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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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2
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Ren R, Guo J, Liu G, Kang H, Machens HG, Schilling AF, Slobodianski A, Zhang Z. Nucleic acid direct delivery to fibroblasts: a review of nucleofection and applications. J Biol Eng 2022; 16:30. [PMID: 36329479 PMCID: PMC9635183 DOI: 10.1186/s13036-022-00309-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Accepted: 10/24/2022] [Indexed: 11/06/2022] Open
Abstract
The fibroblast is one of the ideal target cell candidates for cell-based gene therapy approaches to promote tissue repair. Gene delivery to fibroblasts by viral transfection has been confirmed to have high transfection efficiency. However, in addition to immunogenic effects of viruses, the random integration of viral genes may damage the genome, affect the cell phenotype or even cause cancerous mutations in the transfected cells. Due to these potential biohazards and unknown long-term risks, the clinical use of viral transfection has been very limited. In contrast, initial non-viral transfection methods have been simple and safe to implement, with low immunogenicity, insertional mutagenesis, and risk of carcinogenesis, but their transfection efficiency has been relatively low. Nucleofection, a more recent non-viral transfection method, now combines the advantages of high transfection efficiency and direct nucleic acid delivery to the nucleus with a high safety.Here, we reviewed recent articles on fibroblast nucleofection, summarized different research points, improved methods and application scopes, and opened up ideas for promoting the further improvement and development of fibroblast nucleofection to meet the needs of a variety of disease research and clinical applications.
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Affiliation(s)
- Ranyue Ren
- grid.412793.a0000 0004 1799 5032Department of Orthopedics, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei China
| | - Jiachao Guo
- grid.412793.a0000 0004 1799 5032Department of Pediatric Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei China
| | - Guangwu Liu
- grid.412793.a0000 0004 1799 5032Department of Orthopedics, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei China
| | - Hao Kang
- grid.412793.a0000 0004 1799 5032Department of Orthopedics, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei China
| | - Hans-Günther Machens
- grid.15474.330000 0004 0477 2438Department of Plastic Surgery and Hand Surgery, Faculty of Medicine, Klinikum Rechts Der Isar, Technische Universität München, Munich, Germany
| | - Arndt F. Schilling
- grid.411984.10000 0001 0482 5331Department of Trauma Surgery, Orthopaedics and Plastic Surgery, University Medical Center Göttingen, Göttingen, Germany
| | - Alex Slobodianski
- grid.15474.330000 0004 0477 2438Department of Plastic Surgery and Hand Surgery, Faculty of Medicine, Klinikum Rechts Der Isar, Technische Universität München, Munich, Germany
| | - Ziyang Zhang
- grid.412793.a0000 0004 1799 5032Department of Orthopedics, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei China
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3
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Black JB, Gersbach CA. Synthetic transcription factors for cell fate reprogramming. Curr Opin Genet Dev 2018; 52:13-21. [PMID: 29803990 DOI: 10.1016/j.gde.2018.05.001] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Revised: 04/30/2018] [Accepted: 05/06/2018] [Indexed: 12/22/2022]
Abstract
The ability to reprogram cell lineage specification through the activity of master regulatory transcription factors has transformed disease modeling, drug screening, and cell therapy for regenerative medicine. Recent advances in the engineering of synthetic transcription factors to modulate endogenous gene expression networks and chromatin states have generated a new set of tools with unique advantages to study and enhance cell reprogramming methods. Several studies have applied synthetic transcription factors in various cell reprogramming paradigms in human and murine cells. Moreover, the adaption of CRISPR-based transcription factors for high-throughput screening will enable the systematic identification of optimal factors and gene network perturbations to improve current reprogramming protocols and enable conversion to more diverse, highly specified, and mature cell types. The rapid development of next-generation technologies with more robust and versatile functionality will continue to expand the application of synthetic transcription factors for cell reprogramming.
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Affiliation(s)
- Joshua B Black
- Department of Biomedical Engineering, Duke University, Durham, NC 27708, USA; Center for Genomic and Computational Biology, Duke University, Durham, NC 27708, USA
| | - Charles A Gersbach
- Department of Biomedical Engineering, Duke University, Durham, NC 27708, USA; Center for Genomic and Computational Biology, Duke University, Durham, NC 27708, USA; Department of Orthopaedic Surgery, Duke University Medical Center, Durham, NC 27710, USA.
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4
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Cherif K, Gérard C, Rousseau J, Ouellet DL, Chapdelaine P, Tremblay JP. Increased Frataxin Expression Induced in Friedreich Ataxia Cells by Platinum TALE-VP64s or Platinum TALE-SunTag. MOLECULAR THERAPY-NUCLEIC ACIDS 2018; 12:19-32. [PMID: 30195758 PMCID: PMC6019861 DOI: 10.1016/j.omtn.2018.04.009] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Revised: 04/24/2018] [Accepted: 04/24/2018] [Indexed: 11/28/2022]
Abstract
Frataxin gene (FXN) expression is reduced in Friedreich’s ataxia patients due to an increase in the number of GAA trinucleotides in intron 1. The frataxin protein, encoded by that gene, plays an important role in mitochondria’s iron metabolism. Platinum TALE (plTALE) proteins targeting the regulatory region of the FXN gene, fused with a transcriptional activator (TA) such as VP64 or P300, were used to increase the expression of that gene. Many effectors, plTALEVP64, plTALEp300, and plTALESunTag, targeting 14 sequences of the FXN gene promoter or intron 1 were produced. This permitted selection of 3 plTALEVP64s and 2 plTALESunTag that increased FXN gene expression by up to 19-fold in different Friedreich ataxia (FRDA) primary fibroblasts. Adeno-associated viruses were used to deliver the best effectors to the YG8R mouse model to validate their efficiencies in vivo. Our results showed that these selected plTALEVP64s or plTALESunTag induced transcriptional activity of the endogenous FXN gene as well as expression of the frataxin protein in YG8R mouse heart by 10-fold and in skeletal muscles by up to 35-fold. The aconitase activity was positively modulated by the frataxin level in mitochondria, and it was, thus, increased in vitro and in vivo by the increased frataxin expression.
