleic acid based chemical antibodies, also known as aptamers, are ideal for this application given their small size, lack of immunogenicity and in vitro production. As aptamers have begun to demonstrate their promise through targeting Epithelial Cell Adhesion Molecule (EpCAM), as well as a number of ovarian cancer biomarkers, in in vivo and in vitro models, their clinical applicability is slowly being realised. This review explores some of the current progress of aptamers targeting cancer biomarkers and their potential role as ovarian cancer therapeutics.
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Affiliation(s)
- Justin Liam Henri
- School of Medicine and Centre for Molecular and Medical Research, Deakin University, 75 Pigdons Road, Waurn Ponds, Victoria 3216, Australia
| | - Joanna Macdonald
- School of Medicine and Centre for Molecular and Medical Research, Deakin University, 75 Pigdons Road, Waurn Ponds, Victoria 3216, Australia
| | - Mia Strom
- School of Medicine and Centre for Molecular and Medical Research, Deakin University, 75 Pigdons Road, Waurn Ponds, Victoria 3216, Australia
| | - Wei Duan
- School of Medicine and Centre for Molecular and Medical Research, Deakin University, 75 Pigdons Road, Waurn Ponds, Victoria 3216, Australia
| | - Sarah Shigdar
- School of Medicine and Centre for Molecular and Medical Research, Deakin University, 75 Pigdons Road, Waurn Ponds, Victoria 3216, Australia.
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25
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Cancer induction and suppression with transcriptional control and epigenome editing technologies. J Hum Genet 2017; 63:187-194. [PMID: 29215091 DOI: 10.1038/s10038-017-0377-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2017] [Revised: 09/27/2017] [Accepted: 10/10/2017] [Indexed: 12/22/2022]
Abstract
Cancer epigenetics is one of the most important research subjects in dissecting cancer mechanisms and therapeutic targets because the emergence and malignant transformation of various cancers are caused by unnatural expression of cancer-related genes attributed to their epigenetic errors. The original concept of cancer epigenetics basically stands on the analysis of the epigenetic status in naturally occurring cancer cells; however, the rapidly emerging technology called epigenome editing would change this situation drastically. Epigenome editing, the most promising derivative technology of genome editing, can modify the epigenetic states at the pre-defined genomic locus using the programmable effectors, consisting of various epigenetic factors combined with site-specific DNA-binding domains. This technology can be utilized in a reversible manner; i.e., cancer modeling can be achieved by introducing aberrant epigenetic marks in normal cells, and cancer suppression can be achieved by correcting the epigenetic errors in cancer cells. In this review, we summarize the basics of epigenome editing and cancer epigenetics, followed by the current examples of cancer induction and suppression with the transcriptional control and epigenome editing technologies.
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26
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Mari-Alexandre J, Diaz-Lagares A, Villalba M, Juan O, Crujeiras AB, Calvo A, Sandoval J. Translating cancer epigenomics into the clinic: focus on lung cancer. Transl Res 2017. [PMID: 28644958 DOI: 10.1016/j.trsl.2017.05.008] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Epigenetic deregulation is increasingly being recognized as a hallmark of cancer. Recent studies have identified many new epigenetic biomarkers, some of which are being introduced into clinical practice for diagnosis, molecular classification, prognosis or prediction of response to therapies. O-6-methylguanine-DNA methyltransferase gene is the most clinically advanced epigenetic biomarker as it predicts the response to temozolomide and carmustine in gliomas. Therefore, epigenomics may represent a novel and promising tool for precision medicine, and in particular, the detection of epigenomic biomarkers in liquid biopsies will be of great interest for monitoring diseases in patients. Of particular relevance is the identification of epigenetic biomarkers in lung cancer, one of the most prevalent and deadly types of cancer. DNA methylation of SHOX2 and RASSF1A could be used as diagnostic markers to differentiate between normal and tumor samples. MicroRNA and long noncoding RNA signatures associated with lung cancer development or tobacco smoke have also been identified. In addition to the field of biomarkers, therapeutic approaches using DNA methylation and histone deacetylation inhibitors are being tested in clinical trials for several cancer types. Moreover, new DNA editing techniques based on zinc finger and CRISPR/Cas9 technologies allow specific modification of aberrant methylation found in oncogenes or tumor suppressor genes. We envision that epigenomics will translate into the clinical field and will have an impact on lung cancer diagnosis/prognosis and treatment.
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Affiliation(s)
- Josep Mari-Alexandre
- Unit of Inherited Cardiovascular Diseases, Sudden Death and Mechanisms of Disease, Health Research Institute La Fe, Valencia, Spain
| | - Angel Diaz-Lagares
- Translational Medical Oncology (Oncomet), Health Research Institute of Santiago (IDIS), University Clinical Hospital of Santiago (CHUS), CIBERONC, Santiago de Compostela, Spain
| | - Maria Villalba
- Department of Histology and Pathology, School of Medicine, University of Navarra, Pamplona, Navarra, Spain; CIBERONC, IDISNA and Program in Solid Tumors and Biomarkers, Center for Applied Medical Research (CIMA), University of Navarra, Pamplona, Navarra, Spain
| | - Oscar Juan
- Biomarkers and Precision Medicine Unit. Health Research Institute La Fe, Valencia, Spain
| | - Ana B Crujeiras
- Laboratory of Molecular and Cellular Endocrinology, Health Research Institute of Santiago de Compostela (IDIS), Complejo Hospitalario Universitario de Santiago (CHUS) and Santiago de Compostela University (USC), Santiago de Compostela, Spain; CIBER Physiopathology of Obesity and Nutrition (CIBERobn), Madrid, Spain.
| | - Alfonso Calvo
- Department of Histology and Pathology, School of Medicine, University of Navarra, Pamplona, Navarra, Spain; CIBERONC, IDISNA and Program in Solid Tumors and Biomarkers, Center for Applied Medical Research (CIMA), University of Navarra, Pamplona, Navarra, Spain.
| | - Juan Sandoval
- Biomarkers and Precision Medicine Unit. Health Research Institute La Fe, Valencia, Spain.
