151
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Nakamura M, Gao Y, Dominguez AA, Qi LS. CRISPR technologies for precise epigenome editing. Nat Cell Biol 2021; 23:11-22. [PMID: 33420494 DOI: 10.1038/s41556-020-00620-7] [Citation(s) in RCA: 191] [Impact Index Per Article: 63.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Accepted: 11/30/2020] [Indexed: 01/29/2023]
Abstract
The epigenome involves a complex set of cellular processes governing genomic activity. Dissecting this complexity necessitates the development of tools capable of specifically manipulating these processes. The repurposing of prokaryotic CRISPR systems has allowed for the development of diverse technologies for epigenome engineering. Here, we review the state of currently achievable epigenetic manipulations along with corresponding applications. With future optimization, CRISPR-based epigenomic editing stands as a set of powerful tools for understanding and controlling biological function.
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Affiliation(s)
- Muneaki Nakamura
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Yuchen Gao
- Department of Bioengineering, Stanford University, Stanford, CA, USA.,Cancer Biology Program, Stanford University, Stanford, CA, USA.,Mammoth Biosciences, South San Francisco, CA, USA
| | - Antonia A Dominguez
- Department of Bioengineering, Stanford University, Stanford, CA, USA.,Sana Biotechnology, South San Francisco, CA, USA
| | - Lei S Qi
- Department of Bioengineering, Stanford University, Stanford, CA, USA. .,Department of Chemical and Systems Biology, Stanford University, Stanford, CA, USA. .,Stanford ChEM-H Institute, Stanford University, Stanford, CA, USA.
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152
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Kondrashov A, Karpova E. Notes on Functional Modules in the Assembly of CRISPR/Cas9-Mediated Epigenetic Modifiers. Methods Mol Biol 2021; 2198:401-428. [PMID: 32822047 DOI: 10.1007/978-1-0716-0876-0_30] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
CRISPR/cas9 is a popular tool, widely used today for genome editing. However, the modular organization of this tool allows it to be used not only for DNA modifications but also for introducing epigenetic modifications both in DNA (methylation/demethylation) and in histones (acetylation/deacetylation). In these notes we will concentrate on the ways to adapt the CRISPR/cas9 system for epigenetic DNA modification of specific regions of interest. The modular organization represents a universal principal, that allows to create infinite number of functions with a limited number of tools. CRISPR/cas9, in which each subunit can be adapted for a particular task, is an excellent example of this rule. Made of two main subunits, it can be modified for targeted delivery of foreign activity (effector, an epigenetic enzyme in our case) to a selected part of the genome. In doing this the CRISPR/cas9 system represents a unique method that allows the introduction of both genomic and epigenetic modifications. This chapter gives a detailed review of how to prepare DNA for the fully functional CRISPR/cas9 system, able to introduce required modifications in the region of interest. We will discuss specific requirements for each structural component of the system as well as for auxiliary elements (modules), which are needed to ensure efficient expression of the elements of the system within the cell and the needs of selection and visualization.
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Affiliation(s)
- Alexander Kondrashov
- Division of Cancer and Stem Cells, School of Medicine, University of Nottingham Biodiscovery Institute, Nottingham, UK.
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153
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Xu CF, Chen GJ, Luo YL, Zhang Y, Zhao G, Lu ZD, Czarna A, Gu Z, Wang J. Rational designs of in vivo CRISPR-Cas delivery systems. Adv Drug Deliv Rev 2021; 168:3-29. [PMID: 31759123 DOI: 10.1016/j.addr.2019.11.005] [Citation(s) in RCA: 98] [Impact Index Per Article: 32.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Revised: 11/09/2019] [Accepted: 11/19/2019] [Indexed: 02/08/2023]
Abstract
The CRISPR-Cas system initiated a revolution in genome editing when it was, for the first time, demonstrated success in the mammalian cells. Today, scientists are able to readily edit genomes, regulate gene transcription, engineer posttranscriptional events, and image nucleic acids using CRISPR-Cas-based tools. However, to efficiently transport CRISPR-Cas into target tissues/cells remains challenging due to many extra- and intra-cellular barriers, therefore largely limiting the applications of CRISPR-based therapeutics in vivo. In this review, we summarize the features of plasmid-, RNA- and ribonucleoprotein (RNP)-based CRISPR-Cas therapeutics. Then, we survey the current in vivo delivery systems. We specify the requirements for efficient in vivo delivery in clinical settings, and highlight both efficiency and safety for different CRISPR-Cas tools.
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154
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Anani M, Nobuhisa I, Taga T. Sry-related High Mobility Group Box 17 Functions as a Tumor Suppressor by Antagonizing the Wingless-related Integration Site Pathway. J Cancer Prev 2020; 25:204-212. [PMID: 33409253 PMCID: PMC7783240 DOI: 10.15430/jcp.2020.25.4.204] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2020] [Revised: 12/01/2020] [Accepted: 12/05/2020] [Indexed: 11/16/2022] Open
Abstract
A transcription factor Sry-related high mobility group box (Sox) 17 is involved in developmental processes including spermatogenesis, cardiovascular system, endoderm formation, and so on. In this article, we firstly review the studies on the relation between the Sox17 expression and tumor malignancy. Although Sox17 positively promotes various tissue development, most of the cancers associated with Sox17 show decreased expression levels of Sox17, and an inverse correlation between Sox17 expression and malignancy is revealed. We briefly discuss the mechanism of such Sox17 down-regulation by focusing on DNA methylation of CpG sites located in the Sox17 gene promoter. Next, we overview the function of Sox17 in the fetal hematopoiesis, particularly in the dorsal aorta in midgestation mouse embryos. The Sox17 expression in hematopoietic stem cell (HSC)-containing intra-aortic hematopoietic cell cluster (IAHCs) is important for the cluster formation with the hematopoietic ability. The sustained expression of Sox17 in adult bone marrow HSCs and the cells in IAHCs of the dorsal aorta indicate abnormalities that are low lymphocyte chimerism and the aberrant proliferation of common myeloid progenitors in transplantation experiments. We then summarize the perspectives of Sox17 research in cancer control.
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Affiliation(s)
- Maha Anani
- Department of Clinical Pathology, Faculty of Medicine, Suez Canal University, Ismailia, Egypt
| | - Ikuo Nobuhisa
- Department of Stem Cell Regulation, Medical Research Institute, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
| | - Tetsuya Taga
- Department of Stem Cell Regulation, Medical Research Institute, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
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155
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Design and construction of chimeric linker library with controllable flexibilities for precision protein engineering. Methods Enzymol 2020; 647:23-49. [PMID: 33482990 DOI: 10.1016/bs.mie.2020.12.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Linkers play essential roles in the engineering of fusion proteins, and have been extensively demonstrated to affect protein properties such as expression level, solubility, and biological functions. For linker design and optimization, one of the key factors is the flexibility or rigidity of linkers, which describes the tendency of a linker to maintain a stable conformation when expressed, and can directly contribute to the physical distance between domains of a fusion protein. In this chapter, we discuss the design and engineering of linkers in fusion proteins, and describe a library-based method for optimization of linker flexibility. This approach is based on chimeric linkers, which are composed of both flexible and rigid (helix-forming) linker motifs. We demonstrate that the chimeric linker library capable of controlling the flexibility in a wide range can fill the gap between flexible and rigid linkers by molecular dynamics simulation and fluorescence resonance energy transfer experiments, as well as its applications in fusion protein optimization.
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156
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157
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Ghoshal B, Vong B, Picard CL, Feng S, Tam JM, Jacobsen SE. A viral guide RNA delivery system for CRISPR-based transcriptional activation and heritable targeted DNA demethylation in Arabidopsis thaliana. PLoS Genet 2020; 16:e1008983. [PMID: 33315895 PMCID: PMC7769603 DOI: 10.1371/journal.pgen.1008983] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Revised: 12/28/2020] [Accepted: 11/02/2020] [Indexed: 01/01/2023] Open
Abstract
Plant RNA viruses are used as delivery vectors for their high level of accumulation and efficient spread during virus multiplication and movement. Utilizing this concept, several viral-based guide RNA delivery platforms for CRISPR-Cas9 genome editing have been developed. The CRISPR-Cas9 system has also been adapted for epigenome editing. While systems have been developed for CRISPR-Cas9 based gene activation or site-specific DNA demethylation, viral delivery of guide RNAs remains to be developed for these purposes. To address this gap we have developed a tobacco rattle virus (TRV)-based single guide RNA delivery system for epigenome editing in Arabidopsis thaliana. Because tRNA-like sequences have been shown to facilitate the cell-to-cell movement of RNAs in plants, we used the tRNA-guide RNA expression system to express guide RNAs from the viral genome to promote heritable epigenome editing. We demonstrate that the tRNA-gRNA system with TRV can be used for both transcriptional activation and targeted DNA demethylation of the FLOWERING WAGENINGEN gene in Arabidopsis. We achieved up to ~8% heritability of the induced demethylation phenotype in the progeny of virus inoculated plants. We did not detect the virus in the next generation, indicating effective clearance of the virus from plant tissues. Thus, TRV delivery, combined with a specific tRNA-gRNA architecture, provides for fast and effective epigenome editing.
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Affiliation(s)
- Basudev Ghoshal
- Department of Molecular, Cell and Developmental Biology, University of California at Los Angeles, Los Angeles, California, United States of America
| | - Brandon Vong
- Department of Molecular, Cell and Developmental Biology, University of California at Los Angeles, Los Angeles, California, United States of America
| | - Colette L. Picard
- Department of Molecular, Cell and Developmental Biology, University of California at Los Angeles, Los Angeles, California, United States of America
| | - Suhua Feng
- Department of Molecular, Cell and Developmental Biology, University of California at Los Angeles, Los Angeles, California, United States of America
- Eli and Edyth Broad Center of Regenerative Medicine and Stem Cell Research, University of California at Los Angeles, Los Angeles, California, United States of America
| | - Janet M. Tam
- Department of Molecular, Cell and Developmental Biology, University of California at Los Angeles, Los Angeles, California, United States of America
| | - Steven E. Jacobsen
- Department of Molecular, Cell and Developmental Biology, University of California at Los Angeles, Los Angeles, California, United States of America
- Eli and Edyth Broad Center of Regenerative Medicine and Stem Cell Research, University of California at Los Angeles, Los Angeles, California, United States of America
- Howard Hughes Medical Institute, University of California at Los Angeles, Los Angeles, California, United States of America
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158
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Kuscu C, Kuscu C, Bajwa A, Eason JD, Maluf D, Mas VR. Applications of CRISPR technologies in transplantation. Am J Transplant 2020; 20:3285-3293. [PMID: 32484284 PMCID: PMC8109183 DOI: 10.1111/ajt.16095] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Revised: 04/22/2020] [Accepted: 05/19/2020] [Indexed: 01/25/2023]
Abstract
In transplantation, the ever-increasing number of an organ's demand and long-term graft dysfunction constitute some of the major problems. Therefore, alternative solutions to increase the quantity and quality of the organ supply for transplantation are desired. On this subject, revolutionary Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) technology holds enormous potential for the scientific community with its expanding toolbox. In this minireview, we summarize the history and mechanism of CRISPR/Cas9 systems and explore its potential applications in cellular- and organ-level transplantation. The last part of this review includes future opportunities as well as the challenges in the transplantation field.
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Affiliation(s)
- Cem Kuscu
- Transplant Research Institute, James D. Eason Transplant Institute, Department of Surgery, School of Medicine, University of Tennessee Health Science Center, Memphis, TN
| | - Canan Kuscu
- Transplant Research Institute, James D. Eason Transplant Institute, Department of Surgery, School of Medicine, University of Tennessee Health Science Center, Memphis, TN
| | - Amandeep Bajwa
- Transplant Research Institute, James D. Eason Transplant Institute, Department of Surgery, School of Medicine, University of Tennessee Health Science Center, Memphis, TN
| | - James D. Eason
- Transplant Research Institute, James D. Eason Transplant Institute, Department of Surgery, School of Medicine, University of Tennessee Health Science Center, Memphis, TN
| | - Daniel Maluf
- Transplant Research Institute, James D. Eason Transplant Institute, Department of Surgery, School of Medicine, University of Tennessee Health Science Center, Memphis, TN
| | - Valeria R. Mas
- Transplant Research Institute, James D. Eason Transplant Institute, Department of Surgery, School of Medicine, University of Tennessee Health Science Center, Memphis, TN
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159
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Maroufi F, Maali A, Abdollahpour-Alitappeh M, Ahmadi MH, Azad M. CRISPR-mediated modification of DNA methylation pattern in the new era of cancer therapy. Epigenomics 2020; 12:1845-1859. [PMID: 33185489 DOI: 10.2217/epi-2020-0110] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
In the last 2 decades, a wide variety of studies have been conducted on epigenetics and its role in various cancers. A major mechanism of epigenetic regulation is DNA methylation, including aberrant DNA methylation variations such as hypermethylation and hypomethylation in the promoters of critical genes, which are commonly detected in tumors and mark the early stages of cancer development. Therefore, epigenetic therapy has been of special importance in the last decade for cancer treatment. In epigenetic therapy, all efforts are made to modulate gene expression to the normal status. Importantly, recent studies have shown that epigenetic therapy is focusing on the new gene editing technology, CRISPR-Cas9. This tool was found to be able to effectively modulate gene expression and alter almost any sequence in the genome of cells, resulting in events such as a change in acetylation, methylation, or histone modifications. Of note, the CRISPR-Cas9 system can be used for the treatment of cancers caused by epigenetic alterations. The CRISPR-Cas9 system has greater advantages than other available methods, including potent activity, easy design and high velocity as well as the ability to target any DNA or RNA site. In this review, we described epigenetic modulators, which can be used in the CRISPR-Cas9 system, as well as their functions in gene expression alterations that lead to cancer initiation and progression. In addition, we surveyed various species of CRISPR-dead Cas9 (dCas9) systems, a mutant version of Cas9 with no endonuclease activity. Such systems are applicable in epigenetic therapy for gene expression modulation through chemical group editing on nucleosomes and chromatin remodeling, which finally return the cell to the normal status and prevent cancer progression.