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Affiliation(s)
- Khadija Cherif
- Centre de Recherche du CHU, Québec-Université Laval, Québec, QC, Canada; Département de Médecine Moléculaire, l'Université Laval Québec, Québec, QC, Canada
| | - Catherine Gérard
- Centre de Recherche du CHU, Québec-Université Laval, Québec, QC, Canada; Département de Médecine Moléculaire, l'Université Laval Québec, Québec, QC, Canada
| | - Joël Rousseau
- Centre de Recherche du CHU, Québec-Université Laval, Québec, QC, Canada; Département de Médecine Moléculaire, l'Université Laval Québec, Québec, QC, Canada
| | - Dominique L Ouellet
- Centre de Recherche du CHU, Québec-Université Laval, Québec, QC, Canada; Département de Médecine Moléculaire, l'Université Laval Québec, Québec, QC, Canada
| | - Pierre Chapdelaine
- Centre de Recherche du CHU, Québec-Université Laval, Québec, QC, Canada; Département de Médecine Moléculaire, l'Université Laval Québec, Québec, QC, Canada
| | - Jacques P Tremblay
- Centre de Recherche du CHU, Québec-Université Laval, Québec, QC, Canada; Département de Médecine Moléculaire, l'Université Laval Québec, Québec, QC, Canada.
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5
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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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6
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Erwin GS, Grieshop MP, Ali A, Qi J, Lawlor M, Kumar D, Ahmad I, McNally A, Teider N, Worringer K, Sivasankaran R, Syed DN, Eguchi A, Ashraf M, Jeffery J, Xu M, Park PMC, Mukhtar H, Srivastava AK, Faruq M, Bradner JE, Ansari AZ. Synthetic transcription elongation factors license transcription across repressive chromatin. Science 2017; 358:1617-1622. [PMID: 29192133 PMCID: PMC6037176 DOI: 10.1126/science.aan6414] [Citation(s) in RCA: 95] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2017] [Accepted: 11/15/2017] [Indexed: 12/22/2022]
Abstract
The release of paused RNA polymerase II into productive elongation is highly regulated, especially at genes that affect human development and disease. To exert control over this rate-limiting step, we designed sequence-specific synthetic transcription elongation factors (Syn-TEFs). These molecules are composed of programmable DNA-binding ligands flexibly tethered to a small molecule that engages the transcription elongation machinery. By limiting activity to targeted loci, Syn-TEFs convert constituent modules from broad-spectrum inhibitors of transcription into gene-specific stimulators. Here we present Syn-TEF1, a molecule that actively enables transcription across repressive GAA repeats that silence frataxin expression in Friedreich's ataxia, a terminal neurodegenerative disease with no effective therapy. The modular design of Syn-TEF1 defines a general framework for developing a class of molecules that license transcription elongation at targeted genomic loci.
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Affiliation(s)
- Graham S Erwin
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Matthew P Grieshop
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Asfa Ali
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Jun Qi
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Matthew Lawlor
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Deepak Kumar
- Department of Neurology, All India Institute of Medical Sciences, New Delhi, India
- Genomics and Molecular Medicine, Council of Scientific and Industrial Research (CSIR)-Institute of Genomics and Integrative Biology (IGIB), New Delhi, India
| | - Istaq Ahmad
- Department of Neurology, All India Institute of Medical Sciences, New Delhi, India
- Genomics and Molecular Medicine, Council of Scientific and Industrial Research (CSIR)-Institute of Genomics and Integrative Biology (IGIB), New Delhi, India
| | - Anna McNally
- Novartis Institutes for BioMedical Research (NIBR), Cambridge, MA 02139, USA
| | - Natalia Teider
- Novartis Institutes for BioMedical Research (NIBR), Cambridge, MA 02139, USA
| | - Katie Worringer
- Novartis Institutes for BioMedical Research (NIBR), Cambridge, MA 02139, USA
| | - Rajeev Sivasankaran
- Novartis Institutes for BioMedical Research (NIBR), Cambridge, MA 02139, USA
| | - Deeba N Syed
- Department of Dermatology, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Asuka Eguchi
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Md Ashraf
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Justin Jeffery
- Small Animal Imaging Facility, University of Wisconsin Carbone Cancer Center, Madison, WI 53792, USA
| | - Mousheng Xu
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Paul M C Park
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Hasan Mukhtar
- Department of Dermatology, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Achal K Srivastava
- Department of Neurology, All India Institute of Medical Sciences, New Delhi, India
| | - Mohammed Faruq
- Genomics and Molecular Medicine, Council of Scientific and Industrial Research (CSIR)-Institute of Genomics and Integrative Biology (IGIB), New Delhi, India
| | - James E Bradner
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Novartis Institutes for BioMedical Research (NIBR), Cambridge, MA 02139, USA
| | - Aseem Z Ansari
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA.