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27
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Imm J, Kerrigan TL, Jeffries A, Lunnon K. Using induced pluripotent stem cells to explore genetic and epigenetic variation associated with Alzheimer's disease. Epigenomics 2017; 9:1455-1468. [DOI: 10.2217/epi-2017-0076] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
It is thought that both genetic and epigenetic variation play a role in Alzheimer's disease initiation and progression. With the advent of somatic cell reprogramming into induced pluripotent stem cells it is now possible to generate patient-derived cells that are able to more accurately model and recapitulate disease. Furthermore, by combining this with recent advances in (epi)genome editing technologies, it is possible to begin to examine the functional consequence of previously nominated genetic variants and infer epigenetic causality from recently identified epigenetic variants. In this review, we explore the role of genetic and epigenetic variation in Alzheimer's disease and how the functional relevance of nominated loci can be investigated using induced pluripotent stem cells and (epi)genome editing techniques.
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Affiliation(s)
- Jennifer Imm
- Institute of Clinical and Biomedical Science, University of Exeter Medical School, Exeter University, Exeter, UK
| | - Talitha L Kerrigan
- Institute of Clinical and Biomedical Science, University of Exeter Medical School, Exeter University, Exeter, UK
| | - Aaron Jeffries
- Institute of Clinical and Biomedical Science, University of Exeter Medical School, Exeter University, Exeter, UK
| | - Katie Lunnon
- Institute of Clinical and Biomedical Science, University of Exeter Medical School, Exeter University, Exeter, UK
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28
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Malankhanova TB, Malakhova AA, Medvedev SP, Zakian SM. Modern Genome Editing Technologies in Huntington's Disease Research. J Huntingtons Dis 2017; 6:19-31. [PMID: 28128770 PMCID: PMC5389024 DOI: 10.3233/jhd-160222] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
The development of new revolutionary technologies for directed gene editing has made it possible to thoroughly model and study NgAgo human diseases at the cellular and molecular levels. Gene editing tools like ZFN, TALEN, CRISPR-based systems, NgAgo and SGN can introduce different modifications. In gene sequences and regulate gene expression in different types of cells including induced pluripotent stem cells (iPSCs). These tools can be successfully used for Huntington's disease (HD) modeling, for example, to generate isogenic cell lines bearing different numbers of CAG repeats or to correct the mutation causing the disease. This review presents common genome editing technologies and summarizes the progress made in using them in HD and other hereditary diseases. Furthermore, we will discuss prospects and limitations of genome editing in understanding HD pathology.
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Affiliation(s)
- Tuyana B Malankhanova
- The Federal Research Center Institute of Cytology and Genetics, The Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia.,Novosibirsk State University, Novosibirsk, Russia.,State Research Institute of Circulation Pathology, Ministry of Healthcare of the Russian Federation, Novosibirsk, Russia.,Institute of Chemical Biology and Fundamental Medicine, The Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Anastasia A Malakhova
- The Federal Research Center Institute of Cytology and Genetics, The Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia.,State Research Institute of Circulation Pathology, Ministry of Healthcare of the Russian Federation, Novosibirsk, Russia.,Institute of Chemical Biology and Fundamental Medicine, The Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Sergey P Medvedev
- The Federal Research Center Institute of Cytology and Genetics, The Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia.,Novosibirsk State University, Novosibirsk, Russia.,State Research Institute of Circulation Pathology, Ministry of Healthcare of the Russian Federation, Novosibirsk, Russia.,Institute of Chemical Biology and Fundamental Medicine, The Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Suren M Zakian
- The Federal Research Center Institute of Cytology and Genetics, The Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia.,Novosibirsk State University, Novosibirsk, Russia.,State Research Institute of Circulation Pathology, Ministry of Healthcare of the Russian Federation, Novosibirsk, Russia.,Institute of Chemical Biology and Fundamental Medicine, The Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
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29
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Stepper P, Kungulovski G, Jurkowska RZ, Chandra T, Krueger F, Reinhardt R, Reik W, Jeltsch A, Jurkowski TP. Efficient targeted DNA methylation with chimeric dCas9-Dnmt3a-Dnmt3L methyltransferase. Nucleic Acids Res 2017; 45:1703-1713. [PMID: 27899645 PMCID: PMC5389507 DOI: 10.1093/nar/gkw1112] [Citation(s) in RCA: 192] [Impact Index Per Article: 27.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2016] [Accepted: 10/28/2016] [Indexed: 12/19/2022] Open
Abstract
DNA methylation plays a critical role in the regulation and maintenance of cell-type specific transcriptional programs. Targeted epigenome editing is an emerging technology to specifically regulate cellular gene expression in order to modulate cell phenotypes or dissect the epigenetic mechanisms involved in their control. In this work, we employed a DNA methyltransferase Dnmt3a–Dnmt3L construct fused to the nuclease-inactivated dCas9 programmable targeting domain to introduce DNA methylation into the human genome specifically at the EpCAM, CXCR4 and TFRC gene promoters. We show that targeting of these loci with single gRNAs leads to efficient and widespread methylation of the promoters. Multiplexing of several guide RNAs does not increase the efficiency of methylation. Peaks of targeted methylation were observed around 25 bp upstream and 40 bp downstream of the PAM site, while 20–30 bp of the binding site itself are protected against methylation. Potent methylation is dependent on the multimerization of Dnmt3a/Dnmt3L complexes on the DNA. Furthermore, the introduced methylation causes transcriptional repression of the targeted genes. These new programmable epigenetic editors allow unprecedented control of the DNA methylation status in cells and will lead to further advances in the understanding of epigenetic signaling.