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Affiliation(s)
- Faezeh Maroufi
- Department of Medical Laboratory Sciences, Faculty of Allied Medicine, Qazvin University of Medical Sciences, Qazvin, Iran
| | - Amirhosein Maali
- Student Research Committee, Pasteur institute of Iran, Tehran, Iran.,Department of Medical Biotechnology, Faculty of Allied Medicine, Qazvin University of Medical Sciences, Qazvin, Iran
| | | | - Mohammad Hossein Ahmadi
- Department of Medical Laboratory Sciences, Faculty of Allied Medicine, Qazvin University of Medical Sciences, Qazvin, Iran
| | - Mehdi Azad
- Department of Medical Laboratory Sciences, Faculty of Allied Medicine, Qazvin University of Medical Sciences, Qazvin, Iran
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160
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Dong Z, Dai L, Zhang Y, Fang C, Shi G, Chen Y, Li J, Wang Q, Fu J, Yu Y, Wang W, Cheng L, Liu Y, Lin Y, Wang Y, Wang Q, Wang H, Zhang H, Zhang Y, Su X, Zhang S, Wang F, Qiu M, Zhou Z, Deng H. Hypomethylation of GDNF family receptor alpha 1 promotes epithelial-mesenchymal transition and predicts metastasis of colorectal cancer. PLoS Genet 2020; 16:e1009159. [PMID: 33175846 PMCID: PMC7682896 DOI: 10.1371/journal.pgen.1009159] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Revised: 11/23/2020] [Accepted: 09/28/2020] [Indexed: 02/05/2023] Open
Abstract
Tumor metastasis is the major cause of poor prognosis and mortality in colorectal cancer (CRC). However, early diagnosis of highly metastatic CRC is currently difficult. In the present study, we screened for a novel biomarker, GDNF family receptor alpha 1 (GFRA1) based on the expression and methylation data in CRC patients from The Cancer Genome Altlas (TCGA), followed by further analysis of the correlation between the GFRA1 expression, methylation, and prognosis of patients. Our results show DNA hypomethylation-mediated upregulation of GFRA1 in invasive CRC, and it was found to be correlated with poor prognosis of CRC patients. Furthermore, GFRA1 methylation-modified sequences were found to have potential as methylation diagnostic markers of highly metastatic CRC. The targeted demethylation of GFRA1 by dCas9-TET1CD and gRNA promoted CRC metastasis in vivo and in vitro. Mechanistically, demethylation of GFRA1 induces epithelial-mesenchymal transition (EMT) by promoting AKT phosphorylation and increasing c-Jun expression in CRC cells. Collectively, our findings indicate that GFRA1 hypomethylation can promote CRC invasion via inducing EMT, and thus, GFRA1 methylation can be used as a biomarker for the early diagnosis of highly metastasis CRC. Abnormal DNA methylation, one of important characteristics in tumor cells, is exploited as biomarkers for cancer diagnosis and prognosis prediction. Early diagnosis of highly metastatic CRC will be helpful for the clinical management, thus prolongs patient survival. However, it is currently difficult to make early diagnosis of highly metastatic CRC in clinical practice. Currently, we screened a novel biomarker gene, GFRA1, which associated with the invasion and poor prognosis of CRC. The targeted demethylation of GFRA1 exerted a significant promoting effect on CRC metastasis, and GFRA1 methylation-modified sequences are valuable diagnostic biomarker for CRC metastasis risk assessment. Mechanically, demethylation of GFRA1 induced epithelial-mesenchymal transition (EMT) by upregulating AKT phosphorylation and c-Jun expression in CRC cells. Our results demonstrate the promoting effect of GFRA1 demethylation on CRC invasion and GFRA1 methylation may be a potential prognostic marker for predicting metastasis of CRC.
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Affiliation(s)
- Zhexu Dong
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, Sichuan, the People’s Republic of China
| | - Lei Dai
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, Sichuan, the People’s Republic of China
| | - Yong Zhang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, Sichuan, the People’s Republic of China
| | - Chao Fang
- Department of Gastrointestinal Surgery, West China Hospital and State Key Laboratory of Biotherapy, Sichuan University, Chengdu, Sichuan, the People’s Republic of China
| | - Gang Shi
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, Sichuan, the People’s Republic of China
| | - Ye Chen
- Department of Medical Oncology, Cancer Center, the State Key Laboratory of Biotherapy, West China Hospital, West China Medical School, Sichuan University, Chengdu, Sichuan, the People’s Republic of China
| | - Junshu Li
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, Sichuan, the People’s Republic of China
| | - Qin Wang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, Sichuan, the People’s Republic of China
| | - Jiamei Fu
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, Sichuan, the People’s Republic of China
| | - Yan Yu
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, Sichuan, the People’s Republic of China
| | - Wenshuang Wang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, Sichuan, the People’s Republic of China
| | - Lin Cheng
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, Sichuan, the People’s Republic of China
| | - Yi Liu
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, Sichuan, the People’s Republic of China
| | - Yi Lin
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, Sichuan, the People’s Republic of China
| | - Yuan Wang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, Sichuan, the People’s Republic of China
| | - Qingnan Wang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, Sichuan, the People’s Republic of China
| | - Huiling Wang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, Sichuan, the People’s Republic of China
| | - Hantao Zhang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, Sichuan, the People’s Republic of China
| | - Yujing Zhang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, Sichuan, the People’s Republic of China
| | - Xiaolan Su
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, Sichuan, the People’s Republic of China
| | - Shuang Zhang
- Department of biotherapy, Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, Sichuan, the People’s Republic of China
| | - Feng Wang
- Department of Medical Oncology, Cancer Center, the State Key Laboratory of Biotherapy, West China Hospital, West China Medical School, Sichuan University, Chengdu, Sichuan, the People’s Republic of China
- Department of Critical Care Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan, the People’s Republic of China
| | - Meng Qiu
- Department of Medical Oncology, Cancer Center, the State Key Laboratory of Biotherapy, West China Hospital, West China Medical School, Sichuan University, Chengdu, Sichuan, the People’s Republic of China
| | - Zongguang Zhou
- Department of Gastrointestinal Surgery, West China Hospital and State Key Laboratory of Biotherapy, Sichuan University, Chengdu, Sichuan, the People’s Republic of China
| | - Hongxin Deng
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, Sichuan, the People’s Republic of China
- * E-mail:
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161
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Nohara K, Suzuki T, Okamura K. Gestational arsenic exposure and paternal intergenerational epigenetic inheritance. Toxicol Appl Pharmacol 2020; 409:115319. [PMID: 33160984 DOI: 10.1016/j.taap.2020.115319] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2020] [Revised: 10/22/2020] [Accepted: 11/01/2020] [Indexed: 02/09/2023]
Abstract
A growing body of evidence has shown that gestational exposure to environmental factors such as imbalanced diet, environmental chemicals, and stress can lead to late-onset health effects in offspring and that some of these effects are heritable by the next generation and subsequent generations. Furthermore, altered epigenetic modifications in DNA methylation, histone modifications and small RNAs in a single sperm genome have been shown to transmit disease phenotypes acquired from the environment to later generations. Recently, our group found that gestational exposure of F0 pregnant dams to an inorganic arsenic, sodium arsenite, increases the incidence of hepatic tumors in male F2 mice, and the effects are paternally transmitted to the F2. Here, we first overview the epigenetic changes involved in paternal intergenerational and transgenerational inheritance caused by exposure to environmental factors. Then, we discuss our recent studies regarding paternal inheritance of the tumor-augmenting effects in F2 mice by gestational arsenite exposure, in which we investigated alterations of DNA methylation status in F2 tumors and causative F1 sperm. We also discuss the possible targets of the F2 effects. Finally, we discuss future perspectives on the studies that are needed to fully understand the health effects of arsenic exposure.
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Affiliation(s)
- Keiko Nohara
- Center for Health and Environmental Risk Research, National Institute for Environmental Studies, Tsukuba 305-8506, Japan.
| | - Takehiro Suzuki
- Center for Health and Environmental Risk Research, National Institute for Environmental Studies, Tsukuba 305-8506, Japan
| | - Kazuyuki Okamura
- Center for Health and Environmental Risk Research, National Institute for Environmental Studies, Tsukuba 305-8506, Japan
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162
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Weinguny M, Eisenhut P, Klanert G, Virgolini N, Marx N, Jonsson A, Ivansson D, Lövgren A, Borth N. Random epigenetic modulation of CHO cells by repeated knockdown of DNA methyltransferases increases population diversity and enables sorting of cells with higher production capacities. Biotechnol Bioeng 2020; 117:3435-3447. [PMID: 32662873 PMCID: PMC7818401 DOI: 10.1002/bit.27493] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Revised: 05/25/2020] [Accepted: 07/12/2020] [Indexed: 12/15/2022]
Abstract
Chinese hamster ovary (CHO) cells produce a large share of today's biopharmaceuticals. Still, the generation of satisfactory producer cell lines is a tedious undertaking. Recently, it was found that CHO cells, when exposed to new environmental conditions, modify their epigenome, suggesting that cells adapt their gene expression pattern to handle new challenges. The major aim of the present study was to employ artificially induced, random changes in the DNA-methylation pattern of CHO cells to diversify cell populations and consequently increase the finding of cell lines with improved cellular characteristics. To achieve this, DNA methyltransferases and/or the ten-eleven translocation enzymes were downregulated by RNA interference over a time span of ∼16 days. Methylation analysis of the resulting cell pools revealed that the knockdown of DNA methyltransferases was highly effective in randomly demethylating the genome. The same approach, when applied to stable CHO producer cells resulted in (a) an increased productivity diversity in the cell population, and (b) a higher number of outliers within the population, which resulted in higher specific productivity and titer in the sorted cells. These findings suggest that epigenetics play a previously underestimated, but actually important role in defining the overall cellular behavior of production clones.
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Affiliation(s)
- Marcus Weinguny
- ACIB—Austrian Centre of Industrial BiotechnologyGrazAustria,Department of BiotechnologyUniversity of Natural Resources and Life SciencesViennaAustria
| | - Peter Eisenhut
- ACIB—Austrian Centre of Industrial BiotechnologyGrazAustria,Department of BiotechnologyUniversity of Natural Resources and Life SciencesViennaAustria
| | - Gerald Klanert
- ACIB—Austrian Centre of Industrial BiotechnologyGrazAustria
| | | | - Nicolas Marx
- ACIB—Austrian Centre of Industrial BiotechnologyGrazAustria,Department of BiotechnologyUniversity of Natural Resources and Life SciencesViennaAustria
| | | | | | | | - Nicole Borth
- ACIB—Austrian Centre of Industrial BiotechnologyGrazAustria,Department of BiotechnologyUniversity of Natural Resources and Life SciencesViennaAustria
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163
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Neja SA. Site-Specific DNA Demethylation as a Potential Target for Cancer Epigenetic Therapy. Epigenet Insights 2020; 13:2516865720964808. [PMID: 35036833 PMCID: PMC8756105 DOI: 10.1177/2516865720964808] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2020] [Accepted: 09/13/2020] [Indexed: 12/13/2022] Open
Abstract
Aberrant promoter DNA hypermethylation is a typical characteristic of cancer and it is often seen in malignancies. Recent studies showed that regulatory cis-elements found up-stream of many tumor suppressor gene promoter CpG island (CGI) attract DNA methyltransferases (DNMT) that hypermethylates and silence the genes. As epigenetic alterations are potentially reversible, they make attractive targets for therapeutic intervention. The currently used decitabine (DAC) and azacitidine (AZA) are DNMT inhibitors that follow the passive demethylation pathway. However, they lead to genome-wide demethylation of CpGs in cells, which makes difficult to use it for causal effect analysis and treatment of specific epimutations. Demethylation through specific demethylase enzymes is thus critical for epigenetic resetting of silenced genes and modified chromatins. Yet DNA-binding factors likely play a major role to guide the candidate demethylase enzymes upon its fusion. Before the advent of clustered regulatory interspaced short palindromic repeats (CRISPR), both zinc finger proteins (ZNFs) and transcription activator-like effector protein (TALEs) were used as binding platforms for ten-eleven translocation (TET) enzymes and both systems were able to induce transcription at targeted loci in an in vitro as well as in vivo model. Consequently, the development of site-specific and active demethylation molecular trackers becomes more than hypothetical to makes a big difference in the treatment of cancer in the future. This review is thus to recap the novel albeit distinct studies on the potential use of site-specific demethylation for the development of epigenetic based cancer therapy.
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164
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Wang J, Yang J, Li D, Li J. Technologies for targeting DNA methylation modifications: Basic mechanism and potential application in cancer. Biochim Biophys Acta Rev Cancer 2020; 1875:188454. [PMID: 33075468 DOI: 10.1016/j.bbcan.2020.188454] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Revised: 09/14/2020] [Accepted: 10/14/2020] [Indexed: 02/07/2023]
Abstract
DNA methylation abnormalities are regarded as critical event for cancer initiation and development. Tumor-associated genes encompassing aberrant DNA methylation alterations at specific locus are correlated with chromatin remodeling and dysregulation of gene expression in various malignancies. Thus, technologies designed to manipulate DNA methylation at specific loci of genome are necessary for the functional study and therapeutic application in the context of cancer management. Traditionally, the method for DNA methylation modifications demonstrates an unspecific feature, adversely causing global-genome epigenetic alterations and confusing the function of desired gene. Novel approaches for targeted DNA methylation regulation have a great advantage of manipulating gene epigenetic alterations in a more specific and efficient method. In this review, we described different targeting DNA methylation techniques, including both their advantages and limitations. Through a comprehensive understanding of these targeting tools, we hope to open a new perspective for cancer treatment.