- The Genome Center of Wisconsin, University of Wisconsin-Madison, Madison, WI 53706, USA
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7
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Nelson CE, Robinson-Hamm JN, Gersbach CA. Genome engineering: a new approach to gene therapy for neuromuscular disorders. Nat Rev Neurol 2017; 13:647-661. [DOI: 10.1038/nrneurol.2017.126] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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8
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Strawser C, Schadt K, Hauser L, McCormick A, Wells M, Larkindale J, Lin H, Lynch DR. Pharmacological therapeutics in Friedreich ataxia: the present state. Expert Rev Neurother 2017; 17:895-907. [PMID: 28724340 DOI: 10.1080/14737175.2017.1356721] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
INTRODUCTION Friedreich ataxia (FRDA) is a progressive, inherited, neurodegenerative disease for which there is currently no cure or approved treatment. FRDA is caused by deficits in the production and expression of frataxin, a protein found in the mitochondria that is most likely responsible for regulating iron-sulfur cluster enzymes within the cell. A decrease in frataxin causes dysfunction of adenosine triphosphate synthesis, accumulation of mitochondrial iron, and other events leading to downstream cellular dysfunction. Areas covered: Therapeutic development for FRDA currently focuses on improving mitochondrial function and finding ways to increase frataxin expression. Additionally, the authors will review potential approaches aimed at iron modulation and genetic modulation. Finally, gene therapy is progressing rapidly and is being explored as a treatment for FRDA. Expert commentary: The collection of multiple therapeutic approaches provides many possible ways to treat FRDA. Although the mitochondrial approaches are not thought to be curative, as the primary frataxin deficit will remain, they may still produce improvements in quality of life and slowing of progression. Therapies aimed at frataxin restoration are more likely to truly modify the disease, with gene therapy as the best possibility to alter the course of the disease from both a cardiac and neurological perspective.
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Affiliation(s)
| | - Kimberly Schadt
- a Children's Hospital of Philadelphia , Philadelphia , PA , USA
| | - Lauren Hauser
- a Children's Hospital of Philadelphia , Philadelphia , PA , USA
| | | | - McKenzie Wells
- a Children's Hospital of Philadelphia , Philadelphia , PA , USA
| | - Jane Larkindale
- a Children's Hospital of Philadelphia , Philadelphia , PA , USA
| | - Hong Lin
- a Children's Hospital of Philadelphia , Philadelphia , PA , USA
| | - David R Lynch
- a Children's Hospital of Philadelphia , Philadelphia , PA , USA
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9
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Ouellet DL, Cherif K, Rousseau J, Tremblay JP. Deletion of the GAA repeats from the human frataxin gene using the CRISPR-Cas9 system in YG8R-derived cells and mouse models of Friedreich ataxia. Gene Ther 2017; 24:265-274. [PMID: 28024081 DOI: 10.1038/gt.2016.89] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2016] [Accepted: 12/19/2016] [Indexed: 02/07/2023]
Abstract
The Friedreich ataxia is a monogenic disease due to a hyperexpanded GAA triplet located within the first intron of the frataxin gene that causes transcriptional issues. The resulting frataxin protein deficiency leads to a Fe-S cluster biosynthesis dysfunction in the mitochondria and to oxidative stress and cell death. Here we use the CRISPR-Cas9 system to remove the mutated GAA expansion and restore the frataxin gene transcriptional activity and protein level. Both YG8R and YG8sR mouse models and cell lines derived from these mice were used to CRISPR-edited successfully the GAA expansion in vitro and in vivo. Nevertheless, our results suggest the YG8sR as a better and more suitable model for the study of the CRISPR-Cas9 edition of the mutated frataxin gene.
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Affiliation(s)
- D L Ouellet
- Centre de Recherche, Centre Hospitalier, Universitaire de Québec, Quebec City, QC, Canada
- Département de Médecine Moléculaire, Faculté de Médecine, CHU de Québec, Université Laval, Québec City, QC, Canada
| | - K Cherif
- Centre de Recherche, Centre Hospitalier, Universitaire de Québec, Quebec City, QC, Canada
- Département de Médecine Moléculaire, Faculté de Médecine, CHU de Québec, Université Laval, Québec City, QC, Canada
| | - J Rousseau
- Centre de Recherche, Centre Hospitalier, Universitaire de Québec, Quebec City, QC, Canada
- Département de Médecine Moléculaire, Faculté de Médecine, CHU de Québec, Université Laval, Québec City, QC, Canada
| | - J P Tremblay
- Centre de Recherche, Centre Hospitalier, Universitaire de Québec, Quebec City, QC, Canada
- Département de Médecine Moléculaire, Faculté de Médecine, CHU de Québec, Université Laval, Québec City, QC, Canada
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10
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Chapdelaine P, Gérard C, Sanchez N, Cherif K, Rousseau J, Ouellet DL, Jauvin D, Tremblay JP. Development of an AAV9 coding for a 3XFLAG-TALEfrat#8-VP64 able to increase in vivo the human frataxin in YG8R mice. Gene Ther 2016; 23:606-14. [PMID: 27082765 PMCID: PMC4940929 DOI: 10.1038/gt.2016.36] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2015] [Revised: 03/09/2016] [Accepted: 04/07/2016] [Indexed: 02/07/2023]
Abstract
Artificially designed transcription activator-like effector (TALE) proteins fused to a transcription activation domain (TAD), such as VP64, are able to activate specific eukaryotic promoters. They thus provide a good tool for targeted gene regulation as a therapy. However, the efficacy of such an agent in vivo remains to be demonstrated as the majority of studies have been carried out in cell culture. We produced an adeno-associated virus 9 (AAV9) coding for a TALEfrat#8 containing 13 repeat variable diresidues able to bind to the proximal promoter of human frataxin (FXN) gene. This TALEfrat#8 was fused with a 3XFLAG at its N terminal and a VP64 TAD at its C terminal, and driven by a CAG promoter. This AAV9_3XFLAG-TALEfrat#8-VP64 was injected intraperitoneally to 9-day-old and 4-month-old YG8R mice. After 1 month, the heart, muscle and liver were removed and their FXN mRNA and FXN protein were analyzed. The results show that the AAV9_3XFLAG-TALEfrat#8-VP64 increased the FXN mRNA and FXN protein in the three organs studied. These results corroborate our previous in vitro studies in the FRDA human fibroblasts. Our study indicates that an AAV coding for a TALE protein coupled with a TAD may be used to increase gene expression in vivo as a possible treatment not only for FRDA but also for other haploinsufficiency diseases.