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Affiliation(s)
- Peter Stepper
- Institute of Biochemistry, Pfaffenwaldring 55, Faculty of Chemistry, University of Stuttgart, D-70569 Stuttgart, Germany
| | - Goran Kungulovski
- Institute of Biochemistry, Pfaffenwaldring 55, Faculty of Chemistry, University of Stuttgart, D-70569 Stuttgart, Germany
| | - Renata Z Jurkowska
- Institute of Biochemistry, Pfaffenwaldring 55, Faculty of Chemistry, University of Stuttgart, D-70569 Stuttgart, Germany
| | - Tamir Chandra
- Epigenetics Programme, The Babraham Institute, Cambridge CB22 3AT, UK; The Welcome Trust Sanger Institute, Cambridge CB10 1SA, UK
| | | | - Richard Reinhardt
- Max Planck Genome-Centre Cologne, Carl-von-Linné-Weg 10, D-50829 Cologne, Germany
| | - Wolf Reik
- Epigenetics Programme, The Babraham Institute, Cambridge CB22 3AT, UK; The Welcome Trust Sanger Institute, Cambridge CB10 1SA, UK
| | - Albert Jeltsch
- Institute of Biochemistry, Pfaffenwaldring 55, Faculty of Chemistry, University of Stuttgart, D-70569 Stuttgart, Germany
| | - Tomasz P Jurkowski
- Institute of Biochemistry, Pfaffenwaldring 55, Faculty of Chemistry, University of Stuttgart, D-70569 Stuttgart, Germany
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30
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Zheng J, Zhao S, Yu X, Huang S, Liu HY. Simultaneous targeting of CD44 and EpCAM with a bispecific aptamer effectively inhibits intraperitoneal ovarian cancer growth. Theranostics 2017; 7:1373-1388. [PMID: 28435472 PMCID: PMC5399600 DOI: 10.7150/thno.17826] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2016] [Accepted: 01/23/2017] [Indexed: 12/16/2022] Open
Abstract
CD44 and EpCAM play crucial roles in intraperitoneal ovarian cancer development. In this study, we developed an RNA-based bispecific CD44-EpCAM aptamer that is capable of blocking CD44 and EpCAM simultaneously by fusing single CD44 and EpCAM aptamers with a double stranded RNA adaptor. With the aid of a panel of ovarian cancer cell lines, we found that bispecific CD44-EpCAM aptamer was much more effective than either single CD44 or EpCAM aptamer in the ability to inhibit cell growth and to induce apoptosis. When these aptamers were tested in intraperitoneal ovarian cancer xenograft model, bispecific CD44-EpCAM aptamer suppressed intraperitoneal tumor outgrowth much more significantly than single CD44 and EpCAM aptamer either alone or in combination. The enhanced efficacy of bispecific CD44-EpCAM aptamer is most likely to be attributed to its increased circulation time over the single aptamers. Moreover, we showed that bispecific CD44-EpCAM aptamer exhibited no toxicity to the host and was unable to trigger innate immunogenicity. Our study suggests that bispecific CD44-EpCAM aptamer may represent a promising therapeutic agent against advanced ovarian cancer.
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31
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Lo CL, Choudhury SR, Irudayaraj J, Zhou FC. Epigenetic Editing of Ascl1 Gene in Neural Stem Cells by Optogenetics. Sci Rep 2017; 7:42047. [PMID: 28181538 PMCID: PMC5299429 DOI: 10.1038/srep42047] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2016] [Accepted: 01/09/2017] [Indexed: 11/09/2022] Open
Abstract
Enzymes involved in epigenetic processes such as methyltransferases or demethylases are becoming highly utilized for their persistent DNA or histone modifying efficacy. Herein, we have developed an optogenetic toolbox fused to the catalytic domain (CD) of DNA-methyltransferase3A (DNMT3A-CD) or Ten-Eleven Dioxygenase-1 (TET1-CD) for loci-specific alteration of the methylation state at the promoter of Ascl1 (Mash1), a candidate proneuron gene. Optogenetical protein pairs, CRY2 linked to DNMT3A-CD or TET1-CD and CIB1 fused to a Transcription Activator-Like Element (TALE) locating an Ascl1 promoter region, were designed for site specific epigenetic editing. A differentially methylated region at the Ascl1 promoter, isolated from murine dorsal root ganglion (hypermethylated) and striated cells (hypomethylated), was targeted with these optogenetic-epigenetic constructs. Optimized blue-light illumination triggered the co-localization of TALE constructs with DNMT3A-CD or TET1-CD fusion proteins at the targeted site of the Ascl1 promoter. We found that this spatiotemporal association of the fusion proteins selectively alters the methylation state and also regulates gene activity. This proof of concept developed herein holds immense promise for the ability to regulate gene activity via epigenetic modulation with spatiotemporal precision.