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Affiliation(s)
- Jie Wang
- National Center for Clinical Laboratories, Beijing Hospital, National Center of Gerontology; Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, P.R. China; Graduate School of Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, P.R. China; Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, P.R. China
| | - Jing Yang
- National Center for Clinical Laboratories, Beijing Hospital, National Center of Gerontology; Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, P.R. China; Graduate School of Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, P.R. China; Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, P.R. China
| | - Dandan Li
- National Center for Clinical Laboratories, Beijing Hospital, National Center of Gerontology; Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, P.R. China; Graduate School of Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, P.R. China; Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, P.R. China
| | - Jinming Li
- National Center for Clinical Laboratories, Beijing Hospital, National Center of Gerontology; Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, P.R. China; Graduate School of Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, P.R. China; Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, P.R. China.
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165
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Mo J, Chen Z, Qin S, Li S, Liu C, Zhang L, Ran R, Kong Y, Wang F, Liu S, Zhou Y, Zhang X, Weng X, Zhou X. TRADES: Targeted RNA Demethylation by SunTag System. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2020; 7:2001402. [PMID: 33042753 PMCID: PMC7539198 DOI: 10.1002/advs.202001402] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Revised: 07/15/2020] [Indexed: 05/04/2023]
Abstract
N6-methyladenosine (m6A) is rapidly being studied and uncovered to play a significant role in various biological processes as well as in RNA fate and functions, while the effects of defined m6A sites are rarely characterized for the lack of convenient tools. To provide an applicable method to remove m6A modification at specific loci, an m6A editing system called "targeted RNA demethylation by SunTag system (TRADES)" is engineered. In this system, the targeting element dCas13b is fused to ten copies of GCN4 peptides which can recruit multiple scFv-fusion RNA demethylase to demethylate the target m6A site. Owing to this design, TRADES is more flexible to the indistinct m6A sites for its wide editing window. By site-specific demethylation of messenger RNA (mRNA) SON A2699, the lifetime of SON RNA is successfully prolonged in HeLa cells. Meanwhile, TRADES negligibly influences the lifetime of other non-targeted transcripts. TRADES also can regulate the gene expression of target transcript in an m6A-dependent manner. Moreover, the interference occuring for HBV and HIV replications demonstrates that the TRADES system holds potential in viral life cycle regulation and clinical applications.
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Affiliation(s)
- Jing Mo
- College of Chemistry and Molecular SciencesWuhan UniversityWuhan430072China
| | - Zonggui Chen
- The Institute for Advanced StudiesCollege of Life SciencesState Key Laboratory of VirologyWuhan UniversityWuhan430072China
- State Key Laboratory of Freshwater Ecology and BiotechnologyInstitute of HydrobiologyInnovation Academy for Seed DesignChinese Academy of SciencesWuhan430072China
| | - Shanshan Qin
- College of Chemistry and Molecular SciencesWuhan UniversityWuhan430072China
| | - Shu Li
- State Key Laboratory of Virology and Hubei Province Key Laboratory of Allergy and Immunology and Department of ImmunologySchool of MedicineWuhan UniversityWuhan430071China
| | - Chuangang Liu
- State Key Laboratory of Virology and Hubei Province Key Laboratory of Allergy and Immunology and Department of ImmunologySchool of MedicineWuhan UniversityWuhan430071China
| | - Lu Zhang
- State Key Laboratory of Virology and Hubei Province Key Laboratory of Allergy and Immunology and Department of ImmunologySchool of MedicineWuhan UniversityWuhan430071China
| | - Ruoxi Ran
- Department of Clinical LaboratoryCenter for Gene Diagnosis and Program of Clinical LaboratoryZhongnan HospitalWuhan UniversityWuhan430071China
| | - Ying Kong
- State Key Laboratory of Virology and Hubei Province Key Laboratory of Allergy and Immunology and Department of ImmunologySchool of MedicineWuhan UniversityWuhan430071China
| | - Fang Wang
- School of Pharmaceutical SciencesWuhan UniversityWuhan430071China
| | - Songmei Liu
- Department of Clinical LaboratoryCenter for Gene Diagnosis and Program of Clinical LaboratoryZhongnan HospitalWuhan UniversityWuhan430071China
| | - Yu Zhou
- The Institute for Advanced StudiesCollege of Life SciencesState Key Laboratory of VirologyWuhan UniversityWuhan430072China
| | - Xiaolian Zhang
- State Key Laboratory of Virology and Hubei Province Key Laboratory of Allergy and Immunology and Department of ImmunologySchool of MedicineWuhan UniversityWuhan430071China
| | - Xiaocheng Weng
- College of Chemistry and Molecular SciencesWuhan UniversityWuhan430072China
| | - Xiang Zhou
- College of Chemistry and Molecular SciencesWuhan UniversityWuhan430072China
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166
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Suzuki S, Diaz VD, Hermann BP. What has single-cell RNA-seq taught us about mammalian spermatogenesis? Biol Reprod 2020; 101:617-634. [PMID: 31077285 DOI: 10.1093/biolre/ioz088] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2019] [Accepted: 05/09/2019] [Indexed: 12/18/2022] Open
Abstract
Mammalian spermatogenesis is a complex developmental program that transforms mitotic testicular germ cells (spermatogonia) into mature male gametes (sperm) for production of offspring. For decades, it has been known that this several-weeks-long process involves a series of highly ordered and morphologically recognizable cellular changes as spermatogonia proliferate, spermatocytes undertake meiosis, and spermatids develop condensed nuclei, acrosomes, and flagella. Yet, much of the underlying molecular logic driving these processes has remained opaque because conventional characterization strategies often aggregated groups of cells to meet technical requirements or due to limited capability for cell selection. Recently, a cornucopia of single-cell transcriptome studies has begun to lift the veil on the full compendium of gene expression phenotypes and changes underlying spermatogenic development. These datasets have revealed the previously obscured molecular heterogeneity among and between varied spermatogenic cell types and are reinvigorating investigation of testicular biology. This review describes the extent of available single-cell RNA-seq profiles of spermatogenic and testicular somatic cells, how those data were produced and evaluated, their present value for advancing knowledge of spermatogenesis, and their potential future utility at both the benchtop and bedside.
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Affiliation(s)
- Shinnosuke Suzuki
- Department of Biology, University of Texas at San Antonio, San Antonio, Texas
| | - Victoria D Diaz
- Department of Biology, University of Texas at San Antonio, San Antonio, Texas
| | - Brian P Hermann
- Department of Biology, University of Texas at San Antonio, San Antonio, Texas
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167
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Beyer JN, Raniszewski NR, Burslem GM. Advances and Opportunities in Epigenetic Chemical Biology. Chembiochem 2020; 22:17-42. [PMID: 32786101 DOI: 10.1002/cbic.202000459] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Revised: 08/10/2020] [Indexed: 12/13/2022]
Abstract
The study of epigenetics has greatly benefited from the development and application of various chemical biology approaches. In this review, we highlight the key targets for modulation and recent methods developed to enact such modulation. We discuss various chemical biology techniques to study DNA methylation and the post-translational modification of histones as well as their effect on gene expression. Additionally, we address the wealth of protein synthesis approaches to yield histones and nucleosomes bearing epigenetic modifications. Throughout, we highlight targets that present opportunities for the chemical biology community, as well as exciting new approaches that will provide additional insight into the roles of epigenetic marks.
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Affiliation(s)
- Jenna N Beyer
- Department of Biochemistry and Biophysics Perelman School of Medicine, University of Pennsylvania, 422 Curie Blvd., Philadelphia, PA 19104, USA
| | - Nicole R Raniszewski
- Department of Biochemistry and Biophysics Perelman School of Medicine, University of Pennsylvania, 422 Curie Blvd., Philadelphia, PA 19104, USA
| | - George M Burslem
- Department of Biochemistry and Biophysics Perelman School of Medicine, University of Pennsylvania, 422 Curie Blvd., Philadelphia, PA 19104, USA.,Department of Cancer Biology and Epigenetics Institute Perelman School of Medicine, University of Pennsylvania, 422 Curie Blvd., Philadelphia, PA 19104, USA
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168
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Schrauben M, Dempster E, Lunnon K. Applying gene-editing technology to elucidate the functional consequence of genetic and epigenetic variation in Alzheimer's disease. Brain Pathol 2020; 30:992-1004. [PMID: 32654206 PMCID: PMC8018012 DOI: 10.1111/bpa.12881] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Accepted: 04/05/2020] [Indexed: 12/15/2022] Open
Abstract
Recent studies have highlighted a potential role of genetic and epigenetic variation in the development of Alzheimer's disease. Application of the CRISPR-Cas genome-editing platform has enabled investigation of the functional impact that Alzheimer's disease-associated gene mutations have on gene expression. Moreover, recent advances in the technology have led to the generation of CRISPR-Cas-based tools that allow for high-throughput interrogation of different risk variants to elucidate the interplay between genomic regulatory features, epigenetic modifications, and chromatin structure. In this review, we examine the various iterations of the CRISPR-Cas system and their potential application for exploring the complex interactions and disruptions in gene regulatory circuits that contribute to Alzheimer's disease.
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Affiliation(s)
| | - Emma Dempster
- University of Exeter Medical SchoolExeter UniversityExeterUK
| | - Katie Lunnon
- University of Exeter Medical SchoolExeter UniversityExeterUK
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169
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Liu S, Zheng Y, Zhang Y, Zhang J, Xie F, Guo S, Gu J, Yang J, Zheng P, Lai J, Yin L, Wang H. Methylation-mediated LINC00261 suppresses pancreatic cancer progression by epigenetically inhibiting c-Myc transcription. Theranostics 2020; 10:10634-10651. [PMID: 32929371 PMCID: PMC7482811 DOI: 10.7150/thno.44278] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2020] [Accepted: 08/09/2020] [Indexed: 02/07/2023] Open
Abstract
Background: Due to the limitations of strategies for its early diagnosis and treatment, pancreatic cancer (PC) remains a substantial human health threat. We previously discovered a methylation-mediated lncRNA, LINC00261, which is downregulated in PC tissues. However, the underlying role of LINC00261 in PC remains largely unknown. Methods: Quantitative real-time PCR and in situ hybridization were performed to evaluate the expression levels of LINC00261 in PC, adjacent nontumor and normal pancreas tissues. The clinical significance of LINC00261 was assessed in multicenter PC samples. The functions of LINC00261 in PC were investigated by gain- and loss-of-function assays in vitro and in vivo. Potential downstream pathways and mechanisms were explored via RNA sequencing and bioinformatic analyses. RNA immunoprecipitation and chromatin immunoprecipitation assays were used to validate the underlying mechanisms. Pyrosequencing and targeted demethylation of the LINC00261 promoter were performed to explore the upstream epigenetic mechanisms and therapeutic potential. Results: LINC00261 was significantly downregulated in PC tissues, and its expression was positively associated with the prognosis of PC patients. Phenotypic studies indicated that LINC00261 overexpression significantly suppressed PC cell proliferation, migration and metastasis in vitro and in vivo. c-Myc was identified as a downstream target of LINC00261. LINC00261 repressed c-Myc transcription by physically interacting and binding with the bromo domain of p300/CBP, preventing the recruitment of p300/CBP to the promoter region of c-Myc and decreasing the H3K27Ac level. Moreover, the methylation level of the LINC00261 promoter was high in PC tissues and was correlated with poor prognosis. Targeted demethylation of the LINC00261 promoter inhibited PC progression both in vitro and in vivo. Conclusions: Our findings indicate that methylation-mediated LINC00261 suppresses PC progression by epigenetically repressing c-Myc expression. These findings expand the therapeutic potential of LINC00261, possibly providing evidence to support the development of epigenetic drugs or therapeutic strategies. This research adds further insights into the etiology of PC and indicates that LINC00261 may be a prognostic and therapeutic target in PC.