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Affiliation(s)
- P Chapdelaine
- Unité de Génétique Humaine, Axe Neurosciences, Centre de Recherche du Centre Hospitalier de Universitaire de Québec-Université Laval, Québec City, QC, Canada
- Department of Molecular Medicine, Faculty of Medicine, Laval University, Quebec City, QC, Canada
| | - C Gérard
- Unité de Génétique Humaine, Axe Neurosciences, Centre de Recherche du Centre Hospitalier de Universitaire de Québec-Université Laval, Québec City, QC, Canada
- Department of Molecular Medicine, Faculty of Medicine, Laval University, Quebec City, QC, Canada
| | - N Sanchez
- Unité de Génétique Humaine, Axe Neurosciences, Centre de Recherche du Centre Hospitalier de Universitaire de Québec-Université Laval, Québec City, QC, Canada
- Department of Molecular Medicine, Faculty of Medicine, Laval University, Quebec City, QC, Canada
| | - K Cherif
- Unité de Génétique Humaine, Axe Neurosciences, Centre de Recherche du Centre Hospitalier de Universitaire de Québec-Université Laval, Québec City, QC, Canada
- Department of Molecular Medicine, Faculty of Medicine, Laval University, Quebec City, QC, Canada
| | - J Rousseau
- Unité de Génétique Humaine, Axe Neurosciences, Centre de Recherche du Centre Hospitalier de Universitaire de Québec-Université Laval, Québec City, QC, Canada
- Department of Molecular Medicine, Faculty of Medicine, Laval University, Quebec City, QC, Canada
| | - D L Ouellet
- Unité de Génétique Humaine, Axe Neurosciences, Centre de Recherche du Centre Hospitalier de Universitaire de Québec-Université Laval, Québec City, QC, Canada
- Department of Molecular Medicine, Faculty of Medicine, Laval University, Quebec City, QC, Canada
| | - D Jauvin
- Unité de Génétique Humaine, Axe Neurosciences, Centre de Recherche du Centre Hospitalier de Universitaire de Québec-Université Laval, Québec City, QC, Canada
- Department of Molecular Medicine, Faculty of Medicine, Laval University, Quebec City, QC, Canada
| | - J P Tremblay
- Unité de Génétique Humaine, Axe Neurosciences, Centre de Recherche du Centre Hospitalier de Universitaire de Québec-Université Laval, Québec City, QC, Canada
- Department of Molecular Medicine, Faculty of Medicine, Laval University, Quebec City, QC, Canada
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11
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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: 296] [Impact Index Per Article: 37.0] [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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12
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Katsu-Jiménez Y, Loría F, Corona JC, Díaz-Nido J. Gene Transfer of Brain-derived Neurotrophic Factor (BDNF) Prevents Neurodegeneration Triggered by FXN Deficiency. Mol Ther 2016; 24:877-89. [PMID: 26849417 PMCID: PMC4881769 DOI: 10.1038/mt.2016.32] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2015] [Accepted: 01/21/2016] [Indexed: 02/07/2023] Open
Abstract
Friedreich's ataxia is a predominantly neurodegenerative disease caused by recessive mutations that produce a deficiency of frataxin (FXN). Here, we have used a herpesviral amplicon vector carrying a gene encoding for brain-derived neurotrophic factor (BDNF) to drive its overexpression in neuronal cells and test for its effect on FXN-deficient neurons both in culture and in the mouse cerebellum in vivo. Gene transfer of BDNF to primary cultures of mouse neurons prevents the apoptosis which is triggered by the knockdown of FXN gene expression. This neuroprotective effect of BDNF is also observed in vivo in a viral vector-based knockdown mouse cerebellar model. The injection of a lentiviral vector carrying a minigene encoding for a FXN-specific short hairpin ribonucleic acid (shRNA) into the mouse cerebellar cortex triggers a FXN deficit which is accompanied by significant apoptosis of granule neurons as well as loss of calbindin in Purkinje cells. These pathological changes are accompanied by a loss of motor coordination of mice as assayed by the rota-rod test. Coinjection of a herpesviral vector encoding for BDNF efficiently prevents both the development of cerebellar neuropathology and the ataxic phenotype. These data demonstrate the potential therapeutic usefulness of neurotrophins like BDNF to protect FXN-deficient neurons from degeneration.
