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Zhu C, Hao Z, Liu D. Reshaping the Landscape of the Genome: Toolkits for Precise DNA Methylation Manipulation and Beyond. JACS AU 2024; 4:40-57. [PMID: 38274248 PMCID: PMC10806789 DOI: 10.1021/jacsau.3c00671] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 11/26/2023] [Accepted: 12/01/2023] [Indexed: 01/27/2024]
Abstract
DNA methylation plays a pivotal role in various biological processes and is highly related to multiple diseases. The exact functions of DNA methylation are still puzzling due to its uneven distribution, dynamic conversion, and complex interactions with other substances. Current methods such as chemical- and enzyme-based sequencing techniques have enabled us to pinpoint DNA methylation at single-base resolution, which necessitated the manipulation of DNA methylation at comparable resolution to precisely illustrate the correlations and causal relationships between the functions of DNA methylation and its spatiotemporal patterns. Here a perspective on the past, recent process, and future of precise DNA methylation tools is provided. Specifically, genome-wide and site-specific manipulation of DNA methylation methods is discussed, with an emphasis on their principles, limitations, applications, and future developmental directions.
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Affiliation(s)
- Chenyou Zhu
- Engineering
Research Center of Advanced Rare Earth Materials, Ministry of Education,
Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Ziyang Hao
- School
of Pharmaceutical Sciences, Capital Medical
University, Beijing, 100069, PR China
| | - Dongsheng Liu
- Engineering
Research Center of Advanced Rare Earth Materials, Ministry of Education,
Department of Chemistry, Tsinghua University, Beijing 100084, China
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2
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Yagci ZB, Kelkar GR, Johnson TJ, Sen D, Keung AJ. Designing Epigenome Editors: Considerations of Biochemical and Locus Specificities. Methods Mol Biol 2024; 2842:23-55. [PMID: 39012589 DOI: 10.1007/978-1-0716-4051-7_2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/17/2024]
Abstract
The advent of locus-specific protein recruitment technologies has enabled a new class of studies in chromatin biology. Epigenome editors (EEs) enable biochemical modifications of chromatin at almost any specific endogenous locus. Their locus-specificity unlocks unique information including the functional roles of distinct modifications at specific genomic loci. Given the growing interest in using these tools for biological and translational studies, there are many specific design considerations depending on the scientific question or clinical need. Here, we present and discuss important design considerations and challenges regarding the biochemical and locus specificities of epigenome editors. These include how to: account for the complex biochemical diversity of chromatin; control for potential interdependency of epigenome editors and their resultant modifications; avoid sequestration effects; quantify the locus specificity of epigenome editors; and improve locus-specificity by considering concentration, affinity, avidity, and sequestration effects.
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Affiliation(s)
- Z Begum Yagci
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC, USA
| | - Gautami R Kelkar
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC, USA
| | - Tyler J Johnson
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC, USA
| | - Dilara Sen
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC, USA
| | - Albert J Keung
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC, USA.
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3
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Rots MG, Jeltsch A. Development of Locus-Directed Editing of the Epigenome from Basic Mechanistic Engineering to First Clinical Applications. Methods Mol Biol 2024; 2842:3-20. [PMID: 39012588 DOI: 10.1007/978-1-0716-4051-7_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/17/2024]
Abstract
The introduction of CRISPR/Cas systems has resulted in a strong impulse for the field of gene-targeted epigenome/epigenetic reprogramming (EpiEditing), where EpiEditors consisting of a DNA binding part for targeting and an enzymatic part for rewriting of chromatin modifications are applied in cells to alter chromatin modifications at targeted genome loci in a directed manner. Pioneering studies preceding this era indicated causal relationships of chromatin marks instructing gene expression. The accumulating evidence of chromatin reprogramming of a given genomic locus resulting in gene expression changes opened the field for mainstream applications of this technology in basic and clinical research. The growing knowledge on chromatin biology and application of EpiEditing tools, however, also revealed a lack of predictability of the efficiency of EpiEditing in some cases. In this perspective, the dependence of critical parameters such as specificity, effectivity, and sustainability of EpiEditing on experimental settings and conditions including the expression levels and expression times of the EpiEditors, their chromatin binding affinity and specificity, and the crosstalk between EpiEditors and cellular epigenome modifiers are discussed. These considerations highlight the intimate connection between the outcome of epigenome reprogramming and the details of the technical approaches toward EpiEditing, which are the main topic of this volume of Methods in Molecular Biology. Once established in a fully functional "plug-and-play" mode, EpiEditing will allow to better understand gene expression control and to translate such knowledge into therapeutic tools. These expectations are beginning to be met as shown by various in vivo EpiEditing applications published in recent years, several companies aiming to exploit the therapeutic power of EpiEditing and the first clinical trial initiated.
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Affiliation(s)
- Marianne G Rots
- Department Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands.
| | - Albert Jeltsch
- Department of Biochemistry, Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, Stuttgart, Germany.
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4
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Hamilton PJ, Lim CJ, Nestler EJ, Heller EA. Neuroepigenetic Editing. Methods Mol Biol 2024; 2842:129-152. [PMID: 39012593 DOI: 10.1007/978-1-0716-4051-7_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/17/2024]
Abstract
Epigenetic regulation is intrinsic to basic neurobiological function as well as neurological disease. Regulation of chromatin-modifying enzymes in the brain is critical during both development and adulthood and in response to external stimuli. Biochemical studies are complemented by numerous next-generation sequencing (NGS) studies that quantify global changes in gene expression, chromatin accessibility, histone and DNA modifications in neurons and glial cells. Neuroepigenetic editing tools are essential to distinguish between the mere presence and functional relevance of histone and DNA modifications to gene transcription in the brain and animal behavior. This review discusses current advances in neuroepigenetic editing, highlighting methodological considerations pertinent to neuroscience, such as delivery methods and the spatiotemporal specificity of editing and it demonstrates the enormous potential of epigenetic editing for basic neurobiological research and therapeutic application.
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Affiliation(s)
- Peter J Hamilton
- Department of Anatomy & Neurobiology, Virginia Commonwealth University School of Medicine, Richmond, VA, USA
| | - Carissa J Lim
- Department of Systems Pharmacology and Translational Therapeutics, The University of Pennsylvania, Philadelphia, PA, USA
| | - Eric J Nestler
- The Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Elizabeth A Heller
- Department of Systems Pharmacology and Translational Therapeutics, The University of Pennsylvania, Philadelphia, PA, USA.
- Department of Systems Pharmacology and Translational Therapeutics, Institute for Translational Medicine and Therapeutics, Philadelphia, PA, USA.
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5
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Fontana L, Alahouzou Z, Miccio A, Antoniou P. Epigenetic Regulation of β-Globin Genes and the Potential to Treat Hemoglobinopathies through Epigenome Editing. Genes (Basel) 2023; 14:genes14030577. [PMID: 36980849 PMCID: PMC10048329 DOI: 10.3390/genes14030577] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Revised: 02/21/2023] [Accepted: 02/23/2023] [Indexed: 03/03/2023] Open
Abstract
Beta-like globin gene expression is developmentally regulated during life by transcription factors, chromatin looping and epigenome modifications of the β-globin locus. Epigenome modifications, such as histone methylation/demethylation and acetylation/deacetylation and DNA methylation, are associated with up- or down-regulation of gene expression. The understanding of these mechanisms and their outcome in gene expression has paved the way to the development of new therapeutic strategies for treating various diseases, such as β-hemoglobinopathies. Histone deacetylase and DNA methyl-transferase inhibitors are currently being tested in clinical trials for hemoglobinopathies patients. However, these approaches are often uncertain, non-specific and their global effect poses serious safety concerns. Epigenome editing is a recently developed and promising tool that consists of a DNA recognition domain (zinc finger, transcription activator-like effector or dead clustered regularly interspaced short palindromic repeats Cas9) fused to the catalytic domain of a chromatin-modifying enzyme. It offers a more specific targeting of disease-related genes (e.g., the ability to reactivate the fetal γ-globin genes and improve the hemoglobinopathy phenotype) and it facilitates the development of scarless gene therapy approaches. Here, we summarize the mechanisms of epigenome regulation of the β-globin locus, and we discuss the application of epigenome editing for the treatment of hemoglobinopathies.
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Affiliation(s)
- Letizia Fontana
- Laboratory of Chromatin and Gene Regulation during Development, INSERM UMR 1163, Imagine Institute, Université Paris Cité, F-75015 Paris, France
| | - Zoe Alahouzou
- Laboratory of Chromatin and Gene Regulation during Development, INSERM UMR 1163, Imagine Institute, Université Paris Cité, F-75015 Paris, France
| | - Annarita Miccio
- Laboratory of Chromatin and Gene Regulation during Development, INSERM UMR 1163, Imagine Institute, Université Paris Cité, F-75015 Paris, France
- Correspondence: (A.M.); (P.A.)
| | - Panagiotis Antoniou
- Laboratory of Chromatin and Gene Regulation during Development, INSERM UMR 1163, Imagine Institute, Université Paris Cité, F-75015 Paris, France
- Genome Engineering, Discovery Sciences, BioPharmaceuticals R&D Unit, AstraZeneca, 431 50 Gothenburg, Sweden
- Correspondence: (A.M.); (P.A.)
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PIWI-Interacting RNA (piRNA) and Epigenetic Editing in Environmental Health Sciences. Curr Environ Health Rep 2022; 9:650-660. [PMID: 35917009 DOI: 10.1007/s40572-022-00372-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/28/2022] [Indexed: 01/31/2023]
Abstract
PURPOSE OF REVIEW: The epigenome modulates gene expression in response to environmental stimuli. Modifications to the epigenome are potentially reversible, making them a promising therapeutic approach to mitigate environmental exposure effects on human health. This review details currently available genome and epigenome editing technologies and highlights ncRNA, including piRNA, as potential tools for targeted epigenome editing. RECENT FINDINGS: Zinc finger nuclease (ZFN), transcription activator-like effector nuclease (TALEN), and clustered regularly interspaced short palindromic repeats (CRISPR) associated nuclease (CRISPR/Cas) research has significantly advanced genome editing technology, with broad promise in genetic research and targeted therapies. Initial epigenome-directed therapies relied on global modification and suffered from limited specificity. Adapted from current genome editing tools, zinc finger protein (ZFP), TALE, and CRISPR/nuclease-deactivated Cas (dCas) systems now confer locus-specific epigenome editing, with promising applicability in the field of environmental health sciences. However, high incidence of off-target effects and time taken for screening limit their use. FUTURE DEVELOPMENT: ncRNA serve as a versatile biomarker with well-characterized regulatory mechanisms that can easily be adapted to edit the epigenome. For instance, the transposon silencing mechanism of germline PIWI-interacting RNAs (piRNA) could be engineered to specifically methylate a given gene, overcoming pitfalls of current global modifiers. Future developments in epigenome editing technologies will inform risk assessment through mechanistic investigation and serve as potential modes of intervention to mitigate environmentally induced adverse health outcomes later in life.