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Affiliation(s)
- Chiao-Ling Lo
- Department of Anatomy &Cell Biology, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Samrat Roy Choudhury
- Bindley Bioscience Center, Department of Agricultural &Biological Engineering, Purdue University, West Lafayette, IN, USA
| | - Joseph Irudayaraj
- Bindley Bioscience Center, Department of Agricultural &Biological Engineering, Purdue University, West Lafayette, IN, USA
| | - Feng C Zhou
- Department of Anatomy &Cell Biology, Indiana University School of Medicine, Indianapolis, IN, USA.,Stark Institute of Neuroscience Research, Indiana University School of Medicine, Indianapolis, IN, USA
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32
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Deng J, Qu X, Lu P, Yang X, Zhu Y, Ji H, Wang Y, Jiang Z, Li X, Zhong Y, Yang H, Pan H, Young WB, Zhu H. Specific and Stable Suppression of HIV Provirus Expression In Vitro by Chimeric Zinc Finger DNA Methyltransferase 1. MOLECULAR THERAPY. NUCLEIC ACIDS 2017; 6:233-242. [PMID: 28325289 PMCID: PMC5363508 DOI: 10.1016/j.omtn.2017.01.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/17/2016] [Revised: 12/20/2016] [Accepted: 01/09/2017] [Indexed: 12/25/2022]
Abstract
HIV-1 inserts its proviral DNA into the infected host cells, by which HIV proviral DNA can then be duplicated along with each cell division. Thus, provirus cannot be eradicated completely by current antiretroviral therapy. We have developed an innovative strategy to silence the HIV provirus by targeted DNA methylation on the HIV promoter region. We genetically engineered a chimeric DNA methyltransferase 1 composed of designed zinc-finger proteins to become ZF2 DNMT1. After transient transfection of the molecular clone encoding this chimeric protein into HIV-1 infected or latently infected cells, efficient suppression of HIV-1 expression by the methylation of CpG islands in 5′-LTR was observed and quantified. The effective suppression of HIV in latently infected cells by ZF2-DNMT1 is stable and can last through about 40 cell passages. Cytotoxic caused by ZF2-DNMT1 was only observed during cellular proliferation. Taken together, our results demonstrate the potential of this novel approach for anti-HIV-1 therapy.
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Affiliation(s)
- Junxiao Deng
- State Key Laboratory of Genetic Engineering, Institute of Genetics, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Xiying Qu
- State Key Laboratory of Genetic Engineering, Institute of Genetics, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Panpan Lu
- State Key Laboratory of Genetic Engineering, Institute of Genetics, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Xinyi Yang
- State Key Laboratory of Genetic Engineering, Institute of Genetics, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Yuqi Zhu
- State Key Laboratory of Genetic Engineering, Institute of Genetics, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Haiyan Ji
- State Key Laboratory of Genetic Engineering, Institute of Genetics, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Yanan Wang
- State Key Laboratory of Genetic Engineering, Institute of Genetics, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Zhengtao Jiang
- State Key Laboratory of Genetic Engineering, Institute of Genetics, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Xian Li
- State Key Laboratory of Genetic Engineering, Institute of Genetics, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Yangcheng Zhong
- State Key Laboratory of Genetic Engineering, Institute of Genetics, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - He Yang
- State Key Laboratory of Genetic Engineering, Institute of Genetics, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Hanyu Pan
- State Key Laboratory of Genetic Engineering, Institute of Genetics, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Won-Bin Young
- Department of Radiology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15219, USA
| | - Huanzhang Zhu
- State Key Laboratory of Genetic Engineering, Institute of Genetics, School of Life Sciences, Fudan University, Shanghai 200438, China.
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33
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Abstract
Epigenome editing aims for an introduction or removal of chromatin marks at a defined genomic region using artificial EpiEffectors resulting in a modulation of the activity of the targeted functional DNA elements. Rationally designed EpiEffectors consist of a targeting DNA-binding module (such as a zinc finger protein, TAL effector, or CRISPR/Cas complex) and usually, but not exclusively, a catalytic domain of a chromatin-modifying enzyme. Epigenome editing opens a completely new strategy for basic research of the central nervous system and causal treatment of psychiatric and neurological diseases, because rewriting of epigenetic information can lead to the direct and durable control of the expression of disease-associated genes. Here, we review current advances in the design of locus- and allele-specific DNA-binding modules, approaches for spatial, and temporal control of EpiEffectors and discuss some examples of existing and propose new potential therapeutic strategies based on epigenome editing for treatment of neurodegenerative and psychiatric diseases. These include the targeted silencing of disease-associated genes or activation of neuroprotective genes which may be applied in Alzheimer's and Parkinson's diseases or the control of addiction and depression. Moreover, we discuss allele-specific epigenome editing as novel therapeutic approach for imprinting disorders, Huntington's disease and Rett syndrome.
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34
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Song J, Cano-Rodriquez D, Winkle M, Gjaltema RAF, Goubert D, Jurkowski TP, Heijink IH, Rots MG, Hylkema MN. Targeted epigenetic editing of SPDEF reduces mucus production in lung epithelial cells. Am J Physiol Lung Cell Mol Physiol 2016; 312:L334-L347. [PMID: 28011616 DOI: 10.1152/ajplung.00059.2016] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2016] [Revised: 12/20/2016] [Accepted: 12/20/2016] [Indexed: 11/22/2022] Open
Abstract
Airway mucus hypersecretion contributes to the morbidity and mortality in patients with chronic inflammatory lung diseases. Reducing mucus production is crucial for improving patients' quality of life. The transcription factor SAM-pointed domain-containing Ets-like factor (SPDEF) plays a critical role in the regulation of mucus production and, therefore, represents a potential therapeutic target. This study aims to reduce lung epithelial mucus production by targeted silencing SPDEF using the novel strategy, epigenetic editing. Zinc fingers and CRISPR/dCas platforms were engineered to target repressors (KRAB, DNA methyltransferases, histone methyltransferases) to the SPDEF promoter. All constructs were able to effectively suppress both SPDEF mRNA and protein expression, which was accompanied by inhibition of downstream mucus-related genes [anterior gradient 2 (AGR2), mucin 5AC (MUC5AC)]. For the histone methyltransferase G9A, and not its mutant or other effectors, the obtained silencing was mitotically stable. These results indicate efficient SPDEF silencing and downregulation of mucus-related gene expression by epigenetic editing, in human lung epithelial cells. This opens avenues for epigenetic editing as a novel therapeutic strategy to induce long-lasting mucus inhibition.