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MESH Headings
- Aged
- Animals
- Apoptosis/genetics
- Carcinoma, Pancreatic Ductal/genetics
- Carcinoma, Pancreatic Ductal/mortality
- Carcinoma, Pancreatic Ductal/pathology
- Carcinoma, Pancreatic Ductal/surgery
- Cell Line, Tumor
- Cell Movement/genetics
- Cell Proliferation/genetics
- DNA Methylation
- Disease Progression
- Disease-Free Survival
- Down-Regulation
- Epigenesis, Genetic
- Epithelial-Mesenchymal Transition/genetics
- Female
- Follow-Up Studies
- Gene Expression Regulation, Neoplastic
- Histones/genetics
- Humans
- Male
- Mice
- Middle Aged
- Pancreas/pathology
- Pancreas/surgery
- Pancreatectomy
- Pancreatic Neoplasms/genetics
- Pancreatic Neoplasms/mortality
- Pancreatic Neoplasms/pathology
- Pancreatic Neoplasms/surgery
- Prognosis
- Promoter Regions, Genetic/genetics
- Proto-Oncogene Proteins c-myc/genetics
- RNA, Long Noncoding/genetics
- RNA, Long Noncoding/metabolism
- RNA-Seq
- Transcription, Genetic
- Xenograft Model Antitumor Assays
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Affiliation(s)
- Songsong Liu
- Institute of Hepatopancreatobiliary Surgery, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, P. R. China
| | - Yao Zheng
- Institute of Hepatopancreatobiliary Surgery, Chongqing General Hospital, University of Chinese Academy of Sciences, Chongqing, P. R. China
| | - Yujun Zhang
- Institute of Hepatopancreatobiliary Surgery, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, P. R. China
| | - Junfeng Zhang
- Institute of Hepatopancreatobiliary Surgery, Chongqing General Hospital, University of Chinese Academy of Sciences, Chongqing, P. R. China
| | - Fuming Xie
- Institute of Hepatopancreatobiliary Surgery, Chongqing General Hospital, University of Chinese Academy of Sciences, Chongqing, P. R. China
| | - Shixiang Guo
- Institute of Hepatopancreatobiliary Surgery, Chongqing General Hospital, University of Chinese Academy of Sciences, Chongqing, P. R. China
| | - Jianyou Gu
- Department of First Hepatobiliary Surgery, Zhujiang Hospital, Southern Medical University, Guangzhou, Guangdong, P. R. China
| | - Jiali Yang
- Institute of Hepatopancreatobiliary Surgery, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, P. R. China
| | - Ping Zheng
- Institute of Hepatopancreatobiliary Surgery, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, P. R. China
| | - Jiejuan Lai
- Institute of Hepatopancreatobiliary Surgery, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, P. R. China
| | - Liangyu Yin
- Institute of Hepatopancreatobiliary Surgery, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, P. R. China
- Department of Clinical Nutrition, Daping Hospital, Third Military Medical University (Army Medical University), Chongqing, P. R. China
| | - Huaizhi Wang
- Institute of Hepatopancreatobiliary Surgery, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, P. R. China
- Institute of Hepatopancreatobiliary Surgery, Chongqing General Hospital, University of Chinese Academy of Sciences, Chongqing, P. R. China
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170
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Weichenhan D, Lipka DB, Lutsik P, Goyal A, Plass C. Epigenomic technologies for precision oncology. Semin Cancer Biol 2020; 84:60-68. [PMID: 32822861 DOI: 10.1016/j.semcancer.2020.08.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Revised: 07/28/2020] [Accepted: 08/03/2020] [Indexed: 12/15/2022]
Abstract
Epigenetic patterns in a cell control the expression of genes and consequently determine the phenotype of a cell. Cancer cells possess altered epigenomes which include aberrant patterns of DNA methylation, histone tail modifications, nucleosome positioning and of the three-dimensional chromatin organization within a nucleus. These altered epigenetic patterns are potential useful biomarkers to detect cancer cells and to classify tumor types. In addition, the cancer epigenome dictates the response of a cancer cell to therapeutic intervention and, therefore its knowledge, will allow to predict response to different therapeutic approaches. Here we review the current state-of-the-art technologies that have been developed to decipher epigenetic patterns on the genomic level and discuss how these methods are potentially useful for precision oncology.
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Affiliation(s)
- Dieter Weichenhan
- German Cancer Research Center Heidelberg, Cancer Epigenomics (B370), Im Neuenheimer Feld 280, D-69120, Heidelberg, Germany.
| | - Daniel B Lipka
- Section of Translational Cancer Epigenomics, Division of Translational Medical Oncology, National Center for Tumor Diseases Heidelberg & German Cancer Research Center, Im Neuenheimer Feld 581, D-69120, Heidelberg, Germany; Faculty of Medicine, Medical Center, Otto-von-Guericke-University, Leipziger Straße 44, D-39120, Magdeburg, Germany.
| | - Pavlo Lutsik
- German Cancer Research Center Heidelberg, Cancer Epigenomics (B370), Im Neuenheimer Feld 280, D-69120, Heidelberg, Germany.
| | - Ashish Goyal
- German Cancer Research Center Heidelberg, Cancer Epigenomics (B370), Im Neuenheimer Feld 280, D-69120, Heidelberg, Germany.
| | - Christoph Plass
- German Cancer Research Center Heidelberg, Cancer Epigenomics (B370), Im Neuenheimer Feld 280, D-69120, Heidelberg, Germany.
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171
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Li J, Chen Z, Chen F, Xie G, Ling Y, Peng Y, Lin Y, Luo N, Chiang CM, Wang H. Targeted mRNA demethylation using an engineered dCas13b-ALKBH5 fusion protein. Nucleic Acids Res 2020; 48:5684-5694. [PMID: 32356894 PMCID: PMC7261189 DOI: 10.1093/nar/gkaa269] [Citation(s) in RCA: 146] [Impact Index Per Article: 36.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Revised: 04/01/2020] [Accepted: 04/08/2020] [Indexed: 12/14/2022] Open
Abstract
Studies on biological functions of N6-methyladenosine (m6A) modification in mRNA have drawn significant attention in recent years. Here we describe the construction and characterization of a CRISPR-Cas13b-based tool for targeted demethylation of specific mRNA. A fusion protein, named dm6ACRISPR, was created by linking a catalytically inactive Type VI-B Cas13 enzyme from Prevotella sp. P5-125 (dPspCas13b) to m6A demethylase AlkB homolog 5 (ALKBH5). dm6ACRISPR specifically demethylates m6A of targeted mRNA such as cytochrome b5 form A (CYB5A) to increase its mRNA stability. It can also demethylate β-catenin-encoding CTNNB1 mRNA that contains multiple m6A sites to trigger its translation. In addition, the dm6ACRISPR system incurs efficient demethylation of targeted epitranscriptome transcripts with limited off-target effects. Targeted demethylation of transcripts coding for oncoproteins such as epidermal growth factor receptor (EGFR) and MYC can suppress proliferation of cancer cells. Together, we provide a programmable and in vivo manipulation tool to study mRNA modification of specific genes and their related biological functions.
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Affiliation(s)
- Jiexin Li
- Guangdong Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, Guangdong 510006, China
| | - Zhuojia Chen
- Sun Yat-sen University Cancer Center; State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou 510060, China
| | - Feng Chen
- Guangdong Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, Guangdong 510006, China
| | - Guoyou Xie
- Guangdong Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, Guangdong 510006, China
| | - Yuyi Ling
- Guangdong Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, Guangdong 510006, China
| | - Yanxi Peng
- Guangdong Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, Guangdong 510006, China
| | - Yu Lin
- Guangdong Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, Guangdong 510006, China.,Guangdong Provincial Key Laboratory of Gastroenterology, Department of Gastroenterology, Nanfang Hospital,Southern Medical University, Guangzhou, Guangdong 510006, China
| | - Nan Luo
- Guangdong Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, Guangdong 510006, China
| | - Cheng-Ming Chiang
- Simmons Comprehensive Cancer Center, Department of Pharmacology, and Department of Biochemistry, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390, USA
| | - Hongsheng Wang
- Guangdong Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, Guangdong 510006, China
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172
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Casalino L, Verde P. Multifaceted Roles of DNA Methylation in Neoplastic Transformation, from Tumor Suppressors to EMT and Metastasis. Genes (Basel) 2020; 11:E922. [PMID: 32806509 PMCID: PMC7463745 DOI: 10.3390/genes11080922] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 07/30/2020] [Accepted: 08/10/2020] [Indexed: 12/12/2022] Open
Abstract
Among the major mechanisms involved in tumorigenesis, DNA methylation is an important epigenetic modification impacting both genomic stability and gene expression. Methylation of promoter-proximal CpG islands (CGIs) and transcriptional silencing of tumor suppressors represent the best characterized epigenetic changes in neoplastic cells. The global cancer-associated effects of DNA hypomethylation influence chromatin architecture and reactivation of repetitive elements. Moreover, recent analyses of cancer cell methylomes highlight the role of the DNA hypomethylation of super-enhancer regions critically controlling the expression of key oncogenic players. We will first summarize some basic aspects of DNA methylation in tumorigenesis, along with the role of dysregulated DNA methyltransferases and TET (Ten-Eleven Translocation)-family methylcytosine dioxygenases. We will then examine the potential contribution of epimutations to causality and heritability of cancer. By reviewing some representative genes subjected to hypermethylation-mediated silencing, we will survey their oncosuppressor functions and roles as biomarkers in various types of cancer. Epithelial-to-mesenchymal transition (EMT) and the gain of stem-like properties are critically involved in cancer cell dissemination, metastasis, and therapeutic resistance. However, the driver vs passenger roles of epigenetic changes, such as DNA methylation in EMT, are still poorly understood. Therefore, we will focus our attention on several aspects of DNA methylation in control of EMT and metastasis suppressors, including both protein-coding and noncoding genes.
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Affiliation(s)
- Laura Casalino
- Institute of Genetics and Biophysics “Adriano Buzzati Traverso”, CNR, 80100 Naples, Italy
| | - Pasquale Verde
- Institute of Genetics and Biophysics “Adriano Buzzati Traverso”, CNR, 80100 Naples, Italy
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173
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Rittiner JE, Moncalvo M, Chiba-Falek O, Kantor B. Gene-Editing Technologies Paired With Viral Vectors for Translational Research Into Neurodegenerative Diseases. Front Mol Neurosci 2020; 13:148. [PMID: 32903507 PMCID: PMC7437156 DOI: 10.3389/fnmol.2020.00148] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2020] [Accepted: 07/16/2020] [Indexed: 12/20/2022] Open
Abstract
Diseases of the central nervous system (CNS) have historically been among the most difficult to treat using conventional pharmacological approaches. This is due to a confluence of factors, including the limited regenerative capacity and overall complexity of the brain, problems associated with repeated drug administration, and difficulties delivering drugs across the blood-brain barrier (BBB). Viral-mediated gene transfer represents an attractive alternative for the delivery of therapeutic cargo to the nervous system. Crucially, it usually requires only a single injection, whether that be a gene replacement strategy for an inherited disorder or the delivery of a genome- or epigenome-modifying construct for treatment of CNS diseases and disorders. It is thus understandable that considerable effort has been put towards the development of improved vector systems for gene transfer into the CNS. Different viral vectors are of course tailored to their specific applications, but they generally should share several key properties. The ideal viral vector incorporates a high-packaging capacity, efficient gene transfer paired with robust and sustained expression, lack of oncogenicity, toxicity and pathogenicity, and scalable manufacturing for clinical applications. In this review, we will devote attention to viral vectors derived from human immunodeficiency virus type 1 (lentiviral vectors; LVs) and adeno-associated virus (AAVs). The high interest in these viral delivery systems vectors is due to: (i) robust delivery and long-lasting expression; (ii) efficient transduction into postmitotic cells, including the brain; (iii) low immunogenicity and toxicity; and (iv) compatibility with advanced manufacturing techniques. Here, we will outline basic aspects of LV and AAV biology, particularly focusing on approaches and techniques aiming to enhance viral safety. We will also allocate a significant portion of this review to the development and use of LVs and AAVs for delivery into the CNS, with a focus on the genome and epigenome-editing tools based on clustered regularly interspaced short palindromic repeats/CRISPR-associated protein 9 (CRISPR/Cas 9) and the development of novel strategies for the treatment of neurodegenerative diseases (NDDs).
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Affiliation(s)
- Joseph Edward Rittiner
- Department of Neurobiology, Duke University Medical Center, Durham, NC, United States
- Viral Vector Core, Duke University Medical Center, Durham, NC, United States
- Duke Center for Advanced Genomic Technologies, Durham, NC, United States
| | - Malik Moncalvo
- Department of Neurobiology, Duke University Medical Center, Durham, NC, United States
- Viral Vector Core, Duke University Medical Center, Durham, NC, United States
- Duke Center for Advanced Genomic Technologies, Durham, NC, United States
| | - Ornit Chiba-Falek
- Department of Neurology, Division of Translational Brain Sciences, Duke University Medical Center, Durham, NC, United States
- Center for Genomic and Computational Biology, Duke University Medical Center, Durham, NC, United States
| | - Boris Kantor
- Department of Neurobiology, Duke University Medical Center, Durham, NC, United States
- Viral Vector Core, Duke University Medical Center, Durham, NC, United States
- Duke Center for Advanced Genomic Technologies, Durham, NC, United States
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174
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Shakirova KM, Ovchinnikova VY, Dashinimaev EB. Cell Reprogramming With CRISPR/Cas9 Based Transcriptional Regulation Systems. Front Bioeng Biotechnol 2020; 8:882. [PMID: 32850737 PMCID: PMC7399070 DOI: 10.3389/fbioe.2020.00882] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Accepted: 07/09/2020] [Indexed: 12/22/2022] Open
Abstract
The speed of reprogramming technologies evolution is rising dramatically in modern science. Both the scientific community and health workers depend on such developments due to the lack of safe autogenic cells and tissues for regenerative medicine, genome editing tools and reliable screening techniques. To perform experiments efficiently and to propel the fundamental science it is important to keep up with novel modifications and techniques that are being discovered almost weekly. One of them is CRISPR/Cas9 based genome and transcriptome editing. The aim of this article is to summarize currently existing CRISPR/Cas9 applications for cell reprogramming, mainly, to compare them with other non-CRISPR approaches and to highlight future perspectives and opportunities.
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Affiliation(s)
- Ksenia M Shakirova
- Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia.,Koltzov Institute of Developmental Biology, Russian Academy of Sciences, Moscow, Russia.,Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, Moscow, Russia
| | - Viktoriia Y Ovchinnikova
- Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia.,Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, Moscow, Russia
| | - Erdem B Dashinimaev
- Koltzov Institute of Developmental Biology, Russian Academy of Sciences, Moscow, Russia.,Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, Moscow, Russia
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175
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Lin X, Chemparathy A, La Russa M, Daley T, Qi LS. Computational Methods for Analysis of Large-Scale CRISPR Screens. Annu Rev Biomed Data Sci 2020. [DOI: 10.1146/annurev-biodatasci-020520-113523] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Large-scale CRISPR-Cas pooled screens have shown great promise to investigate functional links between genotype and phenotype at the genome-wide scale. In addition to technological advancement, there is a need to develop computational methods to analyze the large datasets obtained from high-throughput CRISPR screens. Many computational methods have been developed to identify reliable gene hits from various screens. In this review, we provide an overview of the technology development of CRISPR screening platforms, with a focus on recent advances in computational methods to identify and model gene effects using CRISPR screen datasets. We also discuss existing challenges and opportunities for future computational methods development.