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de Mendoza A, Nguyen TV, Ford E, Poppe D, Buckberry S, Pflueger J, Grimmer MR, Stolzenburg S, Bogdanovic O, Oshlack A, Farnham PJ, Blancafort P, Lister R. Large-scale manipulation of promoter DNA methylation reveals context-specific transcriptional responses and stability. Genome Biol 2022; 23:163. [PMID: 35883107 PMCID: PMC9316731 DOI: 10.1186/s13059-022-02728-5] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Accepted: 07/06/2022] [Indexed: 12/22/2022] Open
Abstract
Background Cytosine DNA methylation is widely described as a transcriptional repressive mark with the capacity to silence promoters. Epigenome engineering techniques enable direct testing of the effect of induced DNA methylation on endogenous promoters; however, the downstream effects have not yet been comprehensively assessed. Results Here, we simultaneously induce methylation at thousands of promoters in human cells using an engineered zinc finger-DNMT3A fusion protein, enabling us to test the effect of forced DNA methylation upon transcription, chromatin accessibility, histone modifications, and DNA methylation persistence after the removal of the fusion protein. We find that transcriptional responses to DNA methylation are highly context-specific, including lack of repression, as well as cases of increased gene expression, which appears to be driven by the eviction of methyl-sensitive transcriptional repressors. Furthermore, we find that some regulatory networks can override DNA methylation and that promoter methylation can cause alternative promoter usage. DNA methylation deposited at promoter and distal regulatory regions is rapidly erased after removal of the zinc finger-DNMT3A fusion protein, in a process combining passive and TET-mediated demethylation. Finally, we demonstrate that induced DNA methylation can exist simultaneously on promoter nucleosomes that possess the active histone modification H3K4me3, or DNA bound by the initiated form of RNA polymerase II. Conclusions These findings have important implications for epigenome engineering and demonstrate that the response of promoters to DNA methylation is more complex than previously appreciated. Supplementary Information The online version contains supplementary material available at 10.1186/s13059-022-02728-5.
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Affiliation(s)
- Alex de Mendoza
- Australian Research Council Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Perth, WA, 6009, Australia. .,Harry Perkins Institute of Medical Research, QEII Medical Centre and Centre for Medical Research, The University of Western Australia, Perth, WA, 6009, Australia. .,School of Biological and Behavioural Sciences, Queen Mary University of London, Mile End Road, London, E1 4NS, UK.
| | - Trung Viet Nguyen
- Australian Research Council Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Perth, WA, 6009, Australia.,Harry Perkins Institute of Medical Research, QEII Medical Centre and Centre for Medical Research, The University of Western Australia, Perth, WA, 6009, Australia
| | - Ethan Ford
- Australian Research Council Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Perth, WA, 6009, Australia.,Harry Perkins Institute of Medical Research, QEII Medical Centre and Centre for Medical Research, The University of Western Australia, Perth, WA, 6009, Australia
| | - Daniel Poppe
- Australian Research Council Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Perth, WA, 6009, Australia.,Harry Perkins Institute of Medical Research, QEII Medical Centre and Centre for Medical Research, The University of Western Australia, Perth, WA, 6009, Australia
| | - Sam Buckberry
- Australian Research Council Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Perth, WA, 6009, Australia.,Harry Perkins Institute of Medical Research, QEII Medical Centre and Centre for Medical Research, The University of Western Australia, Perth, WA, 6009, Australia
| | - Jahnvi Pflueger
- Australian Research Council Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Perth, WA, 6009, Australia.,Harry Perkins Institute of Medical Research, QEII Medical Centre and Centre for Medical Research, The University of Western Australia, Perth, WA, 6009, Australia
| | - Matthew R Grimmer
- Department of Biochemistry and Molecular Medicine, University of Southern California, 1450 Biggy St, Los Angeles, CA, 90089, USA.,Integrated Genetics and Genomics, University of California, Davis, 451 Health Sciences Dr, Davis, CA, 95616, USA.,Department of Neurological Surgery, University of California, 1450 3rd St, San Francisco, CA, 94158, USA
| | - Sabine Stolzenburg
- School of Anatomy, Physiology and Human Biology, The University of Western Australia, 35 Stirling Hwy, Crawley, WA, 6009, Australia
| | - Ozren Bogdanovic
- Australian Research Council Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Perth, WA, 6009, Australia.,Genomics and Epigenetics Division, Garvan Institute of Medical Research, Sydney, New South Wales, Australia.,School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales, 2052, Australia
| | - Alicia Oshlack
- The Peter MacCallum Cancer Centre, 305 Grattan St, Melbourne, VIC, 3000, Australia.,School of BioScience, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Peggy J Farnham
- Department of Biochemistry and Molecular Medicine, University of Southern California, 1450 Biggy St, Los Angeles, CA, 90089, USA
| | - Pilar Blancafort
- Harry Perkins Institute of Medical Research, QEII Medical Centre and Centre for Medical Research, The University of Western Australia, Perth, WA, 6009, Australia.,School of Anatomy, Physiology and Human Biology, The University of Western Australia, 35 Stirling Hwy, Crawley, WA, 6009, Australia.,The Greehey Children's Cancer Research Institute, The University of Texas Health Science Center at San Antonio, San Antonio, TX, USA
| | - Ryan Lister
- Australian Research Council Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Perth, WA, 6009, Australia. .,Harry Perkins Institute of Medical Research, QEII Medical Centre and Centre for Medical Research, The University of Western Australia, Perth, WA, 6009, Australia.
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Wang J, Li D, Yang J, Chang L, Zhang R, Li J. CRISPR/Cas9-mediated epigenetic editing tool: An optimized strategy for targeting de novo DNA methylation with stable status via homology directed repair pathway. Biochimie 2022; 202:190-205. [DOI: 10.1016/j.biochi.2022.07.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Revised: 07/07/2022] [Accepted: 07/22/2022] [Indexed: 11/30/2022]
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Pacheco MB, Camilo V, Henrique R, Jerónimo C. Epigenetic Editing in Prostate Cancer: Challenges and Opportunities. Epigenetics 2021; 17:564-588. [PMID: 34130596 DOI: 10.1080/15592294.2021.1939477] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Abstract
Epigenome editing consists of fusing a predesigned DNA recognition unit to the catalytic domain of a chromatin modifying enzyme leading to the introduction or removal of an epigenetic mark at a specific locus. These platforms enabled the study of the mechanisms and roles of epigenetic changes in several research domains such as those addressing pathogenesis and progression of cancer. Despite the continued efforts required to overcome some limitations, which include specificity, off-target effects, efficacy, and longevity, these tools have been rapidly progressing and improving.Since prostate cancer is characterized by multiple genetic and epigenetic alterations that affect different signalling pathways, epigenetic editing constitutes a promising strategy to hamper cancer progression. Therefore, by modulating chromatin structure through epigenome editing, its conformation might be better understood and events that drive prostate carcinogenesis might be further unveiled.This review describes the different epigenome engineering tools, their mechanisms concerning gene's expression and regulation, highlighting the challenges and opportunities concerning prostate cancer research.
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Affiliation(s)
- Mariana Brütt Pacheco
- Cancer Biology and Epigenetics Group, Research Center (GEBC CI-IPOP), Portuguese Oncology Institute of Porto (IPO Porto) & Porto Comprehensive Cancer Center (P.CCC), R. Dr. António Bernardino de Almeida, Porto, Portugal
| | - Vânia Camilo
- Cancer Biology and Epigenetics Group, Research Center (GEBC CI-IPOP), Portuguese Oncology Institute of Porto (IPO Porto) & Porto Comprehensive Cancer Center (P.CCC), R. Dr. António Bernardino de Almeida, Porto, Portugal
| | - Rui Henrique
- Cancer Biology and Epigenetics Group, Research Center (GEBC CI-IPOP), Portuguese Oncology Institute of Porto (IPO Porto) & Porto Comprehensive Cancer Center (P.CCC), R. Dr. António Bernardino de Almeida, Porto, Portugal.,Department of Pathology, Portuguese Oncology Institute of Porto (IPOP), R. DR. António Bernardino De Almeida, Porto, Portugal.,Department of Pathology and Molecular Immunology, School of Medicine & Biomedical Sciences, University of Porto (ICBAS-UP), Rua Jorge Viterbo Ferreira 228, Porto, Portugal
| | - Carmen Jerónimo
- Cancer Biology and Epigenetics Group, Research Center (GEBC CI-IPOP), Portuguese Oncology Institute of Porto (IPO Porto) & Porto Comprehensive Cancer Center (P.CCC), R. Dr. António Bernardino de Almeida, Porto, Portugal.,Department of Pathology and Molecular Immunology, School of Medicine & Biomedical Sciences, University of Porto (ICBAS-UP), Rua Jorge Viterbo Ferreira 228, Porto, Portugal
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Taylor JT, Ellison S, Pandele A, Wood S, Nathan E, Forte G, Parker H, Zindy E, Elvin M, Dickson A, Williams KJ, Karabatsou K, McCabe M, McBain C, Bigger BW. Actinomycin D downregulates Sox2 and improves survival in preclinical models of recurrent glioblastoma. Neuro Oncol 2021; 22:1289-1301. [PMID: 32227096 PMCID: PMC7523458 DOI: 10.1093/neuonc/noaa051] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Glioblastoma (GBM) has been extensively researched over the last few decades, yet despite aggressive multimodal treatment, recurrence is inevitable and second-line treatment options are limited. Here, we demonstrate how high-throughput screening (HTS) in multicellular spheroids can generate physiologically relevant patient chemosensitivity data using patient-derived cells in a rapid and cost-effective manner. Our HTS system identified actinomycin D (ACTD) to be highly cytotoxic over a panel of 12 patient-derived glioma stemlike cell (GSC) lines. ACTD is an antineoplastic antibiotic used in the treatment of childhood cancers. Here, we validate ACTD as a potential repurposed therapeutic for GBM in 3-dimensional GSC cultures and patient-derived xenograft models of recurrent glioblastoma. METHODS Twelve patient-derived GSC lines were screened at 10 µM, as multicellular spheroids, in a 384-well serum-free assay with 133 FDA-approved compounds. GSCs were then treated in vitro with ACTD at established half-maximal inhibitory concentrations (IC50). Downregulation of sex determining region Y-box 2 (Sox2), a stem cell transcription factor, was investigated via western blot and through immunohistological assessment of murine brain tissue. RESULTS Treatment with ACTD was shown to significantly reduce tumor growth in 2 recurrent GBM patient-derived models and significantly increased survival. ACTD is also shown to specifically downregulate the expression of Sox2 both in vitro and in vivo. CONCLUSION These findings indicate that, as predicted by our HTS, ACTD could deplete the cancer stem cell population within the tumor mass, ultimately leading to a delay in tumor progression. KEY POINTS 1. High-throughput chemosensitivity data demonstrated the broad efficacy of actinomycin D, which was validated in 3 preclinical models of glioblastoma.2. Actinomycin D downregulated Sox2 in vitro and in vivo, indicating that this agent could target the stem cell population of GBM tumors.
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Affiliation(s)
- Jessica T Taylor
- Brain Tumor Research Group, Stem Cell and Neurotherapies Laboratory, Division of Cell Matrix Biology and Regenerative Medicine, University of Manchester, Manchester, UK
| | - Stuart Ellison
- Brain Tumor Research Group, Stem Cell and Neurotherapies Laboratory, Division of Cell Matrix Biology and Regenerative Medicine, University of Manchester, Manchester, UK
| | - Alina Pandele
- Brain Tumor Research Group, Stem Cell and Neurotherapies Laboratory, Division of Cell Matrix Biology and Regenerative Medicine, University of Manchester, Manchester, UK
| | - Shaun Wood
- Brain Tumor Research Group, Stem Cell and Neurotherapies Laboratory, Division of Cell Matrix Biology and Regenerative Medicine, University of Manchester, Manchester, UK
| | - Erica Nathan
- CRUK Cambridge Institute, Li Ka Shing Centre, Cambridge, UK
| | - Gabriella Forte
- Brain Tumor Research Group, Stem Cell and Neurotherapies Laboratory, Division of Cell Matrix Biology and Regenerative Medicine, University of Manchester, Manchester, UK
| | - Helen Parker
- Brain Tumor Research Group, Stem Cell and Neurotherapies Laboratory, Division of Cell Matrix Biology and Regenerative Medicine, University of Manchester, Manchester, UK
| | - Egor Zindy
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - Mark Elvin
- Manchester Institute of Biotechnology, Faculty of Science and Engineering, University of Manchester, Manchester, UK
| | - Alan Dickson
- Manchester Institute of Biotechnology, Faculty of Science and Engineering, University of Manchester, Manchester, UK
| | - Kaye J Williams
- Division of Pharmacy and Optometry, School of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | | | - Martin McCabe
- Division of Cancer Sciences, University of Manchester, Manchester, UK
| | - Catherine McBain
- Department of Clinical Oncology, The Christie NHS FT, Manchester, UK
| | - Brian W Bigger
- Brain Tumor Research Group, Stem Cell and Neurotherapies Laboratory, Division of Cell Matrix Biology and Regenerative Medicine, University of Manchester, Manchester, UK
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Scott TA, O’Meally D, Grepo NA, Soemardy C, Lazar DC, Zheng Y, Weinberg MS, Planelles V, Morris KV. Broadly active zinc finger protein-guided transcriptional activation of HIV-1. Mol Ther Methods Clin Dev 2021; 20:18-29. [PMID: 33335944 PMCID: PMC7726486 DOI: 10.1016/j.omtm.2020.10.018] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Accepted: 10/21/2020] [Indexed: 12/14/2022]
Abstract
Human immunodeficiency virus type 1 (HIV-1) causes a persistent viral infection resulting in the demise of immune regulatory cells. Clearance of HIV-1 infection results in integration of proviral DNA into the genome of host cells, which provides a means for evasion and long-term persistence. A therapeutic compound that specifically targets and sustainably activates a latent HIV-1 provirus could be transformative and is the goal for the "shock-and-kill" approach to a functional cure for HIV-1. Substantial progress has been made toward the development of recombinant proteins that target specific genomic loci for gene activation, repression, or inactivation by directed mutations. However, most of these modalities are too large or too complex for efficient therapeutic application. We describe here the development and testing of a novel recombinant zinc finger protein transactivator, ZFP-362-VPR, which specifically and potently enhances proviral HIV-1 transcription both in established latency models and activity across different viral clades. Additionally, ZFP-362-VPR-activated HIV-1 reporter gene expression in a well-established primary human CD4+ T cell latency model and off-target pathways were determined by transcriptome analyses. This study provides clear proof of concept for the application of a novel, therapeutically relevant, protein transactivator to purge cellular reservoirs of HIV-1.