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Affiliation(s)
- Juan Song
- University of Groningen, University Medical Center Groningen, Department of Pathology and Medical Biology, Groningen, The Netherlands.,University of Groningen, University Medical Center Groningen, Groningen Research Institute for Asthma and COPD, Groningen, The Netherlands.,Tianjin Medical University, School of Basic Medical Sciences, Department of Biochemistry and Molecular Biology, Department of Immunology, Tianjin, China; and
| | - David Cano-Rodriquez
- University of Groningen, University Medical Center Groningen, Department of Pathology and Medical Biology, Groningen, The Netherlands
| | - Melanie Winkle
- University of Groningen, University Medical Center Groningen, Department of Pathology and Medical Biology, Groningen, The Netherlands
| | - Rutger A F Gjaltema
- University of Groningen, University Medical Center Groningen, Department of Pathology and Medical Biology, Groningen, The Netherlands
| | - Désirée Goubert
- University of Groningen, University Medical Center Groningen, Department of Pathology and Medical Biology, Groningen, The Netherlands
| | - Tomasz P Jurkowski
- Institute of Biochemistry, Faculty of Chemistry, University of Stuttgart, Stuttgart, Germany
| | - Irene H Heijink
- University of Groningen, University Medical Center Groningen, Department of Pathology and Medical Biology, Groningen, The Netherlands.,University of Groningen, University Medical Center Groningen, Groningen Research Institute for Asthma and COPD, Groningen, The Netherlands
| | - Marianne G Rots
- University of Groningen, University Medical Center Groningen, Department of Pathology and Medical Biology, Groningen, The Netherlands
| | - Machteld N Hylkema
- University of Groningen, University Medical Center Groningen, Department of Pathology and Medical Biology, Groningen, The Netherlands; .,University of Groningen, University Medical Center Groningen, Groningen Research Institute for Asthma and COPD, Groningen, The Netherlands
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35
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Morrow JD, Cho MH, Hersh CP, Pinto-Plata V, Celli B, Marchetti N, Criner G, Bueno R, Washko G, Glass K, Choi AMK, Quackenbush J, Silverman EK, DeMeo DL. DNA methylation profiling in human lung tissue identifies genes associated with COPD. Epigenetics 2016; 11:730-739. [PMID: 27564456 PMCID: PMC5094634 DOI: 10.1080/15592294.2016.1226451] [Citation(s) in RCA: 61] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2016] [Revised: 08/05/2016] [Accepted: 08/10/2016] [Indexed: 10/21/2022] Open
Abstract
Chronic obstructive pulmonary disease (COPD) is a smoking-related disease characterized by genetic and phenotypic heterogeneity. Although association studies have identified multiple genomic regions with replicated associations to COPD, genetic variation only partially explains the susceptibility to lung disease, and suggests the relevance of epigenetic investigations. We performed genome-wide DNA methylation profiling in homogenized lung tissue samples from 46 control subjects with normal lung function and 114 subjects with COPD, all former smokers. The differentially methylated loci were integrated with previous genome-wide association study results. The top 535 differentially methylated sites, filtered for a minimum mean methylation difference of 5% between cases and controls, were enriched for CpG shelves and shores. Pathway analysis revealed enrichment for transcription factors. The top differentially methylated sites from the intersection with previous GWAS were in CHRM1, GLT1D1, and C10orf11; sorted by GWAS P-value, the top sites included FRMD4A, THSD4, and C10orf11. Epigenetic association studies complement genetic association studies to identify genes potentially involved in COPD pathogenesis. Enrichment for genes implicated in asthma and lung function and for transcription factors suggests the potential pathogenic relevance of genes identified through differential methylation and the intersection with a broader range of GWAS associations.
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Affiliation(s)
- Jarrett D. Morrow
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Michael H. Cho
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Craig P. Hersh
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | | | - Bartolome Celli
- Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Nathaniel Marchetti
- Division of Pulmonary and Critical Care Medicine, Temple University, Philadelphia, PA, USA
| | - Gerard Criner
- Division of Pulmonary and Critical Care Medicine, Temple University, Philadelphia, PA, USA
| | - Raphael Bueno
- Division of Thoracic Surgery, Brigham and Women's Hospital, Boston, MA, USA
| | - George Washko
- Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Kimberly Glass
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Augustine M. K. Choi
- Department of Medicine, New York Presbyterian/Weill Cornell Medical Center, New York, NY, USA
| | - John Quackenbush
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Edwin K. Silverman
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Dawn L. DeMeo
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, MA, USA
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36
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Abstract
Genome targeting has quickly developed as one of the most promising fields in science. By using programmable DNA-binding platforms and nucleases, scientists are now able to accurately edit the genome. These DNA-binding tools have recently also been applied to engineer the epigenome for gene expression modulation. Such epigenetic editing constructs have firmly demonstrated the causal role of epigenetics in instructing gene expression. Another focus of epigenome engineering is to understand the order of events of chromatin remodeling in gene expression regulation. Groundbreaking approaches in this field are beginning to yield novel insights into the function of individual chromatin marks in the context of maintaining cellular phenotype and regulating transient gene expression changes. This review focuses on recent advances in the field of epigenetic editing and highlights its promise for sustained gene expression reprogramming.
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37
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Yi L, Li J. CRISPR-Cas9 therapeutics in cancer: promising strategies and present challenges. Biochim Biophys Acta Rev Cancer 2016; 1866:197-207. [PMID: 27641687 DOI: 10.1016/j.bbcan.2016.09.002] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2016] [Revised: 09/13/2016] [Accepted: 09/14/2016] [Indexed: 01/05/2023]
Abstract
Cancer is characterized by multiple genetic and epigenetic alterations that drive malignant cell proliferation and confer chemoresistance. The ability to correct or ablate such mutations holds immense promise for combating cancer. Recently, because of its high efficiency and accuracy, the CRISPR-Cas9 genome editing technique has been widely used in cancer therapeutic explorations. Several studies used CRISPR-Cas9 to directly target cancer cell genomic DNA in cellular and animal cancer models which have shown therapeutic potential in expanding our anticancer protocols. Moreover, CRISPR-Cas9 can also be employed to fight oncogenic infections, explore anticancer drugs, and engineer immune cells and oncolytic viruses for cancer immunotherapeutic applications. Here, we summarize these preclinical CRISPR-Cas9-based therapeutic strategies against cancer, and discuss the challenges and improvements in translating therapeutic CRISPR-Cas9 into clinical use, which will facilitate better application of this technique in cancer research. Further, we propose potential directions of the CRISPR-Cas9 system in cancer therapy.