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Affiliation(s)
- Xueqiu Lin
- Department of Bioengineering, Stanford University, Stanford, California 94305, USA
| | | | - Marie La Russa
- Department of Bioengineering, Stanford University, Stanford, California 94305, USA
| | - Timothy Daley
- Department of Bioengineering, Stanford University, Stanford, California 94305, USA
- Department of Statistics, Stanford University, Stanford, California 94305, USA
| | - Lei S. Qi
- Department of Bioengineering, Stanford University, Stanford, California 94305, USA
- Department of Chemical and Systems Biology and ChEM-H (Chemistry, Engineering, and Medicine for Human Health), Stanford University, Stanford, California 94305, USA
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176
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Moses C, Hodgetts SI, Nugent F, Ben-Ary G, Park KK, Blancafort P, Harvey AR. Transcriptional repression of PTEN in neural cells using CRISPR/dCas9 epigenetic editing. Sci Rep 2020; 10:11393. [PMID: 32647121 PMCID: PMC7347541 DOI: 10.1038/s41598-020-68257-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Accepted: 06/19/2020] [Indexed: 12/11/2022] Open
Abstract
After damage to the adult mammalian central nervous system (CNS), surviving neurons have limited capacity to regenerate and restore functional connectivity. Conditional genetic deletion of PTEN results in robust CNS axon regrowth, while PTEN repression with short hairpin RNA (shRNA) improves regeneration but to a lesser extent, likely due to suboptimal PTEN mRNA knockdown using this approach. Here we employed the CRISPR/dCas9 system to repress PTEN transcription in neural cells. We targeted the PTEN proximal promoter and 5' untranslated region with dCas9 fused to the repressor protein Krüppel-associated box (KRAB). dCas9-KRAB delivered in a lentiviral vector with one CRISPR guide RNA (gRNA) achieved potent and specific PTEN repression in human cell line models and neural cells derived from human iPSCs, and induced histone (H)3 methylation and deacetylation at the PTEN promoter. The dCas9-KRAB system outperformed a combination of four shRNAs targeting the PTEN transcript, a construct previously used in CNS injury models. The CRISPR system also worked more effectively than shRNAs for Pten repression in rat neural crest-derived PC-12 cells, and enhanced neurite outgrowth after nerve growth factor stimulation. PTEN silencing with CRISPR/dCas9 epigenetic editing may provide a new option for promoting axon regeneration and functional recovery after CNS trauma.
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Affiliation(s)
- C Moses
- School of Human Sciences, Faculty of Science, The University of Western Australia, 35 Stirling Highway, Perth, WA, 6009, Australia
- Cancer Epigenetics Laboratory, The Harry Perkins Institute of Medical Research, 6 Verdun Street, Nedlands, WA, 6009, Australia
| | - S I Hodgetts
- School of Human Sciences, Faculty of Science, The University of Western Australia, 35 Stirling Highway, Perth, WA, 6009, Australia
- Perron Institute for Neurological and Translational Science, 8 Verdun Street, Nedlands, WA, 6009, Australia
| | - F Nugent
- Cancer Epigenetics Laboratory, The Harry Perkins Institute of Medical Research, 6 Verdun Street, Nedlands, WA, 6009, Australia
- School of Molecular Sciences, Faculty of Science, The University of Western Australia, 35 Stirling Highway, Perth, WA, 6009, Australia
| | - G Ben-Ary
- School of Human Sciences, Faculty of Science, The University of Western Australia, 35 Stirling Highway, Perth, WA, 6009, Australia
| | - K K Park
- Department of Neurological Surgery, Miami Project to Cure Paralysis, University of Miami Miller School of Medicine, Miami, FL, 33136, USA
| | - P Blancafort
- School of Human Sciences, Faculty of Science, The University of Western Australia, 35 Stirling Highway, Perth, WA, 6009, Australia.
- Cancer Epigenetics Laboratory, The Harry Perkins Institute of Medical Research, 6 Verdun Street, Nedlands, WA, 6009, Australia.
- Greehey Children's Cancer Research Institute, UT Health San Antonio, 8403 Floyd Curl Drive, San Antonio, TX, 78229, USA.
| | - A R Harvey
- School of Human Sciences, Faculty of Science, The University of Western Australia, 35 Stirling Highway, Perth, WA, 6009, Australia.
- Perron Institute for Neurological and Translational Science, 8 Verdun Street, Nedlands, WA, 6009, Australia.
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177
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Gjaltema RAF, Rots MG. Advances of epigenetic editing. Curr Opin Chem Biol 2020; 57:75-81. [PMID: 32619853 DOI: 10.1016/j.cbpa.2020.04.020] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Revised: 04/22/2020] [Accepted: 04/30/2020] [Indexed: 12/11/2022]
Abstract
Epigenetic editing refers to the locus-specific targeting of epigenetic enzymes to rewrite the local epigenetic landscape of an endogenous genomic site, often with the aim of transcriptional reprogramming. Implementing clustered regularly interspaced short palindromic repeat-dCas9 greatly accelerated the advancement of epigenetic editing, yielding preclinical therapeutic successes using a variety of epigenetic enzymes. Here, we review the current applications of these epigenetic editing tools in mammals and shed light on biochemical improvements that facilitate versatile applications.
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Affiliation(s)
- Rutger A F Gjaltema
- Otto-Warburg-Laboratory, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Marianne G Rots
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands.
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178
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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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179
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Dahlet T, Argüeso Lleida A, Al Adhami H, Dumas M, Bender A, Ngondo RP, Tanguy M, Vallet J, Auclair G, Bardet AF, Weber M. Genome-wide analysis in the mouse embryo reveals the importance of DNA methylation for transcription integrity. Nat Commun 2020; 11:3153. [PMID: 32561758 PMCID: PMC7305168 DOI: 10.1038/s41467-020-16919-w] [Citation(s) in RCA: 75] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Accepted: 05/29/2020] [Indexed: 12/20/2022] Open
Abstract
Mouse embryos acquire global DNA methylation of their genome during implantation. However the exact roles of DNA methyltransferases (DNMTs) in embryos have not been studied comprehensively. Here we systematically analyze the consequences of genetic inactivation of Dnmt1, Dnmt3a and Dnmt3b on the methylome and transcriptome of mouse embryos. We find a strict division of function between DNMT1, responsible for maintenance methylation, and DNMT3A/B, solely responsible for methylation acquisition in development. By analyzing severely hypomethylated embryos, we uncover multiple functions of DNA methylation that is used as a mechanism of repression for a panel of genes including not only imprinted and germline genes, but also lineage-committed genes and 2-cell genes. DNA methylation also suppresses multiple retrotransposons and illegitimate transcripts from cryptic promoters in transposons and gene bodies. Our work provides a thorough analysis of the roles of DNA methyltransferases and the importance of DNA methylation for transcriptome integrity in mammalian embryos.
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Affiliation(s)
- Thomas Dahlet
- University of Strasbourg, Strasbourg, France
- Biotechnology and Cell Signaling, CNRS UMR7242, 300 Bd Sébastien Brant, 67412, Illkirch, Cedex, France
| | - Andrea Argüeso Lleida
- University of Strasbourg, Strasbourg, France
- Biotechnology and Cell Signaling, CNRS UMR7242, 300 Bd Sébastien Brant, 67412, Illkirch, Cedex, France
| | - Hala Al Adhami
- University of Strasbourg, Strasbourg, France
- Biotechnology and Cell Signaling, CNRS UMR7242, 300 Bd Sébastien Brant, 67412, Illkirch, Cedex, France
| | - Michael Dumas
- University of Strasbourg, Strasbourg, France
- Biotechnology and Cell Signaling, CNRS UMR7242, 300 Bd Sébastien Brant, 67412, Illkirch, Cedex, France
| | - Ambre Bender
- University of Strasbourg, Strasbourg, France
- Biotechnology and Cell Signaling, CNRS UMR7242, 300 Bd Sébastien Brant, 67412, Illkirch, Cedex, France
| | - Richard P Ngondo
- University of Strasbourg, Strasbourg, France
- Biotechnology and Cell Signaling, CNRS UMR7242, 300 Bd Sébastien Brant, 67412, Illkirch, Cedex, France
- IBMP, CNRS UPR2357, 67084, Strasbourg, France
| | - Manon Tanguy
- University of Strasbourg, Strasbourg, France
- Biotechnology and Cell Signaling, CNRS UMR7242, 300 Bd Sébastien Brant, 67412, Illkirch, Cedex, France
| | - Judith Vallet
- University of Strasbourg, Strasbourg, France
- Biotechnology and Cell Signaling, CNRS UMR7242, 300 Bd Sébastien Brant, 67412, Illkirch, Cedex, France
| | - Ghislain Auclair
- University of Strasbourg, Strasbourg, France
- Biotechnology and Cell Signaling, CNRS UMR7242, 300 Bd Sébastien Brant, 67412, Illkirch, Cedex, France
| | - Anaïs F Bardet
- University of Strasbourg, Strasbourg, France
- Biotechnology and Cell Signaling, CNRS UMR7242, 300 Bd Sébastien Brant, 67412, Illkirch, Cedex, France
| | - Michael Weber
- University of Strasbourg, Strasbourg, France.
- Biotechnology and Cell Signaling, CNRS UMR7242, 300 Bd Sébastien Brant, 67412, Illkirch, Cedex, France.
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180
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Du M, Jillette N, Zhu JJ, Li S, Cheng AW. CRISPR artificial splicing factors. Nat Commun 2020; 11:2973. [PMID: 32532987 PMCID: PMC7293279 DOI: 10.1038/s41467-020-16806-4] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Accepted: 05/22/2020] [Indexed: 12/26/2022] Open
Abstract
Alternative splicing allows expression of mRNA isoforms from a single gene, expanding the diversity of the proteome. Its prevalence in normal biological and disease processes warrant precise tools for modulation. Here we report the engineering of CRISPR Artificial Splicing Factors (CASFx) based on RNA-targeting CRISPR-Cas systems. We show that simultaneous exon inclusion and exclusion can be induced at distinct targets by differential positioning of CASFx. We also create inducible CASFx (iCASFx) using the FKBP-FRB chemical-inducible dimerization domain, allowing small molecule control of alternative splicing. Finally, we demonstrate the activation of SMN2 exon 7 splicing in spinal muscular atrophy (SMA) patient fibroblasts, suggesting a potential application of the CASFx system.
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Affiliation(s)
- Menghan Du
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, 06032, USA
- Department of Genetics and Genome Sciences, University of Connecticut Health Center, Farmington, CT, 06030, USA
| | | | | | - Sheng Li
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, 06032, USA
- Department of Genetics and Genome Sciences, University of Connecticut Health Center, Farmington, CT, 06030, USA
- The Jackson Laboratory Cancer Center, Bar Harbor, ME, 04609, USA
- Department of Computer Science and Engineering, University of Connecticut, Storrs, CT, 06269, USA
| | - Albert Wu Cheng
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, 06032, USA.
- Department of Genetics and Genome Sciences, University of Connecticut Health Center, Farmington, CT, 06030, USA.
- The Jackson Laboratory Cancer Center, Bar Harbor, ME, 04609, USA.
- Institute for Systems Genomics, University of Connecticut Health Center, Farmington, CT, 06030, USA.
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181
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Breunig CT, Köferle A, Neuner AM, Wiesbeck MF, Baumann V, Stricker SH. CRISPR Tools for Physiology and Cell State Changes: Potential of Transcriptional Engineering and Epigenome Editing. Physiol Rev 2020; 101:177-211. [PMID: 32525760 DOI: 10.1152/physrev.00034.2019] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Given the large amount of genome-wide data that have been collected during the last decades, a good understanding of how and why cells change during development, homeostasis, and disease might be expected. Unfortunately, the opposite is true; triggers that cause cellular state changes remain elusive, and the underlying molecular mechanisms are poorly understood. Although genes with the potential to influence cell states are known, the historic dependency on methods that manipulate gene expression outside the endogenous chromatin context has prevented us from understanding how cells organize, interpret, and protect cellular programs. Fortunately, recent methodological innovations are now providing options to answer these outstanding questions, by allowing to target and manipulate individual genomic and epigenomic loci. In particular, three experimental approaches are now feasible due to DNA targeting tools, namely, activation and/or repression of master transcription factors in their endogenous chromatin context; targeting transcription factors to endogenous, alternative, or inaccessible sites; and finally, functional manipulation of the chromatin context. In this article, we discuss the molecular basis of DNA targeting tools and review the potential of these new technologies before we summarize how these have already been used for the manipulation of cellular states and hypothesize about future applications.