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Affiliation(s)
- Tristan A. Scott
- Center for Gene Therapy, City of Hope, Beckman Research Institute and Hematological Malignancy and Stem Cell Transplantation Institute at the City of Hope, 1500 E. Duarte Rd., Duarte, CA 91010, USA
| | - Denis O’Meally
- Center for Gene Therapy, City of Hope, Beckman Research Institute and Hematological Malignancy and Stem Cell Transplantation Institute at the City of Hope, 1500 E. Duarte Rd., Duarte, CA 91010, USA
| | - Nicole Anne Grepo
- Center for Gene Therapy, City of Hope, Beckman Research Institute and Hematological Malignancy and Stem Cell Transplantation Institute at the City of Hope, 1500 E. Duarte Rd., Duarte, CA 91010, USA
| | - Citradewi Soemardy
- Center for Gene Therapy, City of Hope, Beckman Research Institute and Hematological Malignancy and Stem Cell Transplantation Institute at the City of Hope, 1500 E. Duarte Rd., Duarte, CA 91010, USA
| | - Daniel C. Lazar
- Department of Immunology and Infectious Disease, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Yue Zheng
- University of Utah School of Medicine, Division of Microbiology and Immunology, Department of Pathology, Salt Lake City, UT 92037, USA
| | - Marc S. Weinberg
- Department of Immunology and Infectious Disease, The Scripps Research Institute, La Jolla, CA 92037, USA
- Wits-SAMRC Antiviral Gene Therapy Research Unit, Department of Molecular Medicine & Hematology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- HIV Pathogenesis Research Unit, Department of Molecular Medicine and Haematology, School of Pathology, University of the Witwatersrand, Johannesburg, South Africa
| | - Vicente Planelles
- University of Utah School of Medicine, Division of Microbiology and Immunology, Department of Pathology, Salt Lake City, UT 92037, USA
| | - Kevin V. Morris
- Center for Gene Therapy, City of Hope, Beckman Research Institute and Hematological Malignancy and Stem Cell Transplantation Institute at the City of Hope, 1500 E. Duarte Rd., Duarte, CA 91010, USA
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12
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Broche J, Kungulovski G, Bashtrykov P, Rathert P, Jeltsch A. Genome-wide investigation of the dynamic changes of epigenome modifications after global DNA methylation editing. Nucleic Acids Res 2021; 49:158-176. [PMID: 33300025 PMCID: PMC7797067 DOI: 10.1093/nar/gkaa1169] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Revised: 11/05/2020] [Accepted: 11/17/2020] [Indexed: 12/21/2022] Open
Abstract
Chromatin properties are regulated by complex networks of epigenome modifications. Currently, it is unclear how these modifications interact and if they control downstream effects such as gene expression. We employed promiscuous chromatin binding of a zinc finger fused catalytic domain of DNMT3A to introduce DNA methylation in HEK293 cells at many CpG islands (CGIs) and systematically investigated the dynamics of the introduced DNA methylation and the consequent changes of the epigenome network. We observed efficient methylation at thousands of CGIs, but it was unstable at about 90% of them, highlighting the power of genome-wide molecular processes that protect CGIs against DNA methylation. Partially stable methylation was observed at about 1000 CGIs, which showed enrichment in H3K27me3. Globally, the introduced DNA methylation strongly correlated with a decrease in gene expression indicating a direct effect. Similarly, global but transient reductions in H3K4me3 and H3K27ac were observed after DNA methylation but no changes were found for H3K9me3 and H3K36me3. Our data provide a global and time-resolved view on the network of epigenome modifications, their connections with DNA methylation and the responses triggered by artificial DNA methylation revealing a direct repressive effect of DNA methylation in CGIs on H3K4me3, histone acetylation, and gene expression.
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Affiliation(s)
- Julian Broche
- Department of Biochemistry, Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, 70569 Stuttgart, Germany
| | - Goran Kungulovski
- Department of Biochemistry, Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, 70569 Stuttgart, Germany
| | - Pavel Bashtrykov
- Department of Biochemistry, Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, 70569 Stuttgart, Germany
| | - Philipp Rathert
- Department of Biochemistry, Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, 70569 Stuttgart, Germany
| | - Albert Jeltsch
- Department of Biochemistry, Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, 70569 Stuttgart, Germany
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13
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Sgro A, Blancafort P. Epigenome engineering: new technologies for precision medicine. Nucleic Acids Res 2021; 48:12453-12482. [PMID: 33196851 PMCID: PMC7736826 DOI: 10.1093/nar/gkaa1000] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Revised: 10/10/2020] [Accepted: 10/16/2020] [Indexed: 02/07/2023] Open
Abstract
Chromatin adopts different configurations that are regulated by reversible covalent modifications, referred to as epigenetic marks. Epigenetic inhibitors have been approved for clinical use to restore epigenetic aberrations that result in silencing of tumor-suppressor genes, oncogene addictions, and enhancement of immune responses. However, these drugs suffer from major limitations, such as a lack of locus selectivity and potential toxicities. Technological advances have opened a new era of precision molecular medicine to reprogram cellular physiology. The locus-specificity of CRISPR/dCas9/12a to manipulate the epigenome is rapidly becoming a highly promising strategy for personalized medicine. This review focuses on new state-of-the-art epigenome editing approaches to modify the epigenome of neoplasms and other disease models towards a more 'normal-like state', having characteristics of normal tissue counterparts. We highlight biomolecular engineering methodologies to assemble, regulate, and deliver multiple epigenetic effectors that maximize the longevity of the therapeutic effect, and we discuss limitations of the platforms such as targeting efficiency and intracellular delivery for future clinical applications.
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Affiliation(s)
- Agustin Sgro
- Cancer Epigenetics Laboratory, The Harry Perkins Institute of Medical Research, Nedlands, Western Australia 6009, Australia.,School of Human Sciences, The University of Western Australia, Crawley, Perth, Western Australia 6009, Australia
| | - Pilar Blancafort
- Cancer Epigenetics Laboratory, The Harry Perkins Institute of Medical Research, Nedlands, Western Australia 6009, Australia.,School of Human Sciences, The University of Western Australia, Crawley, Perth, Western Australia 6009, Australia.,The Greehey Children's Cancer Research Institute, The University of Texas Health Science Center, San Antonio, TX 78229, USA
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14
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Fal K, Tomkova D, Vachon G, Chabouté ME, Berr A, Carles CC. Chromatin Manipulation and Editing: Challenges, New Technologies and Their Use in Plants. Int J Mol Sci 2021; 22:E512. [PMID: 33419220 PMCID: PMC7825600 DOI: 10.3390/ijms22020512] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Revised: 12/29/2020] [Accepted: 12/30/2020] [Indexed: 12/25/2022] Open
Abstract
An ongoing challenge in functional epigenomics is to develop tools for precise manipulation of epigenetic marks. These tools would allow moving from correlation-based to causal-based findings, a necessary step to reach conclusions on mechanistic principles. In this review, we describe and discuss the advantages and limits of tools and technologies developed to impact epigenetic marks, and which could be employed to study their direct effect on nuclear and chromatin structure, on transcription, and their further genuine role in plant cell fate and development. On one hand, epigenome-wide approaches include drug inhibitors for chromatin modifiers or readers, nanobodies against histone marks or lines expressing modified histones or mutant chromatin effectors. On the other hand, locus-specific approaches consist in targeting precise regions on the chromatin, with engineered proteins able to modify epigenetic marks. Early systems use effectors in fusion with protein domains that recognize a specific DNA sequence (Zinc Finger or TALEs), while the more recent dCas9 approach operates through RNA-DNA interaction, thereby providing more flexibility and modularity for tool designs. Current developments of "second generation", chimeric dCas9 systems, aiming at better targeting efficiency and modifier capacity have recently been tested in plants and provided promising results. Finally, recent proof-of-concept studies forecast even finer tools, such as inducible/switchable systems, that will allow temporal analyses of the molecular events that follow a change in a specific chromatin mark.
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Affiliation(s)
- Kateryna Fal
- Laboratoire de Physiologie Cellulaire et Végétale, Université Grenoble Alpes, CNRS, CEA, INRAE, IRIG-LPCV, 38000 Grenoble, France; (K.F.); (G.V.)
| | - Denisa Tomkova
- Institut de Biologie Moléculaire des Plantes du CNRS, Université de Strasbourg, 12 rue du Général Zimmer, 67084 Strasbourg CEDEX, France; (D.T.); (M.-E.C.)
| | - Gilles Vachon
- Laboratoire de Physiologie Cellulaire et Végétale, Université Grenoble Alpes, CNRS, CEA, INRAE, IRIG-LPCV, 38000 Grenoble, France; (K.F.); (G.V.)
| | - Marie-Edith Chabouté
- Institut de Biologie Moléculaire des Plantes du CNRS, Université de Strasbourg, 12 rue du Général Zimmer, 67084 Strasbourg CEDEX, France; (D.T.); (M.-E.C.)
| | - Alexandre Berr
- Institut de Biologie Moléculaire des Plantes du CNRS, Université de Strasbourg, 12 rue du Général Zimmer, 67084 Strasbourg CEDEX, France; (D.T.); (M.-E.C.)
| | - Cristel C. Carles
- Laboratoire de Physiologie Cellulaire et Végétale, Université Grenoble Alpes, CNRS, CEA, INRAE, IRIG-LPCV, 38000 Grenoble, France; (K.F.); (G.V.)
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15
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Abstract
Methylation of DNA at cytosine bases is an important DNA modification underlying normal development and disease states. Despite decades of research into the biological function of DNA methylation, most of the observations so far have relied primarily on associative data between observed changes in DNA methylation states and local changes in transcriptional activity or chromatin state processes. This is primarily due to the lack of molecular tools to precisely modify DNA methylation in the genome. Recent advances in genome editing technologies have allowed repurposing the CRISPR-Cas9 system for epigenome editing by fusing the catalytically dead Cas9 (dCas9) to epigenome modifying enzymes. Moreover, methods of recruiting multiple protein domains, including the SunTag system, have increased the efficacy of epigenome editing at target sites. Here, we describe an end-to-end protocol for efficient targeted removal of DNA methylation by recruiting multiple catalytic domain of TET1 enzymes to the target sites with the dCas9-SunTag system, including sgRNA design, molecular cloning, delivery of plasmid into mammalian cells, and targeted DNA methylation analysis.