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Affiliation(s)
- Lang Yi
- National Center for Clinical Laboratories, Beijing Hospital, National Center of Gerontology, Beijing, People's Republic of China; Graduate School, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, People's Republic of China; Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, People's Republic of China
| | - Jinming Li
- National Center for Clinical Laboratories, Beijing Hospital, National Center of Gerontology, Beijing, People's Republic of China; Graduate School, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, People's Republic of China; Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, People's Republic of China.
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38
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Abstract
We are entering an era of epigenome engineering. The precision manipulation of chromatin and epigenetic modifications provides new ways to interrogate their influence on genome and cell function and to harness these changes for applications. We review the design and state of epigenome editing tools, highlighting the unique regulatory properties afforded by these systems.
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Affiliation(s)
- Minhee Park
- Department of Biomedical Engineering and Biological Design Center, Boston University, Boston, MA, 02215, USA
| | - Albert J Keung
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC, 27695, USA
| | - Ahmad S Khalil
- Department of Biomedical Engineering and Biological Design Center, Boston University, Boston, MA, 02215, USA. .,Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, 02115, USA.
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39
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Vojta A, Dobrinić P, Tadić V, Bočkor L, Korać P, Julg B, Klasić M, Zoldoš V. Repurposing the CRISPR-Cas9 system for targeted DNA methylation. Nucleic Acids Res 2016; 44:5615-28. [PMID: 26969735 PMCID: PMC4937303 DOI: 10.1093/nar/gkw159] [Citation(s) in RCA: 502] [Impact Index Per Article: 62.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2016] [Revised: 02/29/2016] [Accepted: 03/01/2016] [Indexed: 01/05/2023] Open
Abstract
Epigenetic studies relied so far on correlations between epigenetic marks and gene expression pattern. Technologies developed for epigenome editing now enable direct study of functional relevance of precise epigenetic modifications and gene regulation. The reversible nature of epigenetic modifications, including DNA methylation, has been already exploited in cancer therapy for remodeling the aberrant epigenetic landscape. However, this was achieved non-selectively using epigenetic inhibitors. Epigenetic editing at specific loci represents a novel approach that might selectively and heritably alter gene expression. Here, we developed a CRISPR-Cas9-based tool for specific DNA methylation consisting of deactivated Cas9 (dCas9) nuclease and catalytic domain of the DNA methyltransferase DNMT3A targeted by co-expression of a guide RNA to any 20 bp DNA sequence followed by the NGG trinucleotide. We demonstrated targeted CpG methylation in a ∼35 bp wide region by the fusion protein. We also showed that multiple guide RNAs could target the dCas9-DNMT3A construct to multiple adjacent sites, which enabled methylation of a larger part of the promoter. DNA methylation activity was specific for the targeted region and heritable across mitotic divisions. Finally, we demonstrated that directed DNA methylation of a wider promoter region of the target loci IL6ST and BACH2 decreased their expression.
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Affiliation(s)
- Aleksandar Vojta
- Department of Biology, Division of Molecular Biology, University of Zagreb, Faculty of Science, Zagreb, HR-10000, Croatia
| | - Paula Dobrinić
- Department of Biology, Division of Molecular Biology, University of Zagreb, Faculty of Science, Zagreb, HR-10000, Croatia
| | - Vanja Tadić
- Department of Biology, Division of Molecular Biology, University of Zagreb, Faculty of Science, Zagreb, HR-10000, Croatia
| | - Luka Bočkor
- Department of Biology, Division of Molecular Biology, University of Zagreb, Faculty of Science, Zagreb, HR-10000, Croatia
| | - Petra Korać
- Department of Biology, Division of Molecular Biology, University of Zagreb, Faculty of Science, Zagreb, HR-10000, Croatia
| | - Boris Julg
- Ragon Institute of MGHT, MIT and Harvard, 400 Technology Square, Cambridge, MA, USA
| | - Marija Klasić
- Department of Biology, Division of Molecular Biology, University of Zagreb, Faculty of Science, Zagreb, HR-10000, Croatia
| | - Vlatka Zoldoš
- Department of Biology, Division of Molecular Biology, University of Zagreb, Faculty of Science, Zagreb, HR-10000, Croatia
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40
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Bukowska B, Rogalska A, Forma E, Brys M, Marczak A. Why a Combination of WP 631 and Epo B is an Improvement on the Drugs Singly - Involvement in the Cell Cycle and Mitotic Slippage. Asian Pac J Cancer Prev 2016; 17:1299-308. [DOI: 10.7314/apjcp.2016.17.3.1299] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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41
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Tost J. Engineering of the epigenome: synthetic biology to define functional causality and develop innovative therapies. Epigenomics 2016; 8:153-6. [DOI: 10.2217/epi.15.112] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Affiliation(s)
- Jörg Tost
- Laboratory for Epigenetics & Environment, Centre National de Génotypage, CEA-Institut de Génomique, 2 rue Gaston Crémieux, 91000 Evry, France
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42
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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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43
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Epigenome Editing: State of the Art, Concepts, and Perspectives. Trends Genet 2015; 32:101-113. [PMID: 26732754 DOI: 10.1016/j.tig.2015.12.001] [Citation(s) in RCA: 123] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2015] [Revised: 11/28/2015] [Accepted: 12/01/2015] [Indexed: 12/21/2022]
Abstract
Epigenome editing refers to the directed alteration of chromatin marks at specific genomic loci by using targeted EpiEffectors which comprise designed DNA recognition domains (zinc finger, TAL effector, or modified CRISPR/Cas9 complex) and catalytic domains from a chromatin-modifying enzyme. Epigenome editing is a promising approach for durable gene regulation, with many applications in basic research including the investigation of the regulatory functions and logic of chromatin modifications and cellular reprogramming. From a clinical point of view, targeted regulation of disease-related genes offers novel therapeutic avenues for many diseases. We review here the progress made in this field and discuss open questions in epigenetic regulation and its stability, methods to increase the specificity of epigenome editing, and improved delivery methods for targeted EpiEffectors. Future work will reveal if the approach of epigenome editing fulfills its great promise in basic research and clinical applications.