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Affiliation(s)
- Christopher T Breunig
- MCN Junior Research Group, Munich Center for Neurosciences, Ludwig-Maximilian- Universität, BioMedical Center, Planegg-Martinsried, Germany; and Epigenetic Engineering, Institute of Stem Cell Research, Helmholtz Zentrum, German Research Center for Environmental Health, BioMedical Center, Planegg-Martinsried, Germany
| | - Anna Köferle
- MCN Junior Research Group, Munich Center for Neurosciences, Ludwig-Maximilian- Universität, BioMedical Center, Planegg-Martinsried, Germany; and Epigenetic Engineering, Institute of Stem Cell Research, Helmholtz Zentrum, German Research Center for Environmental Health, BioMedical Center, Planegg-Martinsried, Germany
| | - Andrea M Neuner
- MCN Junior Research Group, Munich Center for Neurosciences, Ludwig-Maximilian- Universität, BioMedical Center, Planegg-Martinsried, Germany; and Epigenetic Engineering, Institute of Stem Cell Research, Helmholtz Zentrum, German Research Center for Environmental Health, BioMedical Center, Planegg-Martinsried, Germany
| | - Maximilian F Wiesbeck
- MCN Junior Research Group, Munich Center for Neurosciences, Ludwig-Maximilian- Universität, BioMedical Center, Planegg-Martinsried, Germany; and Epigenetic Engineering, Institute of Stem Cell Research, Helmholtz Zentrum, German Research Center for Environmental Health, BioMedical Center, Planegg-Martinsried, Germany
| | - Valentin Baumann
- MCN Junior Research Group, Munich Center for Neurosciences, Ludwig-Maximilian- Universität, BioMedical Center, Planegg-Martinsried, Germany; and Epigenetic Engineering, Institute of Stem Cell Research, Helmholtz Zentrum, German Research Center for Environmental Health, BioMedical Center, Planegg-Martinsried, Germany
| | - Stefan H Stricker
- MCN Junior Research Group, Munich Center for Neurosciences, Ludwig-Maximilian- Universität, BioMedical Center, Planegg-Martinsried, Germany; and Epigenetic Engineering, Institute of Stem Cell Research, Helmholtz Zentrum, German Research Center for Environmental Health, BioMedical Center, Planegg-Martinsried, Germany
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182
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Kunii A, Yamamoto T, Sakuma T. Various strategies of effector accumulation to improve the efficiency of genome editing and derivative methodologies. In Vitro Cell Dev Biol Anim 2020; 56:359-366. [PMID: 32514717 DOI: 10.1007/s11626-020-00469-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Accepted: 05/21/2020] [Indexed: 12/30/2022]
Abstract
CRISPR-Cas9 is a sophisticated tool in which Cas9/sgRNA complexes bind to the programmed target sequences and induce DNA double-strand breaks (DSBs) enabling highly efficient genome editing. Moreover, when nuclease-inactive Cas9 (dCas9) is employed, its specific DNA-binding activity provides a variety of derivative technologies such as transcriptional activation/repression, epigenome editing, and chromosome visualization. In these derivative technologies, particular effector molecules are fused with dCas9 or recruited to the target site. However, there had been room for improvement, because both genome editing and derivative technologies require not only the DNA-binding tools but also the additional components for their efficient and flexible outcomes. For genome editing, DSB repair molecules and knock-in donor templates need to act at the DSB sites. Derivative technologies also require their various effector domains to be gathered onto the target sites. Recently, many groups have developed and utilized inventive platforms to accumulate these additional components to the target sequence by modifying Cas9 protein and/or sgRNA. Here, we summarize the strategies of CRISPR-based effector accumulation and the improved methodologies using these creative platforms.
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Affiliation(s)
- Atsushi Kunii
- Department of Mathematical and Life Sciences, Graduate School of Science, Hiroshima University, Hiroshima, 739-8526, Japan
| | - Takashi Yamamoto
- Division of Integrated Sciences for Life, Graduate School of Integrated Sciences for Life, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima, 739-8526, Japan
| | - Tetsushi Sakuma
- Division of Integrated Sciences for Life, Graduate School of Integrated Sciences for Life, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima, 739-8526, Japan.
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183
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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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184
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Uncoupling histone H3K4 trimethylation from developmental gene expression via an equilibrium of COMPASS, Polycomb and DNA methylation. Nat Genet 2020; 52:615-625. [PMID: 32393859 DOI: 10.1038/s41588-020-0618-1] [Citation(s) in RCA: 65] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Accepted: 03/26/2020] [Indexed: 12/20/2022]
Abstract
The COMPASS protein family catalyzes histone H3 Lys 4 (H3K4) methylation and its members are essential for regulating gene expression. MLL2/COMPASS methylates H3K4 on many developmental genes and bivalent clusters. To understand MLL2-dependent transcriptional regulation, we performed a CRISPR-based screen with an MLL2-dependent gene as a reporter in mouse embryonic stem cells. We found that MLL2 functions in gene expression by protecting developmental genes from repression via repelling PRC2 and DNA methylation machineries. Accordingly, repression in the absence of MLL2 is relieved by inhibition of PRC2 and DNA methyltransferases. Furthermore, DNA demethylation on such loci leads to reactivation of MLL2-dependent genes not only by removing DNA methylation but also by opening up previously CpG methylated regions for PRC2 recruitment, diluting PRC2 at Polycomb-repressed genes. These findings reveal how the context and function of these three epigenetic modifiers of chromatin can orchestrate transcriptional decisions and demonstrate that prevention of active repression by the context of the enzyme and not H3K4 trimethylation underlies transcriptional regulation on MLL2/COMPASS targets.
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185
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Encoding quantized fluorescence states with fractal DNA frameworks. Nat Commun 2020; 11:2185. [PMID: 32366822 PMCID: PMC7198603 DOI: 10.1038/s41467-020-16112-z] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2019] [Accepted: 04/14/2020] [Indexed: 02/02/2023] Open
Abstract
Signal amplification in biological systems is achieved by cooperatively recruiting multiple copies of regulatory biomolecules. Nevertheless, the multiplexing capability of artificial fluorescent amplifiers is limited due to the size limit and lack of modularity. Here, we develop Cayley tree-like fractal DNA frameworks to topologically encode the fluorescence states for multiplexed detection of low-abundance targets. Taking advantage of the self-similar topology of Cayley tree, we use only 16 DNA strands to construct n-node (n = 53) structures of up to 5 megadalton. The high level of degeneracy allows encoding 36 colours with 7 nodes by site-specifically anchoring of distinct fluorophores onto a structure. The fractal topology minimises fluorescence crosstalk and allows quantitative decoding of quantized fluorescence states. We demonstrate a spectrum of rigid-yet-flexible super-multiplex structures for encoded fluorescence detection of single-molecule recognition events and multiplexed discrimination of living cells. Thus, the topological engineering approach enriches the toolbox for high-throughput cell imaging. Though DNA framework-based scaffolds for biomolecular assembly are attractive for bioimaging applications, realizing super-multiplex fluorescent amplifiers remains a challenge. Here, the authors report a topological engineering approach to designing fractal DNA frameworks for multiplexed amplifiers.
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186
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Shi J, Clayton C, Tian B. Nano-enabled cellular engineering for bioelectric studies. NANO RESEARCH 2020; 13:1214-1227. [PMID: 34295455 PMCID: PMC8294124 DOI: 10.1007/s12274-019-2580-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Accepted: 11/24/2019] [Indexed: 06/13/2023]
Abstract
Engineered cells have opened up a new avenue for scientists and engineers to achieve specialized biological functions. Nanomaterials, such as silicon nanowires and quantum dots, can establish tight interfaces with cells either extra- or intracellularly, and they have already been widely used to control cellular functions. The future exploration of nanomaterials in cellular engineering may reveal numerous opportunities in both fundamental bioelectric studies and clinic applications. In this review, we highlight several nanomaterials-enabled non-genetic approaches to fabricating engineered cells. First, we briefly review the latest progress in engineered or synthetic cells, such as protocells that create cell-like behaviors from nonliving building blocks, and cells made by genetic or chemical modifications. Next, we illustrate the need for non-genetic cellular engineering with semiconductors and present some examples where chemical synthesis yields complex morphology or functions needed for biointerfaces. We then provide discussions in detail about the semiconductor nanostructure-enabled neural, cardiac, and microbial modulations. We also suggest the need to integrate tissue engineering with semiconductor devices to carry out more complex functions. We end this review by providing our perspectives for future development in non-genetic cellular engineering.
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Affiliation(s)
- Jiuyun Shi
- Department of Chemistry, University of Chicago, Chicago, IL 60637, USA
| | | | - Bozhi Tian
- Department of Chemistry, University of Chicago, Chicago, IL 60637, USA
- The James Franck Institute, University of Chicago, Chicago, IL 60637, USA
- The Institute for Biophysical Dynamics, University of Chicago, Chicago, IL 60637, USA
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187
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Hirakawa M, Krishnakumar R, Timlin J, Carney J, Butler K. Gene editing and CRISPR in the clinic: current and future perspectives. Biosci Rep 2020; 40:BSR20200127. [PMID: 32207531 PMCID: PMC7146048 DOI: 10.1042/bsr20200127] [Citation(s) in RCA: 102] [Impact Index Per Article: 25.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Revised: 03/23/2020] [Accepted: 03/23/2020] [Indexed: 12/26/2022] Open
Abstract
Genome editing technologies, particularly those based on zinc-finger nucleases (ZFNs), transcription activator-like effector nucleases (TALENs), and CRISPR (clustered regularly interspaced short palindromic repeat DNA sequences)/Cas9 are rapidly progressing into clinical trials. Most clinical use of CRISPR to date has focused on ex vivo gene editing of cells followed by their re-introduction back into the patient. The ex vivo editing approach is highly effective for many disease states, including cancers and sickle cell disease, but ideally genome editing would also be applied to diseases which require cell modification in vivo. However, in vivo use of CRISPR technologies can be confounded by problems such as off-target editing, inefficient or off-target delivery, and stimulation of counterproductive immune responses. Current research addressing these issues may provide new opportunities for use of CRISPR in the clinical space. In this review, we examine the current status and scientific basis of clinical trials featuring ZFNs, TALENs, and CRISPR-based genome editing, the known limitations of CRISPR use in humans, and the rapidly developing CRISPR engineering space that should lay the groundwork for further translation to clinical application.
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Affiliation(s)
| | - Raga Krishnakumar
- Systems Biology, Sandia National Laboratories, Livermore, CA 94551, U.S.A
| | - Jerilyn A. Timlin
- Molecular and Microbiology, Sandia National Laboratories, Albuquerque, NM 87185, U.S.A
| | - James P. Carney
- Advanced Materials Laboratory, Sandia National Laboratories, Albuquerque, NM 87185, U.S.A
| | - Kimberly S. Butler
- Molecular and Microbiology, Sandia National Laboratories, Albuquerque, NM 87185, U.S.A
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188
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Xu X, Hulshoff MS, Tan X, Zeisberg M, Zeisberg EM. CRISPR/Cas Derivatives as Novel Gene Modulating Tools: Possibilities and In Vivo Applications. Int J Mol Sci 2020; 21:E3038. [PMID: 32344896 PMCID: PMC7246536 DOI: 10.3390/ijms21093038] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Revised: 04/22/2020] [Accepted: 04/23/2020] [Indexed: 12/18/2022] Open
Abstract
The field of genome editing started with the discovery of meganucleases (e.g., the LAGLIDADG family of homing endonucleases) in yeast. After the discovery of transcription activator-like effector nucleases and zinc finger nucleases, the recently discovered clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR associated proteins (Cas) system has opened a new window of applications in the field of gene editing. Here, we review different Cas proteins and their corresponding features including advantages and disadvantages, and we provide an overview of the different endonuclease-deficient Cas protein (dCas) derivatives. These dCas derivatives consist of an endonuclease-deficient Cas9 which can be fused to different effector domains to perform distinct in vitro applications such as tracking, transcriptional activation and repression, as well as base editing. Finally, we review the in vivo applications of these dCas derivatives and discuss their potential to perform gene activation and repression in vivo, as well as their potential future use in human therapy.
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Affiliation(s)
- Xingbo Xu
- Department of Cardiology and Pneumology, University Medical Center Göttingen, Robert-Koch-Str. 40, 37075 Göttingen, Germany; (X.X.); (M.S.H.)
- German Centre for Cardiovascular Research (DZHK), 37075 Göttingen, Germany; (X.T.); (M.Z.)
| | - Melanie S. Hulshoff
- Department of Cardiology and Pneumology, University Medical Center Göttingen, Robert-Koch-Str. 40, 37075 Göttingen, Germany; (X.X.); (M.S.H.)
- German Centre for Cardiovascular Research (DZHK), 37075 Göttingen, Germany; (X.T.); (M.Z.)
- Department of Pathology and Medical Biology, University Medical Center Groningen, Hanzeplein 1, 9713 GZ Groningen, The Netherlands
| | - Xiaoying Tan
- German Centre for Cardiovascular Research (DZHK), 37075 Göttingen, Germany; (X.T.); (M.Z.)
- Department of Nephrology and Rheumatology, University Medical Center of Göttingen, Robert-Koch-Str. 40, 37075 Göttingen, Germany
| | - Michael Zeisberg
- German Centre for Cardiovascular Research (DZHK), 37075 Göttingen, Germany; (X.T.); (M.Z.)
- Department of Nephrology and Rheumatology, University Medical Center of Göttingen, Robert-Koch-Str. 40, 37075 Göttingen, Germany
| | - Elisabeth M. Zeisberg
- Department of Cardiology and Pneumology, University Medical Center Göttingen, Robert-Koch-Str. 40, 37075 Göttingen, Germany; (X.X.); (M.S.H.)
- German Centre for Cardiovascular Research (DZHK), 37075 Göttingen, Germany; (X.T.); (M.Z.)