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Affiliation(s)
- Trung Viet Nguyen
- ARC Center of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Perth, WA, Australia
- The Harry Perkins Institute of Medical Research, Perth, WA, Australia
| | - Ryan Lister
- ARC Center of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Perth, WA, Australia.
- The Harry Perkins Institute of Medical Research, Perth, WA, Australia.
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16
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Chen M, Zhu H, Mao YJ, Cao N, Yu YL, Li LY, Zhao Q, Wu M, Ye M. Regulation of IL12B Expression in Human Macrophages by TALEN-mediated Epigenome Editing. Curr Med Sci 2020; 40:900-909. [PMID: 33123904 DOI: 10.1007/s11596-020-2249-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2019] [Accepted: 06/22/2020] [Indexed: 10/23/2022]
Abstract
Although the exact etiology of inflammatory bowel disease (IBD) remains unclear, exaggerated immune response in genetically predisposed individuals has been reported. Th1 and Th17 cells mediate IBD development. Macrophages produce IL-12 and IL-23 that share p40 subunit encoded by IL12B gene as heteromer partner to drive Th1 and Th17 differentiation. The available animal and human data strongly support the pathogenic role of IL-12/IL-23 in IBD development and suggest that blocking p40 might be the potential strategy for IBD treatment. Furthermore, aberrant alteration of some cytokines expression via epigenetic mechanisms is involved in pathogenesis of IBD. In this study, we analyzed core promoter region of IL12B gene and investigated whether IL12B expression could be regulated through targeted epigenetic modification with gene editing technology. Transcription activator-like effectors (TALEs) are widely used in the field of genome editing and can specifically target DNA sequence in the host genome. We synthesized the TALE DNA-binding domains that target the promoter of human IL12B gene and fused it with the functional catalytic domains of epigenetic enzymes. Transient expression of these engineered enzymes demonstrated that the TALE-DNMT3A targeted the selected IL12B promoter region, induced loci-specific DNA methylation, and down-regulated IL-12B expression in various human cell lines. Collectively, our data suggested that epigenetic editing of IL12B through methylating DNA on its promoter might be developed as a potential therapeutic strategy for IBD treatment.
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Affiliation(s)
- Meng Chen
- Department of Gastroenterology, Zhongnan Hospital, Wuhan University, Wuhan, 430071, China.,Hubei Clinical Center and Key Lab of Intestinal and Colorectal Diseases, Wuhan, 430071, China
| | - Hua Zhu
- Department of Gastroenterology, Zhongnan Hospital, Wuhan University, Wuhan, 430071, China.,Hubei Clinical Center and Key Lab of Intestinal and Colorectal Diseases, Wuhan, 430071, China
| | - Yu-Juan Mao
- Department of Gastroenterology, Zhongnan Hospital, Wuhan University, Wuhan, 430071, China.,Hubei Clinical Center and Key Lab of Intestinal and Colorectal Diseases, Wuhan, 430071, China
| | - Nan Cao
- Department of Gastroenterology, Zhongnan Hospital, Wuhan University, Wuhan, 430071, China.,Hubei Clinical Center and Key Lab of Intestinal and Colorectal Diseases, Wuhan, 430071, China
| | - Ya-Li Yu
- Department of Gastroenterology, Zhongnan Hospital, Wuhan University, Wuhan, 430071, China.,Hubei Clinical Center and Key Lab of Intestinal and Colorectal Diseases, Wuhan, 430071, China
| | - Lian-Yun Li
- College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Qiu Zhao
- Department of Gastroenterology, Zhongnan Hospital, Wuhan University, Wuhan, 430071, China.,Hubei Clinical Center and Key Lab of Intestinal and Colorectal Diseases, Wuhan, 430071, China
| | - Min Wu
- College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Mei Ye
- College of Life Sciences, Wuhan University, Wuhan, 430072, China.
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17
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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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18
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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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19
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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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20
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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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21
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Urbano A, Smith J, Weeks RJ, Chatterjee A. Gene-Specific Targeting of DNA Methylation in the Mammalian Genome. Cancers (Basel) 2019; 11:cancers11101515. [PMID: 31600992 PMCID: PMC6827012 DOI: 10.3390/cancers11101515] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Revised: 10/02/2019] [Accepted: 10/05/2019] [Indexed: 02/07/2023] Open
Abstract
DNA methylation is the most widely-studied epigenetic modification, playing a critical role in the regulation of gene expression. Dysregulation of DNA methylation is implicated in the pathogenesis of numerous diseases. For example, aberrant DNA methylation in promoter regions of tumor-suppressor genes has been strongly associated with the development and progression of many different tumors. Accordingly, technologies designed to manipulate DNA methylation at specific genomic loci are very important, especially in the context of cancer therapy. Traditionally, epigenomic editing technologies have centered around zinc finger proteins (ZFP)- and transcription activator-like effector protein (TALE)-based targeting. More recently, however, the emergence of clustered regulatory interspaced short palindromic repeats (CRISPR)-deactivated Cas9 (dCas9)-based editing systems have shown to be a more specific and efficient method for the targeted manipulation of DNA methylation. Here, we describe the regulation of the DNA methylome, its significance in cancer and the current state of locus-specific editing technologies for altering DNA methylation.
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Affiliation(s)
- Arthur Urbano
- Department of Pathology, Dunedin School of Medicine, University of Otago, 56 Hanover Street, Dunedin 9054, New Zealand.
| | - Jim Smith
- Department of Pathology, Dunedin School of Medicine, University of Otago, 56 Hanover Street, Dunedin 9054, New Zealand.
| | - Robert J Weeks
- Department of Pathology, Dunedin School of Medicine, University of Otago, 56 Hanover Street, Dunedin 9054, New Zealand.
| | - Aniruddha Chatterjee
- Department of Pathology, Dunedin School of Medicine, University of Otago, 56 Hanover Street, Dunedin 9054, New Zealand.
- Maurice Wilkins Centre for Molecular Biodiscovery, 3A Symonds Street, Private Bag 92019, Auckland, New Zealand.
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22
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Site-specific manipulation of Arabidopsis loci using CRISPR-Cas9 SunTag systems. Nat Commun 2019; 10:729. [PMID: 30760722 PMCID: PMC6374409 DOI: 10.1038/s41467-019-08736-7] [Citation(s) in RCA: 172] [Impact Index Per Article: 34.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2018] [Accepted: 01/23/2019] [Indexed: 01/10/2023] Open
Abstract
Understanding genomic functions requires site-specific manipulation of loci via efficient protein effector targeting systems. However, few approaches for targeted manipulation of the epigenome are available in plants. Here, we adapt the dCas9-SunTag system to engineer targeted gene activation and DNA methylation in Arabidopsis. We demonstrate that a dCas9-SunTag system utilizing the transcriptional activator VP64 drives robust and specific activation of several loci, including protein coding genes and transposable elements, in diverse chromatin contexts. In addition, we present a CRISPR-based methylation targeting system for plants, utilizing a SunTag system with the catalytic domain of the Nicotiana tabacum DRM methyltransferase, which efficiently targets DNA methylation to specific loci, including the FWA promoter, triggering a developmental phenotype, and the SUPERMAN promoter. These SunTag systems represent valuable tools for the site-specific manipulation of plant epigenomes.
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23
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Abstract
The advent of locus-specific protein recruitment technologies has enabled a new class of studies in chromatin biology. Epigenome editors enable biochemical modifications of chromatin at almost any specific endogenous locus. Their locus specificity unlocks unique information including the functional roles of distinct modifications at specific genomic loci. Given the growing interest in using these tools for biological and translational studies, there are many specific design considerations depending on the scientific question or clinical need. Here we present and discuss important design considerations and challenges regarding the biochemical and locus specificities of epigenome editors. These include how to account for the complex biochemical diversity of chromatin; control for potential interdependency of epigenome editors and their resultant modifications; avoid sequestration effects; quantify the locus specificity of epigenome editors; and improve locus specificity by considering concentration, affinity, avidity, and sequestration effects.
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24
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Moses C, Nugent F, Waryah CB, Garcia-Bloj B, Harvey AR, Blancafort P. Activating PTEN Tumor Suppressor Expression with the CRISPR/dCas9 System. MOLECULAR THERAPY. NUCLEIC ACIDS 2018; 14:287-300. [PMID: 30654190 PMCID: PMC6348769 DOI: 10.1016/j.omtn.2018.12.003] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Revised: 12/05/2018] [Accepted: 12/06/2018] [Indexed: 12/22/2022]
Abstract
PTEN expression is lost in many cancers, and even small changes in PTEN activity affect susceptibility and prognosis in a range of highly aggressive malignancies, such as melanoma and triple-negative breast cancer (TNBC). Loss of PTEN expression occurs via multiple mechanisms, including mutation, transcriptional repression and epigenetic silencing. Transcriptional repression of PTEN contributes to resistance to inhibitors used in the clinic, such as B-Raf inhibitors in BRAF mutant melanoma. We aimed to activate PTEN expression using the CRISPR system, specifically dead (d) Cas9 fused to the transactivator VP64-p65-Rta (VPR). dCas9-VPR was directed to the PTEN proximal promoter by single-guide RNAs (sgRNAs), in cancer cells that exhibited low levels of PTEN expression. The dCas9-VPR system increased PTEN expression in melanoma and TNBC cell lines, without transcriptional regulation at predicted off-target sgRNA binding sites. PTEN activation significantly repressed downstream oncogenic pathways, including AKT, mTOR, and MAPK signaling. BRAF V600E mutant melanoma cells transduced with dCas9-VPR displayed reduced migration, as well as diminished colony formation in the presence of B-Raf inhibitors, PI3K/mTOR inhibitors, and with combined PI3K/mTOR and B-Raf inhibition. CRISPR-mediated targeted activation of PTEN may provide an alternative therapeutic approach for highly aggressive cancers that are refractory to current treatments.
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Affiliation(s)
- Colette Moses
- Cancer Epigenetics Laboratory, The Harry Perkins Institute of Medical Research, 6 Verdun Street, Nedlands, WA 6009, Australia; School of Human Sciences, Faculty of Science, The University of Western Australia, 35 Stirling Highway, Perth, WA 6009, Australia
| | - Fiona 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
| | - Charlene Babra Waryah
- Cancer Epigenetics Laboratory, The Harry Perkins Institute of Medical Research, 6 Verdun Street, Nedlands, WA 6009, Australia
| | - Benjamin Garcia-Bloj
- Cancer Epigenetics Laboratory, The Harry Perkins Institute of Medical Research, 6 Verdun Street, Nedlands, WA 6009, Australia; School of Medicine, Faculty of Science, Universidad Mayor, Camino la Piramide 5750, Huechuraba 8580745, Santiago, Chile
| | - Alan 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
| | - Pilar Blancafort
- Cancer Epigenetics Laboratory, The Harry Perkins Institute of Medical Research, 6 Verdun Street, Nedlands, WA 6009, Australia; School of Human Sciences, Faculty of Science, The University of Western Australia, 35 Stirling Highway, Perth, WA 6009, Australia.