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Affiliation(s)
- Yurika Katsu-Jiménez
- Centro de Biología Molecular Severo Ochoa (UAM-CSIC) and Departamento de Biología Molecular, Universidad Autónoma de Madrid (UAM), Madrid, Spain
- Instituto de Investigaciones Sanitarias Hospital Puerta de Hierro-Majadahonda (IDIPHIM), Madrid, Spain
| | - Frida Loría
- Centro de Biología Molecular Severo Ochoa (UAM-CSIC) and Departamento de Biología Molecular, Universidad Autónoma de Madrid (UAM), Madrid, Spain
- Instituto de Investigaciones Sanitarias Hospital Puerta de Hierro-Majadahonda (IDIPHIM), Madrid, Spain
| | - Juan Carlos Corona
- Centro de Biología Molecular Severo Ochoa (UAM-CSIC) and Departamento de Biología Molecular, Universidad Autónoma de Madrid (UAM), Madrid, Spain
- Instituto de Investigaciones Sanitarias Hospital Puerta de Hierro-Majadahonda (IDIPHIM), Madrid, Spain
- Current address: Hospital Infantil de México “Federico Gómez”, México, D.F., México
| | - Javier Díaz-Nido
- Centro de Biología Molecular Severo Ochoa (UAM-CSIC) and Departamento de Biología Molecular, Universidad Autónoma de Madrid (UAM), Madrid, Spain
- Instituto de Investigaciones Sanitarias Hospital Puerta de Hierro-Majadahonda (IDIPHIM), Madrid, Spain
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13
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Piatek A, Mahfouz MM. Targeted genome regulation via synthetic programmable transcriptional regulators. Crit Rev Biotechnol 2016; 37:429-440. [DOI: 10.3109/07388551.2016.1165180] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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14
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Lee HB, Sundberg BN, Sigafoos AN, Clark KJ. Genome Engineering with TALE and CRISPR Systems in Neuroscience. Front Genet 2016; 7:47. [PMID: 27092173 PMCID: PMC4821859 DOI: 10.3389/fgene.2016.00047] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2016] [Accepted: 03/16/2016] [Indexed: 12/26/2022] Open
Abstract
Recent advancement in genome engineering technology is changing the landscape of biological research and providing neuroscientists with an opportunity to develop new methodologies to ask critical research questions. This advancement is highlighted by the increased use of programmable DNA-binding agents (PDBAs) such as transcription activator-like effector (TALE) and RNA-guided clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR associated (Cas) systems. These PDBAs fused or co-expressed with various effector domains allow precise modification of genomic sequences and gene expression levels. These technologies mirror and extend beyond classic gene targeting methods contributing to the development of novel tools for basic and clinical neuroscience. In this Review, we discuss the recent development in genome engineering and potential applications of this technology in the field of neuroscience.
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Affiliation(s)
- Han B Lee
- Neurobiology of Disease Graduate Program, Mayo Graduate School Rochester, MN, USA
| | - Brynn N Sundberg
- Department of Biochemistry and Molecular Biology, Mayo Clinic Rochester, MN, USA
| | - Ashley N Sigafoos
- Department of Biochemistry and Molecular Biology, Mayo Clinic Rochester, MN, USA
| | - Karl J Clark
- Neurobiology of Disease Graduate Program, Mayo Graduate SchoolRochester, MN, USA; Department of Biochemistry and Molecular Biology, Mayo ClinicRochester, MN, USA
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15
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Nabhan JF, Wood KM, Rao VP, Morin J, Bhamidipaty S, LaBranche TP, Gooch RL, Bozal F, Bulawa CE, Guild BC. Intrathecal delivery of frataxin mRNA encapsulated in lipid nanoparticles to dorsal root ganglia as a potential therapeutic for Friedreich's ataxia. Sci Rep 2016; 6:20019. [PMID: 26883577 PMCID: PMC4756688 DOI: 10.1038/srep20019] [Citation(s) in RCA: 95] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2015] [Accepted: 12/04/2015] [Indexed: 12/18/2022] Open
Abstract
In Friedreich's ataxia (FRDA) patients, diminished frataxin (FXN) in sensory neurons is thought to yield the predominant pathology associated with disease. In this study, we demonstrate successful usage of RNA transcript therapy (RTT) as an exogenous human FXN supplementation strategy in vitro and in vivo, specifically to dorsal root ganglia (DRG). Initially, 293 T cells were transfected with codon optimized human FXN mRNA, which was translated to yield FXN protein. Importantly, FXN was rapidly processed into the mature functional form of FXN (mFXN). Next, FXN mRNA, in the form of lipid nanoparticles (LNPs), was administered intravenously in adult mice. Examination of liver homogenates demonstrated efficient FXN LNP uptake in hepatocytes and revealed that the mitochondrial maturation machinery had efficiently processed all FXN protein to mFXN in ~24 h in vivo. Remarkably, greater than 50% mFXN protein derived from LNPs was detected seven days after intravenous administration of FXN LNPs, suggesting that the half-life of mFXN in vivo exceeds one week. Moreover, when FXN LNPs were delivered by intrathecal administration, we detected recombinant human FXN protein in DRG. These observations provide the first demonstration that RTT can be used for the delivery of therapeutic mRNA to DRG.