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44
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Laufer BI, Singh SM. Strategies for precision modulation of gene expression by epigenome editing: an overview. Epigenetics Chromatin 2015; 8:34. [PMID: 26388942 PMCID: PMC4574080 DOI: 10.1186/s13072-015-0023-7] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2015] [Accepted: 08/19/2015] [Indexed: 01/27/2023] Open
Abstract
Genome editing technology has evolved rather quickly and become accessible to most researchers. It has resulted in far reaching implications and a number of novel designer systems including epigenome editing. Epigenome editing utilizes a combination of nuclease-null genome editing systems and effector domains to modulate gene expression. In particular, Zinc Finger, Transcription-Activator-Like Effector, and CRISPR/Cas9 have emerged as modular systems that can be modified to allow for precision manipulation of epigenetic marks without altering underlying DNA sequence. This review contains a comprehensive catalog of effector domains that can be used with components of genome editing systems to achieve epigenome editing. Ultimately, the evidence-based design of epigenome editing offers a novel improvement to the limited attenuation strategies. There is much potential for editing and/or correcting gene expression in somatic cells toward a new era of functional genomics and personalized medicine.
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Affiliation(s)
- Benjamin I Laufer
- Molecular Genetics Unit, Department of Biology, University of Western Ontario, London, ON Canada
| | - Shiva M Singh
- Molecular Genetics Unit, Department of Biology, University of Western Ontario, London, ON Canada
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45
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Abstract
New methods for epigenome editing now make it possible to manipulate the epigenome in living cells with unprecedented specificity and efficiency. These ground-breaking approaches are beginning to yield novel insights into the function of individual chromatin marks in the context of cellular phenotype.
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Affiliation(s)
- Anna Köeferle
- Medical Genomics, UCL Cancer Institute, University College London, 72 Huntley Street, London, WC1E 6BT UK
| | - Stefan H Stricker
- Functional Epigenetics, Institute of Stem Cell Research, Helmholtz Zentrum, German Research Center for Environmental Health, Ingolstädter Landstrasse 1, 85764 Neuherberg, Germany ; Biomedical Center, Ludwig-Maximilian-Universität, Grosshaderner Strasse 9, 82152 Planegg-Martinsried, Germany
| | - Stephan Beck
- Medical Genomics, UCL Cancer Institute, University College London, 72 Huntley Street, London, WC1E 6BT UK
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46
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Kungulovski G, Nunna S, Thomas M, Zanger UM, Reinhardt R, Jeltsch A. Targeted epigenome editing of an endogenous locus with chromatin modifiers is not stably maintained. Epigenetics Chromatin 2015; 8:12. [PMID: 25901185 PMCID: PMC4404288 DOI: 10.1186/s13072-015-0002-z] [Citation(s) in RCA: 69] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2015] [Accepted: 02/09/2015] [Indexed: 01/23/2023] Open
Abstract
Background DNA methylation and histone 3 lysine 9 (H3K9) methylation are considered as epigenetic marks that can be inherited through cell divisions. To explore the functional consequences and stability of these modifications, we employed targeted installment of DNA methylation and H3K9 methylation in the vascular endothelial growth factor A (VEGF-A) promoter using catalytic domains of DNA or H3K9 methyltransferases that are fused to a zinc finger protein which binds a site in the VEGF-A promoter. Results Expression of the targeted DNA and H3K9 methyltransferases caused dense deposition of DNA methylation or H3K9 di- and trimethylation in the promoter of VEGF-A and downregulation of VEGF-A gene expression. We did not observe positive feedback between DNA methylation and H3K9 methylation. Upon loss of the targeted methyltransferases from the cells, the epigenetic marks, chromatin environment, and gene expression levels returned to their original state, indicating that both methylation marks were not stably propagated after their installment. Conclusions The clear anti-correlation between DNA or H3K9 methylation and gene expression suggests a direct role of these marks in transcriptional control. The lack of maintenance of the transiently induced silenced chromatin state suggests that the stability of epigenetic signaling is based on an epigenetic network consisting of several molecular marks. Therefore, for stable reprogramming, either multivalent deposition of functionally related epigenetic marks or longer-lasting trigger stimuli might be necessary. Electronic supplementary material The online version of this article (doi:10.1186/s13072-015-0002-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Goran Kungulovski
- Institute of Biochemistry, Faculty of Chemistry, Stuttgart University, Pfaffenwaldring 55, 70569 Stuttgart, Germany
| | - Suneetha Nunna
- Institute of Biochemistry, Faculty of Chemistry, Stuttgart University, Pfaffenwaldring 55, 70569 Stuttgart, Germany
| | - Maria Thomas
- Dr. Margarete Fischer-Bosch Institute of Clinical Pharmacology, Auerbachstraße 112, 70376 Stuttgart, Germany.,University of Tübingen, Geschwister-Scholl-Platz, 72074 Tübingen, Germany
| | - Ulrich M Zanger
- Dr. Margarete Fischer-Bosch Institute of Clinical Pharmacology, Auerbachstraße 112, 70376 Stuttgart, Germany.,University of Tübingen, Geschwister-Scholl-Platz, 72074 Tübingen, Germany
| | - Richard Reinhardt
- Max-Planck-Genomzentrum Köln, Carl-von-Linné-Weg 10, 50829 Köln, Germany
| | - Albert Jeltsch
- Institute of Biochemistry, Faculty of Chemistry, Stuttgart University, Pfaffenwaldring 55, 70569 Stuttgart, Germany
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47
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Jurkowski TP, Ravichandran M, Stepper P. Synthetic epigenetics-towards intelligent control of epigenetic states and cell identity. Clin Epigenetics 2015; 7:18. [PMID: 25741388 PMCID: PMC4347971 DOI: 10.1186/s13148-015-0044-x] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2014] [Accepted: 01/12/2015] [Indexed: 01/14/2023] Open
Abstract
Epigenetics is currently one of the hottest topics in basic and biomedical research. However, to date, most of the studies have been descriptive in nature, designed to investigate static distribution of various epigenetic modifications in cells. Even though tremendous amount of information has been collected, we are still far from the complete understanding of epigenetic processes, their dynamics or even their direct effects on local chromatin and we still do not comprehend whether these epigenetic states are the cause or the consequence of the transcriptional profile of the cell. In this review, we try to define the concept of synthetic epigenetics and outline the available genome targeting technologies, which are used for locus-specific editing of epigenetic signals. We report early success stories and the lessons we have learned from them, and provide a guide for their application. Finally, we discuss existing limitations of the available technologies and indicate possible areas for further development.