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25
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Geel TM, Ruiters MHJ, Cool RH, Halby L, Voshart DC, Andrade Ruiz L, Niezen-Koning KE, Arimondo PB, Rots MG. The past and presence of gene targeting: from chemicals and DNA via proteins to RNA. Philos Trans R Soc Lond B Biol Sci 2018; 373:20170077. [PMID: 29685979 PMCID: PMC5915719 DOI: 10.1098/rstb.2017.0077] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/28/2017] [Indexed: 12/19/2022] Open
Abstract
The ability to target DNA specifically at any given position within the genome allows many intriguing possibilities and has inspired scientists for decades. Early gene-targeting efforts exploited chemicals or DNA oligonucleotides to interfere with the DNA at a given location in order to inactivate a gene or to correct mutations. We here describe an example towards correcting a genetic mutation underlying Pompe's disease using a nucleotide-fused nuclease (TFO-MunI). In addition to the promise of gene correction, scientists soon realized that genes could be inactivated or even re-activated without inducing potentially harmful DNA damage by targeting transcriptional modulators to a particular gene. However, it proved difficult to fuse protein effector domains to the first generation of programmable DNA-binding agents. The engineering of gene-targeting proteins (zinc finger proteins (ZFPs), transcription activator-like effectors (TALEs)) circumvented this problem. The disadvantage of protein-based gene targeting is that a fusion protein needs to be engineered for every locus. The recent introduction of CRISPR/Cas offers a flexible approach to target a (fusion) protein to the locus of interest using cheap designer RNA molecules. Many research groups now exploit this platform and the first human clinical trials have been initiated: CRISPR/Cas has kicked off a new era of gene targeting and is revolutionizing biomedical sciences.This article is part of a discussion meeting issue 'Frontiers in epigenetic chemical biology'.
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Affiliation(s)
- T M Geel
- Epigenetic Editing, Dept Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, Hanzeplein 1, 9713 GZ Groningen, The Netherlands
| | - M H J Ruiters
- Epigenetic Editing, Dept Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, Hanzeplein 1, 9713 GZ Groningen, The Netherlands
| | - R H Cool
- Chemical and Pharmaceutical Biology, University of Groningen, Antonius Deusinglaan 1, 9713 AV Groningen, The Netherlands
| | - L Halby
- CNRS FRE3600 ETaC, bât IBCG, 31062 Toulouse, France
| | - D C Voshart
- Epigenetic Editing, Dept Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, Hanzeplein 1, 9713 GZ Groningen, The Netherlands
| | - L Andrade Ruiz
- Epigenetic Editing, Dept Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, Hanzeplein 1, 9713 GZ Groningen, The Netherlands
| | - K E Niezen-Koning
- Laboratory of Metabolic Diseases, Dept Laboratory Medicine, University of Groningen, University Medical Center Groningen, Hanzeplein 1, 9713 GZ Groningen, The Netherlands
| | - P B Arimondo
- CNRS FRE3600 ETaC, bât IBCG, 31062 Toulouse, France
| | - M G Rots
- Epigenetic Editing, Dept Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, Hanzeplein 1, 9713 GZ Groningen, The Netherlands
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Rhie SK, Yao L, Luo Z, Witt H, Schreiner S, Guo Y, Perez AA, Farnham PJ. ZFX acts as a transcriptional activator in multiple types of human tumors by binding downstream from transcription start sites at the majority of CpG island promoters. Genome Res 2018; 28:310-320. [PMID: 29429977 PMCID: PMC5848610 DOI: 10.1101/gr.228809.117] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2017] [Accepted: 01/26/2018] [Indexed: 12/29/2022]
Abstract
High expression of the transcription factor ZFX is correlated with proliferation, tumorigenesis, and patient survival in multiple types of human cancers. However, the mechanism by which ZFX influences transcriptional regulation has not been determined. We performed ChIP-seq in four cancer cell lines (representing kidney, colon, prostate, and breast cancers) to identify ZFX binding sites throughout the human genome. We identified roughly 9000 ZFX binding sites and found that most of the sites are in CpG island promoters. Moreover, genes with promoters bound by ZFX are expressed at higher levels than genes with promoters not bound by ZFX. To determine if ZFX contributes to regulation of the promoters to which it is bound, we performed RNA-seq analysis after knockdown of ZFX by siRNA in prostate and breast cancer cells. Many genes with promoters bound by ZFX were down-regulated upon ZFX knockdown, supporting the hypothesis that ZFX acts as a transcriptional activator. Surprisingly, ZFX binds at +240 bp downstream from the TSS of the responsive promoters. Using Nucleosome Occupancy and Methylome Sequencing (NOMe-seq), we show that ZFX binds between the open chromatin region at the TSS and the first downstream nucleosome, suggesting that ZFX may play a critical role in promoter architecture. We have also shown that a closely related zinc finger protein ZNF711 has a similar binding pattern at CpG island promoters, but ZNF711 may play a subordinate role to ZFX. This functional characterization of ZFX provides important new insights into transcription, chromatin structure, and the regulation of the cancer transcriptome.
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Affiliation(s)
- Suhn Kyong Rhie
- Department of Biochemistry and Molecular Medicine and the Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, California 90089, USA
| | - Lijun Yao
- Department of Biochemistry and Molecular Medicine and the Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, California 90089, USA
| | - Zhifei Luo
- Department of Biochemistry and Molecular Medicine and the Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, California 90089, USA
| | - Heather Witt
- Department of Biochemistry and Molecular Medicine and the Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, California 90089, USA
| | - Shannon Schreiner
- Department of Biochemistry and Molecular Medicine and the Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, California 90089, USA
| | - Yu Guo
- Department of Biochemistry and Molecular Medicine and the Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, California 90089, USA
| | - Andrew A Perez
- Department of Biochemistry and Molecular Medicine and the Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, California 90089, USA
| | - Peggy J Farnham
- Department of Biochemistry and Molecular Medicine and the Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, California 90089, USA
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Waking up dormant tumor suppressor genes with zinc fingers, TALEs and the CRISPR/dCas9 system. Oncotarget 2018; 7:60535-60554. [PMID: 27528034 PMCID: PMC5312401 DOI: 10.18632/oncotarget.11142] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2016] [Accepted: 07/19/2016] [Indexed: 12/24/2022] Open
Abstract
The aberrant epigenetic silencing of tumor suppressor genes (TSGs) plays a major role during carcinogenesis and regaining these dormant functions by engineering of sequence-specific epigenome editing tools offers a unique opportunity for targeted therapies. However, effectively normalizing the expression and regaining tumor suppressive functions of silenced TSGs by artificial transcription factors (ATFs) still remains a major challenge. Herein we describe novel combinatorial strategies for the potent reactivation of two class II TSGs, MASPIN and REPRIMO, in cell lines with varying epigenetic states, using the CRISPR/dCas9 associated system linked to a panel of effector domains (VP64, p300, VPR and SAM complex), as well as with protein-based ATFs, Zinc Fingers and TALEs. We found that co-delivery of multiple effector domains using a combination of CRISPR/dCas9 and TALEs or SAM complex maximized activation in highly methylated promoters. In particular, CRISPR/dCas9 VPR with SAM upregulated MASPIN mRNA (22,145-fold change) in H157 lung cancer cells, with accompanying re-expression of MASPIN protein, which led to a concomitant inhibition of cell proliferation and induction of apoptotic cell death. Consistently, CRISPR/dCas9 VP64 with SAM upregulated REPRIMO (680-fold change), which led to phenotypic reprogramming in AGS gastric cancer cells. Altogether, our results outlined novel sequence-specific, combinatorial epigenome editing approaches to reactivate highly methylated TSGs as a promising therapy for cancer and other diseases.
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28
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Kretzmann JA, Evans CW, Norret M, Blancafort P, Swaminathan Iyer K. Non-viral Methodology for Efficient Co-transfection. Methods Mol Biol 2018. [PMID: 29524139 DOI: 10.1007/978-1-4939-7774-1_13] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The potential impact of CRISPR/Cas9, TALE, and zinc finger technology is immense, both with respect to their use as tools for understanding the roles and functions of the genomic elements and epigenome modifications in an endogenous context and as new methods for treatment of diseases. Application of such technologies has drawn attention, however, to the prevailing lack of effective delivery methods. Promising viral and non-viral methods both currently fall short when the efficient delivery of large plasmids or multiple plasmids is required. Therefore, the use of TALE and CRISPR platforms has been severely limited in applications where selection methods to increase the relative proportion of treated cells are not applicable, and it represents a significant bottleneck in the further application of these tools as therapeutics.The protocol presented here describes the synthesis of a dendronized polymer as a highly efficient and nontoxic transfection agent. Furthermore, the optimization of the polymer as a co-transfection reagent for large and multiple plasmids in cell lines is described, in addition to general considerations for co-transfection experiments. Usage of this method has allowed for significantly improved large plasmid co-transfection efficiency over Lipofectamine 2000 in multiple cell lines, allowing an improved delivery of CRISPR/dCas9 and TALE systems.
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Affiliation(s)
- Jessica A Kretzmann
- School of Molecular Sciences, The University of Western Australia, Crawley, WA, Australia
- Cancer Epigenetics Group, Harry Perkins Institute of Medical Research, Nedlands, WA, Australia
| | - Cameron W Evans
- School of Molecular Sciences, The University of Western Australia, Crawley, WA, Australia
| | - Marck Norret
- School of Molecular Sciences, The University of Western Australia, Crawley, WA, Australia
| | - Pilar Blancafort
- Cancer Epigenetics Group, Harry Perkins Institute of Medical Research, Nedlands, WA, Australia.
- School of Human Sciences, The University of Western Australia, Perth, WA, Australia.
| | - K Swaminathan Iyer
- School of Molecular Sciences, The University of Western Australia, Crawley, WA, Australia.
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29
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Waryah CB, Moses C, Arooj M, Blancafort P. Zinc Fingers, TALEs, and CRISPR Systems: A Comparison of Tools for Epigenome Editing. Methods Mol Biol 2018. [PMID: 29524128 DOI: 10.1007/978-1-4939-7774-1_2] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The completion of genome, epigenome, and transcriptome mapping in multiple cell types has created a demand for precision biomolecular tools that allow researchers to functionally manipulate DNA, reconfigure chromatin structure, and ultimately reshape gene expression patterns. Epigenetic editing tools provide the ability to interrogate the relationship between epigenetic modifications and gene expression. Importantly, this information can be exploited to reprogram cell fate for both basic research and therapeutic applications. Three different molecular platforms for epigenetic editing have been developed: zinc finger proteins (ZFs), transcription activator-like effectors (TALEs), and the system of Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) and CRISPR-associated (Cas) proteins. These platforms serve as custom DNA-binding domains (DBDs), which are fused to epigenetic modifying domains to manipulate epigenetic marks at specific sites in the genome. The addition and/or removal of epigenetic modifications reconfigures local chromatin structure, with the potential to provoke long-lasting changes in gene transcription. Here we summarize the molecular structure and mechanism of action of ZF, TALE, and CRISPR platforms and describe their applications for the locus-specific manipulation of the epigenome. The advantages and disadvantages of each platform will be discussed with regard to genomic specificity, potency in regulating gene expression, and reprogramming cell phenotypes, as well as ease of design, construction, and delivery. Finally, we outline potential applications for these tools in molecular biology and biomedicine and identify possible barriers to their future clinical implementation.
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Affiliation(s)
- Charlene Babra Waryah
- Cancer Epigenetics Group, The Harry Perkins Institute of Medical Research, Nedlands, Perth, WA, Australia
| | - Colette Moses
- Cancer Epigenetics Group, The Harry Perkins Institute of Medical Research, Nedlands, Perth, WA, Australia
- School of Human Sciences, The University of Western Australia, Perth, WA, Australia
| | - Mahira Arooj
- Cancer Epigenetics Group, The Harry Perkins Institute of Medical Research, Nedlands, Perth, WA, Australia
- School of Biomedical Sciences, Curtin Health Innovation Research Institute, Curtin University, Perth, WA, Australia
| | - Pilar Blancafort
- Cancer Epigenetics Group, The Harry Perkins Institute of Medical Research, Nedlands, Perth, WA, Australia.
- School of Human Sciences, The University of Western Australia, Perth, WA, Australia.