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Affiliation(s)
- Joseph F. Nabhan
- Rare Disease Research Unit, Pfizer, 610 Main Street, Cambridge, MA 02139, USA
| | - Kristy M. Wood
- Global Biotherapeutics, Pfizer, 610 Main Street, Cambridge, MA 02139, USA
| | - Varada P. Rao
- Comparative Medicine, Pfizer, 1 Burtt Rd, Andover, MA 01810, USA
| | - Jeffrey Morin
- Comparative Medicine, Pfizer, 1 Burtt Rd, Andover, MA 01810, USA
| | - Surya Bhamidipaty
- Drug Safety Research and Development, Pfizer, 1 Burtt Rd, Andover, MA 01810, USA
| | - Timothy P. LaBranche
- Drug Safety Research and Development, Pfizer, 1 Burtt Rd, Andover, MA 01810, USA
| | - Renea L. Gooch
- Rare Disease Research Unit, Pfizer, 610 Main Street, Cambridge, MA 02139, USA
| | - Fazli Bozal
- Rare Disease Research Unit, Pfizer, 610 Main Street, Cambridge, MA 02139, USA
| | - Christine E. Bulawa
- Rare Disease Research Unit, Pfizer, 610 Main Street, Cambridge, MA 02139, USA
| | - Braydon C. Guild
- Global Biotherapeutics, Pfizer, 610 Main Street, Cambridge, MA 02139, USA
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16
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A. Lu M, Rajanala S, Mikkilineni SV, Cahill CM, Brown R, D. Berry J, Rogers JT. The 5’-Untranslated Region of the C9orf72 mRNA Exhibits a Phylogenetic Alignment to the Cis-Aconitase Iron-Responsive Element; Novel Therapies for Amytrophic Lateral Sclerosis. ACTA ACUST UNITED AC 2016. [DOI: 10.4236/nm.2016.71003] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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17
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Anjomani Virmouni S, Ezzatizadeh V, Sandi C, Sandi M, Al-Mahdawi S, Chutake Y, Pook MA. A novel GAA-repeat-expansion-based mouse model of Friedreich's ataxia. Dis Model Mech 2015; 8:225-35. [PMID: 25681319 PMCID: PMC4348561 DOI: 10.1242/dmm.018952] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2014] [Accepted: 02/02/2015] [Indexed: 02/06/2023] Open
Abstract
Friedreich's ataxia (FRDA) is an autosomal recessive neurodegenerative disorder caused by a GAA repeat expansion mutation within intron 1 of the FXN gene, resulting in reduced levels of frataxin protein. We have previously reported the generation of human FXN yeast artificial chromosome (YAC) transgenic FRDA mouse models containing 90-190 GAA repeats, but the presence of multiple GAA repeats within these mice is considered suboptimal. We now describe the cellular, molecular and behavioural characterisation of a newly developed YAC transgenic FRDA mouse model, designated YG8sR, which we have shown by DNA sequencing to contain a single pure GAA repeat expansion. The founder YG8sR mouse contained 120 GAA repeats but, due to intergenerational expansion, we have now established a colony of YG8sR mice that contain ~200 GAA repeats. We show that YG8sR mice have a single copy of the FXN transgene, which is integrated at a single site as confirmed by fluorescence in situ hybridisation (FISH) analysis of metaphase and interphase chromosomes. We have identified significant behavioural deficits, together with a degree of glucose intolerance and insulin hypersensitivity, in YG8sR FRDA mice compared with control Y47R and wild-type (WT) mice. We have also detected increased somatic GAA repeat instability in the brain and cerebellum of YG8sR mice, together with significantly reduced expression of FXN, FAST-1 and frataxin, and reduced aconitase activity, compared with Y47R mice. Furthermore, we have confirmed the presence of pathological vacuoles within neurons of the dorsal root ganglia (DRG) of YG8sR mice. These novel GAA-repeat-expansion-based YAC transgenic FRDA mice, which exhibit progressive FRDA-like pathology, represent an excellent model for the investigation of FRDA disease mechanisms and therapy.