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189
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Syding LA, Nickl P, Kasparek P, Sedlacek R. CRISPR/Cas9 Epigenome Editing Potential for Rare Imprinting Diseases: A Review. Cells 2020; 9:cells9040993. [PMID: 32316223 PMCID: PMC7226972 DOI: 10.3390/cells9040993] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2020] [Revised: 04/14/2020] [Accepted: 04/15/2020] [Indexed: 12/22/2022] Open
Abstract
Imprinting diseases (IDs) are rare congenital disorders caused by aberrant dosages of imprinted genes. Rare IDs are comprised by a group of several distinct disorders that share a great deal of homology in terms of genetic etiologies and symptoms. Disruption of genetic or epigenetic mechanisms can cause issues with regulating the expression of imprinted genes, thus leading to disease. Genetic mutations affect the imprinted genes, duplications, deletions, and uniparental disomy (UPD) are reoccurring phenomena causing imprinting diseases. Epigenetic alterations on methylation marks in imprinting control centers (ICRs) also alters the expression patterns and the majority of patients with rare IDs carries intact but either silenced or overexpressed imprinted genes. Canonical CRISPR/Cas9 editing relying on double-stranded DNA break repair has little to offer in terms of therapeutics for rare IDs. Instead CRISPR/Cas9 can be used in a more sophisticated way by targeting the epigenome. Catalytically dead Cas9 (dCas9) tethered with effector enzymes such as DNA de- and methyltransferases and histone code editors in addition to systems such as CRISPRa and CRISPRi have been shown to have high epigenome editing efficiency in eukaryotic cells. This new era of CRISPR epigenome editors could arguably be a game-changer for curing and treating rare IDs by refined activation and silencing of disturbed imprinted gene expression. This review describes major CRISPR-based epigenome editors and points out their potential use in research and therapy of rare imprinting diseases.
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Affiliation(s)
- Linn Amanda Syding
- Laboratory of Transgenic Models of Diseases, Institute of Molecular Genetics of the CAS, v.v.i, 252 50 Vestec, Czech Republic
| | - Petr Nickl
- Laboratory of Transgenic Models of Diseases, Institute of Molecular Genetics of the CAS, v.v.i, 252 50 Vestec, Czech Republic
| | - Petr Kasparek
- Laboratory of Transgenic Models of Diseases, Institute of Molecular Genetics of the CAS, v.v.i, 252 50 Vestec, Czech Republic
- Czech Centre for Phenogenomics, Institute of Molecular Genetics of the CAS, v.v.i, 252 50 Vestec, Czech Republic
| | - Radislav Sedlacek
- Laboratory of Transgenic Models of Diseases, Institute of Molecular Genetics of the CAS, v.v.i, 252 50 Vestec, Czech Republic
- Czech Centre for Phenogenomics, Institute of Molecular Genetics of the CAS, v.v.i, 252 50 Vestec, Czech Republic
- Correspondence: ; Tel.: +420-325-873-243
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190
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Horii T, Morita S, Hino S, Kimura M, Hino Y, Kogo H, Nakao M, Hatada I. Successful generation of epigenetic disease model mice by targeted demethylation of the epigenome. Genome Biol 2020; 21:77. [PMID: 32234052 PMCID: PMC7110793 DOI: 10.1186/s13059-020-01991-8] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Accepted: 03/08/2020] [Indexed: 01/06/2023] Open
Abstract
BACKGROUND Epigenetic modifications, including DNA methylation, play an important role in gene silencing and genome stability. Consequently, epigenetic dysregulation can cause several diseases, such as cancer, obesity, diabetes, autism, and imprinting disorders. RESULTS We validate three methods for the generation of epigenome-edited mice using the dCas9-SunTag and single-chain variable fragment-TET1 catalytic domain. We generate model mice for Silver-Russell syndrome (SRS), an imprinting disorder, by target-specific DNA demethylation in the H19 differentially methylated region. Like SRS patients, these mice show H19 upregulation and Igf2 downregulation, leading to severe intrauterine and postnatal growth retardation. CONCLUSION This is the first report of an imprinting disease model animal generated by targeted demethylation of specific loci of the epigenome in fertilized eggs. Epigenome-edited animals are also useful for exploring the causative epimutations in epigenetic diseases.
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Affiliation(s)
- Takuro Horii
- Laboratory of Genome Science, Biosignal Genome Resource Center, Institute for Molecular and Cellular Regulation, Gunma University, 3-39-15 Showa-machi, Maebashi, Gunma, 371-8512, Japan
| | - Sumiyo Morita
- Laboratory of Genome Science, Biosignal Genome Resource Center, Institute for Molecular and Cellular Regulation, Gunma University, 3-39-15 Showa-machi, Maebashi, Gunma, 371-8512, Japan
| | - Shinjiro Hino
- Department of Medical Cell Biology, Institute of Molecular Embryology and Genetics, Kumamoto University, 2-2-1 Honjo, Chuo-ku, Kumamoto, 860-0811, Japan
| | - Mika Kimura
- Laboratory of Genome Science, Biosignal Genome Resource Center, Institute for Molecular and Cellular Regulation, Gunma University, 3-39-15 Showa-machi, Maebashi, Gunma, 371-8512, Japan
| | - Yuko Hino
- Department of Medical Cell Biology, Institute of Molecular Embryology and Genetics, Kumamoto University, 2-2-1 Honjo, Chuo-ku, Kumamoto, 860-0811, Japan
| | - Hiroshi Kogo
- Department of Anatomy and Cell Biology, Graduate School of Medicine, Gunma University, 3-39-22 Showa-machi, Maebashi, Gunma, 371-8511, Japan
| | - Mitsuyoshi Nakao
- Department of Medical Cell Biology, Institute of Molecular Embryology and Genetics, Kumamoto University, 2-2-1 Honjo, Chuo-ku, Kumamoto, 860-0811, Japan
| | - Izuho Hatada
- Laboratory of Genome Science, Biosignal Genome Resource Center, Institute for Molecular and Cellular Regulation, Gunma University, 3-39-15 Showa-machi, Maebashi, Gunma, 371-8512, Japan.
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191
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Targeted DNA demethylation of the Fgf21 promoter by CRISPR/dCas9-mediated epigenome editing. Sci Rep 2020; 10:5181. [PMID: 32198422 PMCID: PMC7083849 DOI: 10.1038/s41598-020-62035-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Accepted: 03/06/2020] [Indexed: 11/08/2022] Open
Abstract
Recently, we reported PPARα-dependent DNA demethylation of the Fgf21 promoter in the postnatal mouse liver, where reduced DNA methylation is associated with enhanced gene expression after PPARα activation. However, there is no direct evidence for the effect of site-specific DNA methylation on gene expression. We employed the dCas9-SunTag and single-chain variable fragment (scFv)-TET1 catalytic domain (TET1CD) system to induce targeted DNA methylation of the Fgf21 promoter both in vitro and in vivo. We succeeded in targeted DNA demethylation of the Fgf 21 promoter both in Hepa1-6 cells and PPARα-deficient mice, with increased gene expression response to PPARα synthetic ligand administration and fasting, respectively. This study provides direct evidence that the DNA methylation status of a particular gene may determine the magnitude of the gene expression response to activation cues.
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192
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Imkeller K, Ambrosi G, Boutros M, Huber W. gscreend: modelling asymmetric count ratios in CRISPR screens to decrease experiment size and improve phenotype detection. Genome Biol 2020; 21:53. [PMID: 32122365 PMCID: PMC7052974 DOI: 10.1186/s13059-020-1939-1] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2019] [Accepted: 01/19/2020] [Indexed: 02/06/2023] Open
Abstract
Pooled CRISPR screens are a powerful tool to probe genotype-phenotype relationships at genome-wide scale. However, criteria for optimal design are missing, and it remains unclear how experimental parameters affect results. Here, we report that random decreases in gRNA abundance are more likely than increases due to bottle-neck effects during the cell proliferation phase. Failure to consider this asymmetry leads to loss of detection power. We provide a new statistical test that addresses this problem and improves hit detection at reduced experiment size. The method is implemented in the R package gscreend, which is available at http://bioconductor.org/packages/gscreend.
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Affiliation(s)
- Katharina Imkeller
- German Cancer Research Center (DKFZ) and Heidelberg University, Heidelberg, Germany
- European Molecular Biology Laboratory, Heidelberg, Germany
| | - Giulia Ambrosi
- German Cancer Research Center (DKFZ) and Heidelberg University, Heidelberg, Germany
| | - Michael Boutros
- German Cancer Research Center (DKFZ) and Heidelberg University, Heidelberg, Germany
| | - Wolfgang Huber
- European Molecular Biology Laboratory, Heidelberg, Germany
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193
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Chan RF, Turecki G, Shabalin AA, Guintivano J, Zhao M, Xie LY, van Grootheest G, Kaminsky ZA, Dean B, Penninx BW, Aberg KA, van den Oord EJ. Cell Type-Specific Methylome-wide Association Studies Implicate Neurotrophin and Innate Immune Signaling in Major Depressive Disorder. Biol Psychiatry 2020; 87:431-442. [PMID: 31889537 PMCID: PMC9933050 DOI: 10.1016/j.biopsych.2019.10.014] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Revised: 09/26/2019] [Accepted: 10/10/2019] [Indexed: 01/06/2023]
Abstract
BACKGROUND We sought to characterize methylation changes in brain and blood associated with major depressive disorder (MDD). As analyses of bulk tissue may obscure association signals and hamper the biological interpretation of findings, these changes were studied on a cell type-specific level. METHODS In 3 collections of human postmortem brain (n = 206) and 1 collection of blood samples (N = 1132) of MDD cases and controls, we used epigenomic deconvolution to perform cell type-specific methylome-wide association studies within subpopulations of neurons/glia for the brain data and granulocytes/T cells/B cells/monocytes for the blood data. Sorted neurons/glia from a fourth postmortem brain collection (n = 58) were used for validation purposes. RESULTS Cell type-specific methylome-wide association studies identified multiple findings in neurons/glia that were detected across brain collections and were reproducible in physically sorted nuclei. Cell type-specific analyses in blood samples identified methylome-wide significant associations in T cells, monocytes, and whole blood that replicated findings from a past methylation study of MDD. Pathway analyses implicated p75 neurotrophin receptor/nerve growth factor signaling and innate immune toll-like receptor signaling in MDD. Top results in neurons, glia, bulk brain, T cells, monocytes, and whole blood were enriched for genes supported by genome-wide association studies for MDD and other psychiatric disorders. CONCLUSIONS We both replicated and identified novel MDD-methylation associations in human brain and blood samples at a cell type-specific level. Our results provide mechanistic insights into how the immune system may interact with the brain to affect MDD susceptibility. Importantly, our findings involved associations with MDD in human samples that implicated many closely related biological pathways. These disease-linked sites and pathways represent promising new therapeutic targets for MDD.
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194
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Morita S, Horii T, Kimura M, Hatada I. Synergistic Upregulation of Target Genes by TET1 and VP64 in the dCas9-SunTag Platform. Int J Mol Sci 2020; 21:E1574. [PMID: 32106616 PMCID: PMC7084704 DOI: 10.3390/ijms21051574] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Revised: 02/21/2020] [Accepted: 02/24/2020] [Indexed: 12/14/2022] Open
Abstract
Overexpression of a gene of interest is a general approach used in both basic research and therapeutic applications. However, the conventional approach involving overexpression of exogenous genes has difficulty achieving complete genome coverage, and is also limited by the cloning capacity of viral vectors. Therefore, an alternative approach would be to drive the expression of an endogenous gene using an artificial transcriptional activator. Fusion proteins of dCas9 and a transcription activation domain, such as dCas9-VP64, are widely used for activation of endogenous genes. However, when using a single sgRNA, the activation range is low. Consequently, tiling of several sgRNAs is required for robust transcriptional activation. Here we describe the screening of factors that exhibit the best synergistic activation of gene expression with TET1 in the dCas9-SunTag format. All seven factors examined showed some synergy with TET1. Among them, VP64 gave the best results. Thus, simultaneous tethering of VP64 and TET1 to a target gene using an optimized dCas9-SunTag format synergistically activates gene expression using a single sgRNA.
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Affiliation(s)
| | | | | | - Izuho Hatada
- Laboratory of Genome Science, Biosignal Genome Resource Center, Institute for Molecular and Cellular Regulation, Gunma University, 3-39-15 Showa-machi, Maebashi 371-8512, Japan; (S.M.); (T.H.); (M.K.)
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195
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Devesa-Guerra I, Morales-Ruiz T, Pérez-Roldán J, Parrilla-Doblas JT, Dorado-León M, García-Ortiz MV, Ariza RR, Roldán-Arjona T. DNA Methylation Editing by CRISPR-guided Excision of 5-Methylcytosine. J Mol Biol 2020; 432:2204-2216. [PMID: 32087201 DOI: 10.1016/j.jmb.2020.02.007] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Revised: 02/07/2020] [Accepted: 02/07/2020] [Indexed: 12/22/2022]
Abstract
Tools for actively targeted DNA demethylation are required to increase our knowledge about regulation and specific functions of this important epigenetic modification. DNA demethylation in mammals involves TET-mediated oxidation of 5-methylcytosine (5-meC), which may promote its replication-dependent dilution and/or active removal through base excision repair (BER). However, it is still unclear whether oxidized derivatives of 5-meC are simply DNA demethylation intermediates or rather epigenetic marks on their own. Unlike animals, plants have evolved enzymes that directly excise 5-meC without previous modification. In this work, we have fused the catalytic domain of Arabidopsis ROS1 5-meC DNA glycosylase to a CRISPR-associated null-nuclease (dCas9) and analyzed its capacity for targeted reactivation of methylation-silenced genes, in comparison to other dCas9-effectors. We found that dCas9-ROS1, but not dCas9-TET1, is able to reactivate methylation-silenced genes and induce partial demethylation in a replication-independent manner. We also found that reactivation induced by dCas9-ROS1, as well as that achieved by two different CRISPR-based chromatin effectors (dCas9-VP160 and dCas9-p300), generally decreases with methylation density. Our results suggest that plant 5-meC DNA glycosylases are a valuable addition to the CRISPR-based toolbox for epigenetic editing.