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30
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Rots MG, Jeltsch A. Editing the Epigenome: Overview, Open Questions, and Directions of Future Development. Methods Mol Biol 2018:3-18. [DOI: 10.1007/978-1-4939-7774-1_1] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/30/2023]
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Abstract
Studies of the mammalian nervous system have revealed widespread epigenetic regulation underlying gene expression intrinsic to basic neurobiological function as well as neurological disease. Over the past decade, a critical role has emerged for the neural regulation of chromatin-modifying enzymes during both development and adulthood, and in response to external stimuli. These biochemical data are complemented by numerous next generation sequencing (NGS) studies that quantify the extent of chromatin and DNA modifications in neurons. Neuroepigenetic editing tools can be applied to distinguish between the mere presence and functional relevance of such modifications to neural transcription and animal behavior. This review discusses current advances in neuroepigenetic editing, highlighting methodological considerations pertinent to neuroscience, such as delivery methods and the spatiotemporal specificity of editing. Although neuroepigenetic editing is a nascent field, the studies presented in this review demonstrate the enormous potential of this approach for basic neurobiological research and therapeutic application.
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Affiliation(s)
- Peter J Hamilton
- The Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, NY, New York, USA
| | - Carissa J Lim
- Department of Pharmacology, The University of Pennsylvania, Philadelphia, PA, USA
| | - Eric J Nestler
- The Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, NY, New York, USA
| | - Elizabeth A Heller
- Department of Pharmacology, The University of Pennsylvania, Philadelphia, PA, USA. .,Penn Epigenetics Institute, The University of Pennsylvania, Philadelphia, PA, USA.
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32
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Techniques and strategies employing engineered transcription factors. CURRENT OPINION IN BIOMEDICAL ENGINEERING 2017. [DOI: 10.1016/j.cobme.2017.10.009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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33
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Kretzmann JA, Ho D, Evans CW, Plani-Lam JHC, Garcia-Bloj B, Mohamed AE, O'Mara ML, Ford E, Tan DEK, Lister R, Blancafort P, Norret M, Iyer KS. Synthetically controlling dendrimer flexibility improves delivery of large plasmid DNA. Chem Sci 2017; 8:2923-2930. [PMID: 28451358 PMCID: PMC5376716 DOI: 10.1039/c7sc00097a] [Citation(s) in RCA: 83] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2017] [Accepted: 01/26/2017] [Indexed: 01/10/2023] Open
Abstract
Tools for editing the genome and epigenome have revolutionised the field of molecular biology and represent a new frontier in targeted therapeutic intervention. Although efficiencies and specificities of genome editing technologies have improved with the development of TALEs and CRISPR platforms, intracellular delivery of these larger constructs still remains a challenge using existing delivery agents. Viral vectors, including lentiviruses and adeno-associated viruses, as well as some non-viral strategies, such as cationic polymers and liposomes, are limited by packaging capacity, poor delivery, toxicity, and immunogenicity. We report a highly controlled synthetic strategy to engineer a flexible dendritic polymer using click chemistry to overcome the aforementioned delivery challenges associated with genome engineering technologies. Using a systematic approach, we demonstrate that high transfection efficiencies and packaging capacity can be achieved using this non-viral delivery methodology to deliver zinc fingers, TALEs and CRISPR/dCas9 platforms.
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Affiliation(s)
- Jessica A Kretzmann
- School of Molecular Sciences , The University of Western Australia , 35 Stirling Hwy , Crawley , WA 6009 , Australia . ;
- Harry Perkins Institute of Medical Research , 6 Verdun St , Nedlands , WA 6009 , Australia .
| | - Diwei Ho
- School of Molecular Sciences , The University of Western Australia , 35 Stirling Hwy , Crawley , WA 6009 , Australia . ;
| | - Cameron W Evans
- School of Molecular Sciences , The University of Western Australia , 35 Stirling Hwy , Crawley , WA 6009 , Australia . ;
| | - Janice H C Plani-Lam
- Harry Perkins Institute of Medical Research , 6 Verdun St , Nedlands , WA 6009 , Australia .
| | - Benjamin Garcia-Bloj
- Harry Perkins Institute of Medical Research , 6 Verdun St , Nedlands , WA 6009 , Australia .
| | - A Elaaf Mohamed
- Research School of Chemistry , Australian National University , Canberra , ACT 2601 , Australia
| | - Megan L O'Mara
- Research School of Chemistry , Australian National University , Canberra , ACT 2601 , Australia
| | - Ethan Ford
- School of Molecular Sciences , The University of Western Australia , 35 Stirling Hwy , Crawley , WA 6009 , Australia . ;
- Harry Perkins Institute of Medical Research , 6 Verdun St , Nedlands , WA 6009 , Australia .
- ARC Centre of Excellence in Plant Energy Biology , The University of Western Australia , 35 Stirling Hwy , Crawley , WA 6009 , Australia
| | - Dennis E K Tan
- School of Molecular Sciences , The University of Western Australia , 35 Stirling Hwy , Crawley , WA 6009 , Australia . ;
- Harry Perkins Institute of Medical Research , 6 Verdun St , Nedlands , WA 6009 , Australia .
- ARC Centre of Excellence in Plant Energy Biology , The University of Western Australia , 35 Stirling Hwy , Crawley , WA 6009 , Australia
| | - Ryan Lister
- School of Molecular Sciences , The University of Western Australia , 35 Stirling Hwy , Crawley , WA 6009 , Australia . ;
- Harry Perkins Institute of Medical Research , 6 Verdun St , Nedlands , WA 6009 , Australia .
- ARC Centre of Excellence in Plant Energy Biology , The University of Western Australia , 35 Stirling Hwy , Crawley , WA 6009 , Australia
| | - Pilar Blancafort
- Harry Perkins Institute of Medical Research , 6 Verdun St , Nedlands , WA 6009 , Australia .
- School of Anatomy, Physiology and Human Biology , The University of Western Australia , 35 Stirling Hwy , Crawley , WA 6009 , Australia
| | - Marck Norret
- School of Molecular Sciences , The University of Western Australia , 35 Stirling Hwy , Crawley , WA 6009 , Australia . ;
| | - K Swaminathan Iyer
- School of Molecular Sciences , The University of Western Australia , 35 Stirling Hwy , Crawley , WA 6009 , Australia . ;
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34
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Hossain MA, Shen Y, Knudson I, Thakur S, Stees JR, Qiu Y, Pace BS, Peterson KR, Bungert J. Activation of Fetal γ-globin Gene Expression via Direct Protein Delivery of Synthetic Zinc-finger DNA-Binding Domains. MOLECULAR THERAPY-NUCLEIC ACIDS 2016; 5:e378. [PMID: 27754490 DOI: 10.1038/mtna.2016.85] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2016] [Accepted: 08/29/2016] [Indexed: 12/20/2022]
Abstract
Reactivation of γ-globin expression has been shown to ameliorate disease phenotypes associated with mutations in the adult β-globin gene, including sickle cell disease. Specific mutations in the promoter of the γ-globin genes are known to prevent repression of the genes in the adult and thus lead to hereditary persistence of fetal hemoglobin. One such hereditary persistence of fetal hemoglobin is associated with a sequence located 567 bp upstream of the Gγ-globin gene which assembles a GATA-containing repressor complex. We generated two synthetic zinc-finger DNA-binding domains (ZF-DBDs) targeting this sequence. The -567Gγ ZF-DBDs associated with high affinity and specificity with the target site in the γ-globin gene promoter. We delivered the -567Gγ ZF-DBDs directly to primary erythroid cells. Exposure of these cells to the recombinant -567Gγ ZF-DBDs led to increased expression of the γ-globin gene. Direct protein delivery of ZF-DBDs that compete with transcription regulatory proteins will have broad implications for modulating gene expression in analytical or therapeutic settings.
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Affiliation(s)
- Mir A Hossain
- Department of Biochemistry and Molecular Biology, College of Medicine, University of Florida, Gainesville, Florida, USA
| | - Yong Shen
- Department of Biochemistry and Molecular Biology, College of Medicine, University of Florida, Gainesville, Florida, USA
| | - Isaac Knudson
- Department of Biochemistry and Molecular Biology, College of Medicine, University of Florida, Gainesville, Florida, USA
| | - Shaleen Thakur
- Department of Biochemistry and Molecular Biology, College of Medicine, University of Florida, Gainesville, Florida, USA
| | - Jared R Stees
- Department of Biochemistry and Molecular Biology, College of Medicine, University of Florida, Gainesville, Florida, USA
| | - Yi Qiu
- Department of Anatomy and Cell Biology, College of Medicine, UF Health Cancer Center, Genetics Institute, University of Florida, Gainesville, Florida, USA
| | - Betty S Pace
- Department of Pediatrics, Augusta University, Augusta, Georgia, USA
| | - Kenneth R Peterson
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, Kansas, USA
| | - Jörg Bungert
- Department of Biochemistry and Molecular Biology, College of Medicine, University of Florida, Gainesville, Florida, USA
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Abstract
We are entering an era of epigenome engineering. The precision manipulation of chromatin and epigenetic modifications provides new ways to interrogate their influence on genome and cell function and to harness these changes for applications. We review the design and state of epigenome editing tools, highlighting the unique regulatory properties afforded by these systems.
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Affiliation(s)
- Minhee Park
- Department of Biomedical Engineering and Biological Design Center, Boston University, Boston, MA, 02215, USA
| | - Albert J Keung
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC, 27695, USA
| | - Ahmad S Khalil
- Department of Biomedical Engineering and Biological Design Center, Boston University, Boston, MA, 02215, USA. .,Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, 02115, USA.
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36
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Qi X, Zhang J, Zhao Y, Chen T, Xiang Y, Hui J, Cai D, Liu Y, Xia L, Yu T, Li G. The applications of CRISPR screen in functional genomics. Brief Funct Genomics 2016; 16:34-37. [DOI: 10.1093/bfgp/elw020] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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37
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Hossain MA, Barrow JJ, Shen Y, Haq MI, Bungert J. Artificial zinc finger DNA binding domains: versatile tools for genome engineering and modulation of gene expression. J Cell Biochem 2016; 116:2435-44. [PMID: 25989233 DOI: 10.1002/jcb.25226] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2015] [Accepted: 05/11/2015] [Indexed: 02/01/2023]
Abstract
Genome editing and alteration of gene expression by synthetic DNA binding activities gained a lot of momentum over the last decade. This is due to the development of new DNA binding molecules with enhanced binding specificity. The most commonly used DNA binding modules are zinc fingers (ZFs), TALE-domains, and the RNA component of the CRISPR/Cas9 system. These binding modules are fused or linked to either nucleases that cut the DNA and induce DNA repair processes, or to protein domains that activate or repress transcription of genes close to the targeted site in the genome. This review focuses on the structure, design, and applications of ZF DNA binding domains (ZFDBDs). ZFDBDs are relatively small and have been shown to penetrate the cell membrane without additional tags suggesting that they could be delivered to cells without a DNA or RNA intermediate. Advanced algorithms that are based on extensive knowledge of the mode of ZF/DNA interactions are used to design the amino acid composition of ZFDBDs so that they bind to unique sites in the genome. Off-target binding has been a concern for all synthetic DNA binding molecules. Thus, increasing the specificity and affinity of ZFDBDs will have a significant impact on their use in analytical or therapeutic settings.