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Affiliation(s)
- Sara Anjomani Virmouni
- Ataxia Research Group, Division of Biosciences, Department of Life Sciences, College of Health & Life Sciences, Brunel University London, Uxbridge, UB8 3PH, UK Synthetic Biology Theme, Institute of Environment, Health and Societies, Brunel University London, Uxbridge, UB8 3PH, UK
| | - Vahid Ezzatizadeh
- Ataxia Research Group, Division of Biosciences, Department of Life Sciences, College of Health & Life Sciences, Brunel University London, Uxbridge, UB8 3PH, UK
| | - Chiranjeevi Sandi
- Ataxia Research Group, Division of Biosciences, Department of Life Sciences, College of Health & Life Sciences, Brunel University London, Uxbridge, UB8 3PH, UK
| | - Madhavi Sandi
- Ataxia Research Group, Division of Biosciences, Department of Life Sciences, College of Health & Life Sciences, Brunel University London, Uxbridge, UB8 3PH, UK Synthetic Biology Theme, Institute of Environment, Health and Societies, Brunel University London, Uxbridge, UB8 3PH, UK
| | - Sahar Al-Mahdawi
- Ataxia Research Group, Division of Biosciences, Department of Life Sciences, College of Health & Life Sciences, Brunel University London, Uxbridge, UB8 3PH, UK Synthetic Biology Theme, Institute of Environment, Health and Societies, Brunel University London, Uxbridge, UB8 3PH, UK
| | - Yogesh Chutake
- Department of Pediatrics, Section of Genetics, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
| | - Mark A Pook
- Ataxia Research Group, Division of Biosciences, Department of Life Sciences, College of Health & Life Sciences, Brunel University London, Uxbridge, UB8 3PH, UK Synthetic Biology Theme, Institute of Environment, Health and Societies, Brunel University London, Uxbridge, UB8 3PH, UK
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18
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Shah KA, McGinty RJ, Egorova VI, Mirkin SM. Coupling transcriptional state to large-scale repeat expansions in yeast. Cell Rep 2014; 9:1594-1602. [PMID: 25464841 DOI: 10.1016/j.celrep.2014.10.048] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2014] [Revised: 09/07/2014] [Accepted: 10/19/2014] [Indexed: 11/15/2022] Open
Abstract
Expansions of simple DNA repeats cause numerous hereditary disorders in humans. Replication, repair, and transcription are implicated in the expansion process, but their relative contributions are yet to be distinguished. To separate the roles of replication and transcription in the expansion of Friedreich's ataxia (GAA)n repeats, we designed two yeast genetic systems that utilize a galactose-inducible GAL1 promoter but contain these repeats in either the transcribed or nontranscribed region of a selectable cassette. We found that large-scale repeat expansions can occur in the lack of transcription. Induction of transcription strongly elevated the rate of expansions in both systems, indicating that active transcriptional state rather than transcription through the repeat per se affects this process. Furthermore, replication defects increased the rate of repeat expansions irrespective of transcriptional state. We present a model in which transcriptional state, linked to the nucleosomal density of a region, acts as a modulator of large-scale repeat expansions.
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Affiliation(s)
- Kartik A Shah
- Department of Biology, Tufts University, Medford, MA 02155, USA
| | - Ryan J McGinty
- Department of Biology, Tufts University, Medford, MA 02155, USA
| | - Vera I Egorova
- Department of Biology, Tufts University, Medford, MA 02155, USA
| | - Sergei M Mirkin
- Department of Biology, Tufts University, Medford, MA 02155, USA.
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19
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Sandford E, Burmeister M. Genes and genetic testing in hereditary ataxias. Genes (Basel) 2014; 5:586-603. [PMID: 25055202 PMCID: PMC4198919 DOI: 10.3390/genes5030586] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2014] [Revised: 06/25/2014] [Accepted: 07/01/2014] [Indexed: 12/19/2022] Open
Abstract
Ataxia is a neurological cerebellar disorder characterized by loss of coordination during muscle movements affecting walking, vision, and speech. Genetic ataxias are very heterogeneous, with causative variants reported in over 50 genes, which can be inherited in classical dominant, recessive, X-linked, or mitochondrial fashion. A common mechanism of dominant ataxias is repeat expansions, where increasing lengths of repeated DNA sequences result in non-functional proteins that accumulate in the body causing disease. Greater understanding of all ataxia genes has helped identify several different pathways, such as DNA repair, ubiquitination, and ion transport, which can be used to help further identify new genes and potential treatments. Testing for the most common mutations in these genes is now clinically routine to help with prognosis and treatment decisions, but next generation sequencing will revolutionize how genetic testing will be done. Despite the large number of known ataxia causing genes, however, many individuals with ataxia are unable to obtain a genetic diagnosis, suggesting that more genes need to be discovered. Utilization of next generation sequencing technologies, expression studies, and increased knowledge of ataxia pathways will aid in the identification of new ataxia genes.
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Affiliation(s)
- Erin Sandford
- Molecular & Behavioral Neuroscience Institute, University of Michigan, Ann Arbor, MI 48109, USA.
| | - Margit Burmeister
- Molecular & Behavioral Neuroscience Institute, University of Michigan, Ann Arbor, MI 48109, USA.
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20
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Kabadi AM, Gersbach CA. Engineering synthetic TALE and CRISPR/Cas9 transcription factors for regulating gene expression. Methods 2014; 69:188-97. [PMID: 25010559 DOI: 10.1016/j.ymeth.2014.06.014] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2014] [Revised: 06/26/2014] [Accepted: 06/27/2014] [Indexed: 12/22/2022] Open
Abstract
Engineered DNA-binding proteins that can be targeted to specific sites in the genome to manipulate gene expression have enabled many advances in biomedical research. This includes generating tools to study fundamental aspects of gene regulation and the development of a new class of gene therapies that alter the expression of endogenous genes. Designed transcription factors have entered clinical trials for the treatment of human diseases and others are in preclinical development. High-throughput and user-friendly platforms for designing synthetic DNA-binding proteins present innovative methods for deciphering cell biology and designing custom synthetic gene circuits. We review two platforms for designing synthetic transcription factors for manipulating gene expression: Transcription activator-like effectors (TALEs) and the RNA-guided clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9 system. We present an overview of each technology and a guide for designing and assembling custom TALE- and CRISPR/Cas9-based transcription factors. We also discuss characteristics of each platform that are best suited for different applications.
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Affiliation(s)
- Ami M Kabadi
- Department of Biomedical Engineering, Duke University, Durham, NC 27708, United States
| | - Charles A Gersbach
- Department of Biomedical Engineering, Duke University, Durham, NC 27708, United States; Institute for Genome Sciences and Policy, Duke University, Durham, NC 27708, United States; Department of Orthopaedic Surgery, Duke University Medical Center, Durham, NC 27710, United States.