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Affiliation(s)
- Iván Devesa-Guerra
- Maimónides Biomedical Research Institute of Córdoba (IMIBIC), 14071, Córdoba, Spain; Department of Genetics, University of Córdoba, 14071, Córdoba, Spain; Reina Sofía University Hospital, 14071, Córdoba, Spain
| | - Teresa Morales-Ruiz
- Maimónides Biomedical Research Institute of Córdoba (IMIBIC), 14071, Córdoba, Spain; Department of Genetics, University of Córdoba, 14071, Córdoba, Spain; Reina Sofía University Hospital, 14071, Córdoba, Spain
| | - Juan Pérez-Roldán
- Maimónides Biomedical Research Institute of Córdoba (IMIBIC), 14071, Córdoba, Spain; Department of Genetics, University of Córdoba, 14071, Córdoba, Spain; Reina Sofía University Hospital, 14071, Córdoba, Spain
| | - Jara Teresa Parrilla-Doblas
- Maimónides Biomedical Research Institute of Córdoba (IMIBIC), 14071, Córdoba, Spain; Department of Genetics, University of Córdoba, 14071, Córdoba, Spain; Reina Sofía University Hospital, 14071, Córdoba, Spain
| | - Macarena Dorado-León
- Maimónides Biomedical Research Institute of Córdoba (IMIBIC), 14071, Córdoba, Spain; Department of Genetics, University of Córdoba, 14071, Córdoba, Spain; Reina Sofía University Hospital, 14071, Córdoba, Spain
| | - María Victoria García-Ortiz
- Maimónides Biomedical Research Institute of Córdoba (IMIBIC), 14071, Córdoba, Spain; Department of Genetics, University of Córdoba, 14071, Córdoba, Spain; Reina Sofía University Hospital, 14071, Córdoba, Spain
| | - Rafael R Ariza
- Maimónides Biomedical Research Institute of Córdoba (IMIBIC), 14071, Córdoba, Spain; Department of Genetics, University of Córdoba, 14071, Córdoba, Spain; Reina Sofía University Hospital, 14071, Córdoba, Spain
| | - Teresa Roldán-Arjona
- Maimónides Biomedical Research Institute of Córdoba (IMIBIC), 14071, Córdoba, Spain; Department of Genetics, University of Córdoba, 14071, Córdoba, Spain; Reina Sofía University Hospital, 14071, Córdoba, Spain.
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196
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Kato M, Natarajan R. Epigenetics and epigenomics in diabetic kidney disease and metabolic memory. Nat Rev Nephrol 2020; 15:327-345. [PMID: 30894700 DOI: 10.1038/s41581-019-0135-6] [Citation(s) in RCA: 300] [Impact Index Per Article: 75.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
The development and progression of diabetic kidney disease (DKD), a highly prevalent complication of diabetes mellitus, are influenced by both genetic and environmental factors. DKD is an important contributor to the morbidity of patients with diabetes mellitus, indicating a clear need for an improved understanding of disease aetiology to inform the development of more efficacious treatments. DKD is characterized by an accumulation of extracellular matrix, hypertrophy and fibrosis in kidney glomerular and tubular cells. Increasing evidence shows that genes associated with these features of DKD are regulated not only by classical signalling pathways but also by epigenetic mechanisms involving chromatin histone modifications, DNA methylation and non-coding RNAs. These mechanisms can respond to changes in the environment and, importantly, might mediate the persistent long-term expression of DKD-related genes and phenotypes induced by prior glycaemic exposure despite subsequent glycaemic control, a phenomenon called metabolic memory. Detection of epigenetic events during the early stages of DKD could be valuable for timely diagnosis and prompt treatment to prevent progression to end-stage renal disease. Identification of epigenetic signatures of DKD via epigenome-wide association studies might also inform precision medicine approaches. Here, we highlight the emerging role of epigenetics and epigenomics in DKD and the translational potential of candidate epigenetic factors and non-coding RNAs as biomarkers and drug targets for DKD.
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Affiliation(s)
- Mitsuo Kato
- Department of Diabetes Complications and Metabolism, Diabetes Metabolism Research Institute, Beckman Research Institute of City of Hope, Duarte, CA, USA.
| | - Rama Natarajan
- Department of Diabetes Complications and Metabolism, Diabetes Metabolism Research Institute, Beckman Research Institute of City of Hope, Duarte, CA, USA.
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197
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Lu Z, Liu Z, Mao W, Wang X, Zheng X, Chen S, Cao B, Huang S, Zhang X, Zhou T, Zhang Y, Huang X, Sun Q, Li JD. Locus-specific DNA methylation of Mecp2 promoter leads to autism-like phenotypes in mice. Cell Death Dis 2020; 11:85. [PMID: 32015323 PMCID: PMC6997184 DOI: 10.1038/s41419-020-2290-x] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Revised: 01/15/2020] [Accepted: 01/21/2020] [Indexed: 02/07/2023]
Abstract
Autism spectrum disorder (ASD) is a neurodevelopmental disease with a strong heritability, but recent evidence suggests that epigenetic dysregulation may also contribute to the pathogenesis of ASD. Especially, increased methylation at the MECP2 promoter and decreased MECP2 expression were observed in the brains of ASD patients. However, the causative relationship of MECP2 promoter methylation and ASD has not been established. In this study, we achieved locus-specific methylation at the transcription start site (TSS) of Mecp2 in Neuro-2a cells and in mice, using nuclease-deactivated Cas9 (dCas9) fused with DNA methyltransferase catalytic domains, together with five locus-targeting sgRNAs. This locus-specific epigenetic modification led to a reduced Mecp2 expression and a series of behavioral alterations in mice, including reduced social interaction, increased grooming, enhanced anxiety/depression, and poor performance in memory tasks. We further found that specifically increasing the Mecp2 promoter methylation in the hippocampus was sufficient to induce most of the behavioral changes. Our finding therefore demonstrated for the first time the casual relationship between locus-specific DNA methylation and diseases symptoms in vivo, warranting potential therapeutic application of epigenetic editing.
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Affiliation(s)
- Zongyang Lu
- School of Life Science and Technology, ShanghaiTech University, 100 Haike Rd., Pudong New Area, Shanghai, 201210, China.,CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, 320 Yueyang Road, Shanghai, 200031, China.,University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Zhen Liu
- Institute of Neuroscience, Chinese Academy of Sciences (CAS) Key Laboratory of Primate Neurobiology, CAS Center for Excellence in Brain Science and Intelligence Technology, Shanghai Institutes for Biological Sciences, CAS, Shanghai, 200031, China
| | - Wei Mao
- Hunan Key Laboratory of Animal Models for Human Genetics, School of Life Sciences, Central South University, 110 Xiangya Road, Changsha, 410078, China
| | - Xinying Wang
- Hunan Key Laboratory of Animal Models for Human Genetics, School of Life Sciences, Central South University, 110 Xiangya Road, Changsha, 410078, China
| | - Xiaoguo Zheng
- School of Life Science and Technology, ShanghaiTech University, 100 Haike Rd., Pudong New Area, Shanghai, 201210, China
| | - Shanshan Chen
- Institute of Neuroscience, Chinese Academy of Sciences (CAS) Key Laboratory of Primate Neurobiology, CAS Center for Excellence in Brain Science and Intelligence Technology, Shanghai Institutes for Biological Sciences, CAS, Shanghai, 200031, China
| | - Beibei Cao
- Hunan Key Laboratory of Animal Models for Human Genetics, School of Life Sciences, Central South University, 110 Xiangya Road, Changsha, 410078, China
| | - Shisheng Huang
- School of Life Science and Technology, ShanghaiTech University, 100 Haike Rd., Pudong New Area, Shanghai, 201210, China
| | - Xuliang Zhang
- School of Life Science and Technology, ShanghaiTech University, 100 Haike Rd., Pudong New Area, Shanghai, 201210, China
| | - Tao Zhou
- School of Life Science and Technology, ShanghaiTech University, 100 Haike Rd., Pudong New Area, Shanghai, 201210, China
| | - Yu Zhang
- School of Life Science and Technology, ShanghaiTech University, 100 Haike Rd., Pudong New Area, Shanghai, 201210, China
| | - Xingxu Huang
- School of Life Science and Technology, ShanghaiTech University, 100 Haike Rd., Pudong New Area, Shanghai, 201210, China. .,CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, 320 Yueyang Road, Shanghai, 200031, China.
| | - Qiang Sun
- Institute of Neuroscience, Chinese Academy of Sciences (CAS) Key Laboratory of Primate Neurobiology, CAS Center for Excellence in Brain Science and Intelligence Technology, Shanghai Institutes for Biological Sciences, CAS, Shanghai, 200031, China.
| | - Jia-Da Li
- Hunan Key Laboratory of Animal Models for Human Genetics, School of Life Sciences, Central South University, 110 Xiangya Road, Changsha, 410078, China.
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Epigenetic Control of a Local Chromatin Landscape. Int J Mol Sci 2020; 21:ijms21030943. [PMID: 32023873 PMCID: PMC7038174 DOI: 10.3390/ijms21030943] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Revised: 01/28/2020] [Accepted: 01/29/2020] [Indexed: 12/11/2022] Open
Abstract
Proper regulation of the chromatin landscape is essential for maintaining eukaryotic cell identity and diverse cellular processes. The importance of the epigenome comes, in part, from the ability to influence gene expression through patterns in DNA methylation, histone tail modification, and chromatin architecture. Decades of research have associated this process of chromatin regulation and gene expression with human diseased states. With the goal of understanding how chromatin dysregulation contributes to disease, as well as preventing or reversing this type of dysregulation, a multidisciplinary effort has been launched to control the epigenome. Chemicals that alter the epigenome have been used in labs and in clinics since the 1970s, but more recently there has been a shift in this effort towards manipulating the chromatin landscape in a locus-specific manner. This review will provide an overview of chromatin biology to set the stage for the type of control being discussed, evaluate the recent technological advances made in controlling specific regions of chromatin, and consider the translational applications of these works.
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199
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Editing DNA Methylation in Mammalian Embryos. Int J Mol Sci 2020; 21:ijms21020637. [PMID: 31963664 PMCID: PMC7014263 DOI: 10.3390/ijms21020637] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Revised: 01/15/2020] [Accepted: 01/16/2020] [Indexed: 01/08/2023] Open
Abstract
DNA methylation in mammals is essential for numerous biological functions, such as ensuring chromosomal stability, genomic imprinting, and X-chromosome inactivation through transcriptional regulation. Gene knockout of DNA methyltransferases and demethylation enzymes has made significant contributions to analyzing the functions of DNA methylation in development. By applying epigenome editing, it is now possible to manipulate DNA methylation in specific genomic regions and to understand the functions of these modifications. In this review, we first describe recent DNA methylation editing technology. We then focused on changes in DNA methylation status during mammalian gametogenesis and preimplantation development, and have discussed the implications of applying this technology to early embryos.
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Barrett CM, McCracken R, Elmer J, Haynes KA. Components from the Human c-myb Transcriptional Regulation System Reactivate Epigenetically Repressed Transgenes. Int J Mol Sci 2020; 21:E530. [PMID: 31947658 PMCID: PMC7014047 DOI: 10.3390/ijms21020530] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Revised: 01/07/2020] [Accepted: 01/07/2020] [Indexed: 11/16/2022] Open
Abstract
A persistent challenge for mammalian cell engineering is the undesirable epigenetic silencing of transgenes. Foreign DNA can be incorporated into closed chromatin before and after it has been integrated into a host cell's genome. To identify elements that mitigate epigenetic silencing, we tested components from the c-myb and NF-kB transcriptional regulation systems in transiently transfected DNA and at chromosomally integrated transgenes in PC-3 and HEK 293 cells. DNA binding sites for MYB (c-myb) placed upstream of a minimal promoter enhanced expression from transiently transfected plasmid DNA. We targeted p65 and MYB fusion proteins to a chromosomal transgene, UAS-Tk-luciferase, that was silenced by ectopic Polycomb chromatin complexes. Transient expression of Gal4-MYB induced an activated state that resisted complete re-silencing. We used custom guide RNAs and dCas9-MYB to target MYB to different positions relative to the promoter and observed that transgene activation within ectopic Polycomb chromatin required proximity of dCas9-MYB to the transcriptional start site. Our report demonstrates the use of MYB in the context of the CRISPR-activation system, showing that DNA elements and fusion proteins derived from c-myb can mitigate epigenetic silencing to improve transgene expression in engineered cell lines.
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Affiliation(s)
- Cassandra M. Barrett
- School of Biological and Health Systems Engineering, Arizona State University, 501 East Tyler Mall, Tempe, AZ 85287, USA;
| | - Reilly McCracken
- Department of Chemical Engineering, Villanova University, 217 White Hall, 800 East Lancaster Avenue, Villanova, PA 19085, USA; (R.M.); (J.E.)
| | - Jacob Elmer
- Department of Chemical Engineering, Villanova University, 217 White Hall, 800 East Lancaster Avenue, Villanova, PA 19085, USA; (R.M.); (J.E.)
| | - Karmella A. Haynes
- School of Biological and Health Systems Engineering, Arizona State University, 501 East Tyler Mall, Tempe, AZ 85287, USA;
- Wallace H. Coulter Department of Biomedical Engineering, Emory University, Atlanta, GA 30322, USA
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