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Affiliation(s)
- Mir A Hossain
- Department of Biochemistry and Molecular Biology, College of Medicine, Cancer Center, Genetics Institute, University of Florida, Gainesville, Florida, 32610
| | - Joeva J Barrow
- Department of Biochemistry and Molecular Biology, College of Medicine, Cancer Center, Genetics Institute, University of Florida, Gainesville, Florida, 32610
| | - Yong Shen
- Department of Biochemistry and Molecular Biology, College of Medicine, Cancer Center, Genetics Institute, University of Florida, Gainesville, Florida, 32610
| | - Md Imdadul Haq
- Department of Biochemistry and Molecular Biology, College of Medicine, Cancer Center, Genetics Institute, University of Florida, Gainesville, Florida, 32610
| | - Jörg Bungert
- Department of Biochemistry and Molecular Biology, College of Medicine, Cancer Center, Genetics Institute, University of Florida, Gainesville, Florida, 32610
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38
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Editing the epigenome: technologies for programmable transcription and epigenetic modulation. Nat Methods 2016; 13:127-37. [PMID: 26820547 DOI: 10.1038/nmeth.3733] [Citation(s) in RCA: 284] [Impact Index Per Article: 35.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2015] [Accepted: 12/16/2015] [Indexed: 02/08/2023]
Abstract
Gene regulation is a complex and tightly controlled process that defines cell identity, health and disease, and response to pharmacologic and environmental signals. Recently developed DNA-targeting platforms, including zinc finger proteins, transcription activator-like effectors (TALEs) and the clustered, regularly interspaced, short palindromic repeats (CRISPR)-Cas9 system, have enabled the recruitment of transcriptional modulators and epigenome-modifying factors to any genomic site, leading to new insights into the function of epigenetic marks in gene expression. Additionally, custom transcriptional and epigenetic regulation is facilitating refined control over cell function and decision making. The unique properties of the CRISPR-Cas9 system have created new opportunities for high-throughput genetic screens and multiplexing targets to manipulate complex gene expression patterns. This Review summarizes recent technological developments in this area and their application to biomedical challenges. We also discuss remaining limitations and necessary future directions for this field.
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39
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Epigenome Editing: State of the Art, Concepts, and Perspectives. Trends Genet 2015; 32:101-113. [PMID: 26732754 DOI: 10.1016/j.tig.2015.12.001] [Citation(s) in RCA: 118] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2015] [Revised: 11/28/2015] [Accepted: 12/01/2015] [Indexed: 12/21/2022]
Abstract
Epigenome editing refers to the directed alteration of chromatin marks at specific genomic loci by using targeted EpiEffectors which comprise designed DNA recognition domains (zinc finger, TAL effector, or modified CRISPR/Cas9 complex) and catalytic domains from a chromatin-modifying enzyme. Epigenome editing is a promising approach for durable gene regulation, with many applications in basic research including the investigation of the regulatory functions and logic of chromatin modifications and cellular reprogramming. From a clinical point of view, targeted regulation of disease-related genes offers novel therapeutic avenues for many diseases. We review here the progress made in this field and discuss open questions in epigenetic regulation and its stability, methods to increase the specificity of epigenome editing, and improved delivery methods for targeted EpiEffectors. Future work will reveal if the approach of epigenome editing fulfills its great promise in basic research and clinical applications.
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40
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Huisman C, van der Wijst MGP, Schokker M, Blancafort P, Terpstra MM, Kok K, van der Zee AGJ, Schuuring E, Wisman GBA, Rots MG. Re-expression of Selected Epigenetically Silenced Candidate Tumor Suppressor Genes in Cervical Cancer by TET2-directed Demethylation. Mol Ther 2015; 24:536-47. [PMID: 26686387 DOI: 10.1038/mt.2015.226] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2015] [Accepted: 12/11/2015] [Indexed: 12/18/2022] Open
Abstract
DNA hypermethylation is extensively explored as therapeutic target for gene expression modulation in cancer. Here, we re-activated hypermethylated candidate tumor suppressor genes (TSGs) (C13ORF18, CCNA1, TFPI2, and Maspin) by TET2-induced demethylation in cervical cancer cell lines. To redirect TET2 to hypermethylated TSGs, we engineered zinc finger proteins (ZFPs), which were first fused to the transcriptional activator VP64 to validate effective gene re-expression and confirm TSG function. ChIP-Seq not only revealed enriched binding of ZFPs to their intended sequence, but also considerable off-target binding, especially at promoter regions. Nevertheless, results obtained by targeted re-expression using ZFP-VP64 constructs were in line with cDNA overexpression; both revealed strong growth inhibition for C13ORF18 and TFPI2, but not for CCNA1 and Maspin. To explore effectivity of locus-targeted demethylation, ZFP-TET2 fusions were constructed which efficiently demethylated genes with subsequent gene re-activation. Moreover, targeting TET2 to TFPI2 and C13ORF18, but not CCNA1, significantly decreased cell growth, viability, and colony formation in cervical cancer cells compared to a catalytically inactive mutant of TET2. These data underline that effective re-activation of hypermethylated genes can be achieved through targeted DNA demethylation by TET2, which can assist in realizing sustained re-expression of genes of interest.
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Affiliation(s)
- Christian Huisman
- Department of Pathology and Medical Biology, University Medical Center Groningen (UMCG), University of Groningen, Groningen, The Netherlands.,Current address: Department of Pediatrics, Oregon Health and Science University, Portland, Oregon, USA
| | - Monique G P van der Wijst
- Department of Pathology and Medical Biology, University Medical Center Groningen (UMCG), University of Groningen, Groningen, The Netherlands
| | - Matthijs Schokker
- Department of Pathology and Medical Biology, University Medical Center Groningen (UMCG), University of Groningen, Groningen, The Netherlands
| | - Pilar Blancafort
- Cancer Epigenetics Group, The Harry Perkins Institute for Medical Research, The University of Western Australia, Nedlands, Western Australia, Australia
| | - Martijn M Terpstra
- Department of Genetics, University Medical Center Groningen (UMCG), University of Groningen, Groningen, The Netherlands
| | - Klaas Kok
- Department of Genetics, University Medical Center Groningen (UMCG), University of Groningen, Groningen, The Netherlands
| | - Ate G J van der Zee
- Department of Gynecological Oncology, University Medical Center Groningen (UMCG), University of Groningen, Groningen, The Netherlands
| | - Ed Schuuring
- Department of Pathology and Medical Biology, University Medical Center Groningen (UMCG), University of Groningen, Groningen, The Netherlands
| | - G Bea A Wisman
- Department of Gynecological Oncology, University Medical Center Groningen (UMCG), University of Groningen, Groningen, The Netherlands
| | - Marianne G Rots
- Department of Pathology and Medical Biology, University Medical Center Groningen (UMCG), University of Groningen, Groningen, The Netherlands
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41
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Lim WF, Burdach J, Funnell APW, Pearson RCM, Quinlan KGR, Crossley M. Directing an artificial zinc finger protein to new targets by fusion to a non-DNA-binding domain. Nucleic Acids Res 2015; 44:3118-30. [PMID: 26673701 PMCID: PMC4838343 DOI: 10.1093/nar/gkv1380] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2015] [Accepted: 11/27/2015] [Indexed: 01/05/2023] Open
Abstract
Transcription factors are often regarded as having two separable components: a DNA-binding domain (DBD) and a functional domain (FD), with the DBD thought to determine target gene recognition. While this holds true for DNA binding in vitro, it appears that in vivo FDs can also influence genomic targeting. We fused the FD from the well-characterized transcription factor Krüppel-like Factor 3 (KLF3) to an artificial zinc finger (AZF) protein originally designed to target the Vascular Endothelial Growth Factor-A (VEGF-A) gene promoter. We compared genome-wide occupancy of the KLF3FD-AZF fusion to that observed with AZF. AZF bound to the VEGF-A promoter as predicted, but was also found to occupy approximately 25 000 other sites, a large number of which contained the expected AZF recognition sequence, GCTGGGGGC. Interestingly, addition of the KLF3 FD re-distributes the fusion protein to new sites, with total DNA occupancy detected at around 50 000 sites. A portion of these sites correspond to known KLF3-bound regions, while others contained sequences similar but not identical to the expected AZF recognition sequence. These results show that FDs can influence and may be useful in directing AZF DNA-binding proteins to specific targets and provide insights into how natural transcription factors operate.
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Affiliation(s)
- Wooi F Lim
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, NSW 2052, Australia
| | - Jon Burdach
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, NSW 2052, Australia
| | - Alister P W Funnell
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, NSW 2052, Australia
| | - Richard C M Pearson
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, NSW 2052, Australia
| | - Kate G R Quinlan
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, NSW 2052, Australia
| | - Merlin Crossley
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, NSW 2052, Australia
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42
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Thakore PI, D'Ippolito AM, Song L, Safi A, Shivakumar NK, Kabadi AM, Reddy TE, Crawford GE, Gersbach CA. Highly specific epigenome editing by CRISPR-Cas9 repressors for silencing of distal regulatory elements. Nat Methods 2015; 12:1143-9. [PMID: 26501517 PMCID: PMC4666778 DOI: 10.1038/nmeth.3630] [Citation(s) in RCA: 645] [Impact Index Per Article: 71.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2015] [Accepted: 09/19/2015] [Indexed: 12/17/2022]
Abstract
Epigenome editing with the CRISPR (clustered, regularly interspaced, short palindromic repeats)-Cas9 platform is a promising technology for modulating gene expression to direct cell phenotype and to dissect the causal epigenetic mechanisms of gene regulation. Fusions of nuclease-inactive dCas9 to the Krüppel-associated box (KRAB) repressor (dCas9-KRAB) can silence target gene expression, but the genome-wide specificity and the extent of heterochromatin formation catalyzed by dCas9-KRAB are not known. We targeted dCas9-KRAB to the HS2 enhancer, a distal regulatory element that orchestrates the expression of multiple globin genes, and observed highly specific induction of H3K9 trimethylation (H3K9me3) at the enhancer and decreased chromatin accessibility of both the enhancer and its promoter targets. Targeted epigenetic modification of HS2 silenced the expression of multiple globin genes, with minimal off-target changes in global gene expression. These results demonstrate that repression mediated by dCas9-KRAB is sufficiently specific to disrupt the activity of individual enhancers via local modification of the epigenome.
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Affiliation(s)
- Pratiksha I Thakore
- Department of Biomedical Engineering, Duke University, Durham, North Carolina, USA
- Center for Genomic and Computational Biology, Duke University, Durham, North Carolina, USA
| | - Anthony M D'Ippolito
- Center for Genomic and Computational Biology, Duke University, Durham, North Carolina, USA
- University Program in Genetics and Genomics, Duke University, Durham, North Carolina, USA
| | - Lingyun Song
- Center for Genomic and Computational Biology, Duke University, Durham, North Carolina, USA
- Department of Pediatrics, Division of Medical Genetics, Duke University Medical Center, Durham, North Carolina, USA
| | - Alexias Safi
- Center for Genomic and Computational Biology, Duke University, Durham, North Carolina, USA
- Department of Pediatrics, Division of Medical Genetics, Duke University Medical Center, Durham, North Carolina, USA
| | | | - Ami M Kabadi
- Department of Biomedical Engineering, Duke University, Durham, North Carolina, USA
- Center for Genomic and Computational Biology, Duke University, Durham, North Carolina, USA
| | - Timothy E Reddy
- Center for Genomic and Computational Biology, Duke University, Durham, North Carolina, USA
- Department of Biostatistics &Bioinformatics, Duke University Medical Center, Durham, North Carolina, USA
| | - Gregory E Crawford
- Center for Genomic and Computational Biology, Duke University, Durham, North Carolina, USA
- Department of Pediatrics, Division of Medical Genetics, Duke University Medical Center, Durham, North Carolina, USA
| | - Charles A Gersbach
- Department of Biomedical Engineering, Duke University, Durham, North Carolina, USA
- Center for Genomic and Computational Biology, Duke University, Durham, North Carolina, USA
- Department of Orthopaedic Surgery, Duke University Medical Center, Durham, North Carolina, USA
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43
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Yao L, Berman BP, Farnham PJ. Demystifying the secret mission of enhancers: linking distal regulatory elements to target genes. Crit Rev Biochem Mol Biol 2015; 50:550-73. [PMID: 26446758 PMCID: PMC4666684 DOI: 10.3109/10409238.2015.1087961] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Enhancers are short regulatory sequences bound by sequence-specific transcription factors and play a major role in the spatiotemporal specificity of gene expression patterns in development and disease. While it is now possible to identify enhancer regions genomewide in both cultured cells and primary tissues using epigenomic approaches, it has been more challenging to develop methods to understand the function of individual enhancers because enhancers are located far from the gene(s) that they regulate. However, it is essential to identify target genes of enhancers not only so that we can understand the role of enhancers in disease but also because this information will assist in the development of future therapeutic options. After reviewing models of enhancer function, we discuss recent methods for identifying target genes of enhancers. First, we describe chromatin structure-based approaches for directly mapping interactions between enhancers and promoters. Second, we describe the use of correlation-based approaches to link enhancer state with the activity of nearby promoters and/or gene expression. Third, we describe how to test the function of specific enhancers experimentally by perturbing enhancer–target relationships using high-throughput reporter assays and genome editing. Finally, we conclude by discussing as yet unanswered questions concerning how enhancers function, how target genes can be identified, and how to distinguish direct from indirect changes in gene expression mediated by individual enhancers.