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Affiliation(s)
- Tomasz P Jurkowski
- Laboratory of Molecular Epigenetics, Institute of Biochemistry, Faculty of Chemistry, University of Stuttgart, Pfaffenwaldring 55, D-70569 Stuttgart, Germany
| | - Mirunalini Ravichandran
- Laboratory of Molecular Epigenetics, Institute of Biochemistry, Faculty of Chemistry, University of Stuttgart, Pfaffenwaldring 55, D-70569 Stuttgart, Germany
| | - Peter Stepper
- Laboratory of Molecular Epigenetics, Institute of Biochemistry, Faculty of Chemistry, University of Stuttgart, Pfaffenwaldring 55, D-70569 Stuttgart, Germany
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48
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Stolzenburg S, Beltran AS, Swift-Scanlan T, Rivenbark AG, Rashwan R, Blancafort P. Stable oncogenic silencing in vivo by programmable and targeted de novo DNA methylation in breast cancer. Oncogene 2015; 34:5427-35. [PMID: 25684141 PMCID: PMC4633433 DOI: 10.1038/onc.2014.470] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2014] [Revised: 11/15/2014] [Accepted: 12/09/2014] [Indexed: 12/16/2022]
Abstract
With the recent comprehensive mapping of cancer genomes, there is now a need for functional approaches to edit the aberrant epigenetic state of key cancer drivers to reprogram the epi-pathology of the disease. In this study we utilized a programmable DNA-binding methyltransferase to induce targeted incorporation of DNA methylation (DNAme) in the SOX2 oncogene in breast cancer through a six zinc finger (ZF) protein linked to DNA methyltransferase 3A (ZF-DNMT3A). We demonstrated long-lasting oncogenic repression, which was maintained even after suppression of ZF-DNMT3A expression in tumor cells. The de novo DNAme was faithfully propagated and maintained through cell generations even after the suppression of the expression of the chimeric methyltransferase in the tumor cells. Xenograft studies in NUDE mice demonstrated stable SOX2 repression and long-term breast tumor growth inhibition, which lasted for >100 days post implantation of the tumor cells in mice. This was accompanied with a faithful maintenance of DNAme in the breast cancer implants. In contrast, downregulation of SOX2 by ZF domains engineered with the Krueppel-associated box repressor domain resulted in a transient and reversible suppression of oncogenic gene expression. Our results indicated that targeted de novo DNAme of the SOX2 oncogenic promoter was sufficient to induce long-lasting epigenetic silencing, which was not only maintained during cell division but also significantly delayed the tumorigenic phenotype of cancer cells in vivo, even in the absence of treatment. Here, we outline a genome-based targeting approach to long-lasting tumor growth inhibition with potential applicability to many other oncogenic drivers that are currently refractory to drug design.
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Affiliation(s)
- S Stolzenburg
- Cancer Epigenetics Group, The Harry Perkins Institute of Medical Research, Western Australia & School of Anatomy, Physiology and Human Biology, M309, The University of Western Australia, Nedlands, Western Australia, Australia.,Department of Pharmacology, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - A S Beltran
- Department of Pharmacology, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - T Swift-Scanlan
- Lineberger Comprehensive Cancer Center/School of Nursing, University of North Carolina, Chapel Hill, NC, USA
| | - A G Rivenbark
- Department of Pathology and Laboratory Medicine, University of North Carolina School of Medicine, Chapel Hill, NC, USA
| | - R Rashwan
- Cancer Epigenetics Group, The Harry Perkins Institute of Medical Research, Western Australia & School of Anatomy, Physiology and Human Biology, M309, The University of Western Australia, Nedlands, Western Australia, Australia
| | - P Blancafort
- Cancer Epigenetics Group, The Harry Perkins Institute of Medical Research, Western Australia & School of Anatomy, Physiology and Human Biology, M309, The University of Western Australia, Nedlands, Western Australia, Australia.,Department of Pharmacology, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
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49
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Abstract
As synthetic biology approaches are extended to diverse applications throughout medicine, biotechnology and basic biological research, there is an increasing need to engineer yeast, plant and mammalian cells. Eukaryotic genomes are regulated by the diverse biochemical and biophysical states of chromatin, which brings distinct challenges, as well as opportunities, over applications in bacteria. Recent synthetic approaches, including 'epigenome editing', have allowed the direct and functional dissection of many aspects of physiological chromatin regulation. These studies lay the foundation for biomedical and biotechnological engineering applications that could take advantage of the unique combinatorial and spatiotemporal layers of chromatin regulation to create synthetic systems of unprecedented sophistication.
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50
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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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