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Affiliation(s)
- Lijing Yao
- a Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California , Los Angeles , CA , USA and
| | - Benjamin P Berman
- b Department of Biomedical Sciences , Bioinformatics and Computational Biology Research Center, Cedars-Sinai Medical Center , Los Angeles , CA , USA
| | - Peggy J Farnham
- a Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California , Los Angeles , CA , USA and
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44
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Abstract
Advances in genome engineering technologies have made the precise control over genome sequence and regulation possible across a variety of disciplines. These tools can expand our understanding of fundamental biological processes and create new opportunities for therapeutic designs. The rapid evolution of these methods has also catalyzed a new era of genomics that includes multiple approaches to functionally characterize and manipulate the regulation of genomic information. Here, we review the recent advances of the most widely adopted genome engineering platforms and their application to functional genomics. This includes engineered zinc finger proteins, TALEs/TALENs, and the CRISPR/Cas9 system as nucleases for genome editing, transcription factors for epigenome editing, and other emerging applications. We also present current and potential future applications of these tools, as well as their current limitations and areas for future advances.
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Affiliation(s)
- Isaac B Hilton
- Department of Biomedical Engineering, Duke University, Durham, North Carolina 27708, USA; Center for Genomic and Computational Biology, Duke University, Durham, North Carolina 27708, USA
| | - Charles A Gersbach
- Department of Biomedical Engineering, Duke University, Durham, North Carolina 27708, USA; Center for Genomic and Computational Biology, Duke University, Durham, North Carolina 27708, USA; Department of Orthopaedic Surgery, Duke University Medical Center, Durham, North Carolina 27710, USA
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45
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Laufer BI, Singh SM. Strategies for precision modulation of gene expression by epigenome editing: an overview. Epigenetics Chromatin 2015; 8:34. [PMID: 26388942 PMCID: PMC4574080 DOI: 10.1186/s13072-015-0023-7] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2015] [Accepted: 08/19/2015] [Indexed: 01/27/2023] Open
Abstract
Genome editing technology has evolved rather quickly and become accessible to most researchers. It has resulted in far reaching implications and a number of novel designer systems including epigenome editing. Epigenome editing utilizes a combination of nuclease-null genome editing systems and effector domains to modulate gene expression. In particular, Zinc Finger, Transcription-Activator-Like Effector, and CRISPR/Cas9 have emerged as modular systems that can be modified to allow for precision manipulation of epigenetic marks without altering underlying DNA sequence. This review contains a comprehensive catalog of effector domains that can be used with components of genome editing systems to achieve epigenome editing. Ultimately, the evidence-based design of epigenome editing offers a novel improvement to the limited attenuation strategies. There is much potential for editing and/or correcting gene expression in somatic cells toward a new era of functional genomics and personalized medicine.
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Affiliation(s)
- Benjamin I Laufer
- Molecular Genetics Unit, Department of Biology, University of Western Ontario, London, ON Canada
| | - Shiva M Singh
- Molecular Genetics Unit, Department of Biology, University of Western Ontario, London, ON Canada
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46
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Grimmer MR, Farnham PJ. Can genome engineering be used to target cancer-associated enhancers? Epigenomics 2015; 6:493-501. [PMID: 25431942 DOI: 10.2217/epi.14.30] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Transcriptional misregulation is involved in the development of many diseases, especially neoplastic transformation. Distal regulatory elements, such as enhancers, play a major role in specifying cell-specific transcription patterns in both normal and diseased tissues, suggesting that enhancers may be prime targets for therapeutic intervention. By focusing on modulating gene regulation mediated by cell type-specific enhancers, there is hope that normal epigenetic patterning in an affected tissue could be restored with fewer side effects than observed with treatments employing relatively nonspecific inhibitors such as epigenetic drugs. New methods employing genomic nucleases and site-specific epigenetic regulators targeted to specific genomic regions, using either artificial DNA-binding proteins or RNA-DNA interactions, may allow precise genome engineering at enhancers. However, this field is still in its infancy and further refinements that increase specificity and efficiency are clearly required.
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Affiliation(s)
- Matthew R Grimmer
- Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089-9601, USA
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47
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Huisman C, van der Wijst MGP, Falahi F, Overkamp J, Karsten G, Terpstra MM, Kok K, van der Zee AGJ, Schuuring E, Wisman GBA, Rots MG. Prolonged re-expression of the hypermethylated gene EPB41L3 using artificial transcription factors and epigenetic drugs. Epigenetics 2015; 10:384-96. [PMID: 25830725 DOI: 10.1080/15592294.2015.1034415] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
Abstract
Epigenetic silencing of tumor suppressor genes (TSGs) is considered a significant event in the progression of cancer. For example, EPB41L3, a potential biomarker in cervical cancer, is often silenced by cancer-specific promoter methylation. Artificial transcription factors (ATFs) are unique tools to re-express such silenced TSGs to functional levels; however, the induced effects are considered transient. Here, we aimed to improve the efficiency and sustainability of gene re-expression using engineered zinc fingers fused to VP64 (ZF-ATFs) or DNA methylation modifiers (ZF-Tet2 or ZF-TDG) and/or by co-treatment with epigenetic drugs [5-aza-2'-deoxycytidine or Trichostatin A (TSA)]. The EPB41L3-ZF effectively bound its methylated endogenous locus, as also confirmed by ChIP-seq. ZF-ATFs reactivated the epigenetically silenced target gene EPB41L3 (∼ 10-fold) in breast, ovarian, and cervical cancer cell lines. Prolonged high levels of EPB41L3 (∼ 150-fold) induction could be achieved by short-term co-treatment with epigenetic drugs. Interestingly, for otherwise ineffective ZF-Tet2 or ZF-TDG treatments, TSA facilitated re-expression of EPB41L3 up to twofold. ATF-mediated re-expression demonstrated a tumor suppressive role for EPB41L3 in cervical cancer cell lines. In conclusion, epigenetic reprogramming provides a novel way to improve sustainability of re-expression of epigenetically silenced promoters.
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48
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O'Geen H, Henry IM, Bhakta MS, Meckler JF, Segal DJ. A genome-wide analysis of Cas9 binding specificity using ChIP-seq and targeted sequence capture. Nucleic Acids Res 2015; 43:3389-404. [PMID: 25712100 PMCID: PMC4381059 DOI: 10.1093/nar/gkv137] [Citation(s) in RCA: 156] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2014] [Revised: 02/07/2015] [Accepted: 02/09/2015] [Indexed: 12/26/2022] Open
Abstract
Clustered regularly interspaced short palindromic repeat (CRISPR) RNA-guided nucleases have gathered considerable excitement as a tool for genome engineering. However, questions remain about the specificity of target site recognition. Cleavage specificity is typically evaluated by low throughput assays (T7 endonuclease I assay, target amplification followed by high-throughput sequencing), which are limited to a subset of potential off-target sites. Here, we used ChIP-seq to examine genome-wide CRISPR binding specificity at gRNA-specific and gRNA-independent sites for two guide RNAs. RNA-guided Cas9 binding was highly specific to the target site while off-target binding occurred at much lower intensities. Cas9-bound regions were highly enriched in NGG sites, a sequence required for target site recognition by Streptococcus pyogenes Cas9. To determine the relationship between Cas9 binding and endonuclease activity, we applied targeted sequence capture, which allowed us to survey 1200 genomic loci simultaneously including potential off-target sites identified by ChIP-seq and by computational prediction. A high frequency of indels was observed at both target sites and one off-target site, while no cleavage activity could be detected at other ChIP-bound regions. Our results confirm the high-specificity of CRISPR endonucleases and demonstrate that sequence capture can be used as a high-throughput genome-wide approach to identify off-target activity.
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Affiliation(s)
- Henriette O'Geen
- Genome Center and Department of Biochemistry and Molecular Medicine, University of California, Davis, CA 95616, USA
| | - Isabelle M Henry
- Department of Plant Biology and Genome Center, University of California, Davis, CA 95616, USA
| | - Mital S Bhakta
- Genome Center and Department of Biochemistry and Molecular Medicine, University of California, Davis, CA 95616, USA
| | - Joshua F Meckler
- Genome Center and Department of Biochemistry and Molecular Medicine, University of California, Davis, CA 95616, USA
| | - David J Segal
- Genome Center and Department of Biochemistry and Molecular Medicine, University of California, Davis, CA 95616, USA
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49
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van der Wijst MGP, Huisman C, Mposhi A, Roelfes G, Rots MG. Targeting Nrf2 in healthy and malignant ovarian epithelial cells: Protection versus promotion. Mol Oncol 2015; 9:1259-73. [PMID: 25841766 DOI: 10.1016/j.molonc.2015.03.003] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2014] [Revised: 03/09/2015] [Accepted: 03/11/2015] [Indexed: 12/30/2022] Open
Abstract
Risk factors indicate the importance of oxidative stress during ovarian carcinogenesis. To tolerate oxidative stress, cells activate the transcription factor Nrf2 (Nfe2l2), the master regulator of antioxidant and cytoprotective genes. Indeed, for most cancers, hyperactivity of Nrf2 is observed, and siRNA studies assigned Nrf2 as therapeutic target. However, the cancer-protective role of Nrf2 in healthy cells highlights the requirement for an adequate therapeutic window. We engineered artificial transcription factors to assess the role of Nrf2 in healthy (OSE-C2) and malignant ovarian cells (A2780). Successful NRF2 up- and downregulation correlated with decreased, respectively increased, sensitivity toward oxidative stress. Inhibition of NRF2 reduced the colony forming potential to the same extent in wild-type and BRCA1 knockdown A2780 cells. Only in BRCA1 knockdown A2780 cells, the effect of Nrf2 inhibition could be enhanced when combined with PARP inhibitors. Therefore, we propose that this combination therapy of PARP inhibitors and Nrf2 inhibition can further improve treatment efficacy specifically in BRCA1 mutant cancer cells without acquiring the side-effects associated with previously studied Nrf2 inhibition combinations with either chemotherapy or radiation. Our findings stress the dual role of Nrf2 in carcinogenesis, while offering approaches to exploit Nrf2 as a potent therapeutic target in ovarian cancer.
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Affiliation(s)
- Monique G P van der Wijst
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen (UMCG), Hanzeplein 1 9713 GZ Groningen, The Netherlands.
| | - Christian Huisman
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen (UMCG), Hanzeplein 1 9713 GZ Groningen, The Netherlands.
| | - Archibold Mposhi
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen (UMCG), Hanzeplein 1 9713 GZ Groningen, The Netherlands.
| | - Gerard Roelfes
- Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands.
| | - Marianne G Rots
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen (UMCG), Hanzeplein 1 9713 GZ Groningen, The Netherlands.
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50
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Abstract
As synthetic biology approaches are extended to diverse applications throughout medicine, biotechnology and basic biological research, there is an increasing need to engineer yeast, plant and mammalian cells. Eukaryotic genomes are regulated by the diverse biochemical and biophysical states of chromatin, which brings distinct challenges, as well as opportunities, over applications in bacteria. Recent synthetic approaches, including 'epigenome editing', have allowed the direct and functional dissection of many aspects of physiological chromatin regulation. These studies lay the foundation for biomedical and biotechnological engineering applications that could take advantage of the unique combinatorial and spatiotemporal layers of chromatin regulation to create synthetic systems of unprecedented sophistication.
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