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21
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Nemudryi AA, Valetdinova KR, Medvedev SP, Zakian SM. TALEN and CRISPR/Cas Genome Editing Systems: Tools of Discovery. Acta Naturae 2014; 6:19-40. [PMID: 25349712 PMCID: PMC4207558] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
Precise studies of plant, animal and human genomes enable remarkable opportunities of obtained data application in biotechnology and medicine. However, knowing nucleotide sequences isn't enough for understanding of particular genomic elements functional relationship and their role in phenotype formation and disease pathogenesis. In post-genomic era methods allowing genomic DNA sequences manipulation, visualization and regulation of gene expression are rapidly evolving. Though, there are few methods, that meet high standards of efficiency, safety and accessibility for a wide range of researchers. In 2011 and 2013 novel methods of genome editing appeared - this are TALEN (Transcription Activator-Like Effector Nucleases) and CRISPR (Clustered Regulatory Interspaced Short Palindromic Repeats)/Cas9 systems. Although TALEN and CRISPR/Cas9 appeared recently, these systems have proved to be effective and reliable tools for genome engineering. Here we generally review application of these systems for genome editing in conventional model objects of current biology, functional genome screening, cell-based human hereditary disease modeling, epigenome studies and visualization of cellular processes. Additionally, we review general strategies for designing TALEN and CRISPR/Cas9 and analyzing their activity. We also discuss some obstacles researcher can face using these genome editing tools.
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Affiliation(s)
- A. A. Nemudryi
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Lavrentyev Prosp., 10, Novosibirsk, Russia, 630090
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Lavrentyev Prosp., 8, Novosibirsk, Russia, 630090
- Meshalkin Novosibirsk State Research Institute of Circulation Pathology, Ministry of Health of the Russian Federation, Rechkunovskaya Str., 15, Novosibirsk, Russia, 630055
| | - K. R. Valetdinova
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Lavrentyev Prosp., 10, Novosibirsk, Russia, 630090
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Lavrentyev Prosp., 8, Novosibirsk, Russia, 630090
- Meshalkin Novosibirsk State Research Institute of Circulation Pathology, Ministry of Health of the Russian Federation, Rechkunovskaya Str., 15, Novosibirsk, Russia, 630055
- Novosibirsk State University, Pirogova Str., 2, Novosibirsk, Russia, 630090
| | - S. P. Medvedev
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Lavrentyev Prosp., 10, Novosibirsk, Russia, 630090
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Lavrentyev Prosp., 8, Novosibirsk, Russia, 630090
- Meshalkin Novosibirsk State Research Institute of Circulation Pathology, Ministry of Health of the Russian Federation, Rechkunovskaya Str., 15, Novosibirsk, Russia, 630055
- Novosibirsk State University, Pirogova Str., 2, Novosibirsk, Russia, 630090
| | - S. M. Zakian
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Lavrentyev Prosp., 10, Novosibirsk, Russia, 630090
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Lavrentyev Prosp., 8, Novosibirsk, Russia, 630090
- Meshalkin Novosibirsk State Research Institute of Circulation Pathology, Ministry of Health of the Russian Federation, Rechkunovskaya Str., 15, Novosibirsk, Russia, 630055
- Novosibirsk State University, Pirogova Str., 2, Novosibirsk, Russia, 630090
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22
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Nemudryi AA, Valetdinova KR, Medvedev SP, Zakian SM. TALEN and CRISPR/Cas Genome Editing Systems: Tools of Discovery. Acta Naturae 2014; 85:209-18. [PMID: 25349712 DOI: 10.1007/s11103-014-0188-7] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2014] [Accepted: 03/05/2014] [Indexed: 05/07/2023] Open
Abstract
Precise studies of plant, animal and human genomes enable remarkable opportunities of obtained data application in biotechnology and medicine. However, knowing nucleotide sequences isn't enough for understanding of particular genomic elements functional relationship and their role in phenotype formation and disease pathogenesis. In post-genomic era methods allowing genomic DNA sequences manipulation, visualization and regulation of gene expression are rapidly evolving. Though, there are few methods, that meet high standards of efficiency, safety and accessibility for a wide range of researchers. In 2011 and 2013 novel methods of genome editing appeared - this are TALEN (Transcription Activator-Like Effector Nucleases) and CRISPR (Clustered Regulatory Interspaced Short Palindromic Repeats)/Cas9 systems. Although TALEN and CRISPR/Cas9 appeared recently, these systems have proved to be effective and reliable tools for genome engineering. Here we generally review application of these systems for genome editing in conventional model objects of current biology, functional genome screening, cell-based human hereditary disease modeling, epigenome studies and visualization of cellular processes. Additionally, we review general strategies for designing TALEN and CRISPR/Cas9 and analyzing their activity. We also discuss some obstacles researcher can face using these genome editing tools.
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Affiliation(s)
- A A Nemudryi
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Lavrentyev Prosp., 10, Novosibirsk, Russia, 630090 ; Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Lavrentyev Prosp., 8, Novosibirsk, Russia, 630090 ; Meshalkin Novosibirsk State Research Institute of Circulation Pathology, Ministry of Health of the Russian Federation, Rechkunovskaya Str., 15, Novosibirsk, Russia, 630055
| | - K R Valetdinova
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Lavrentyev Prosp., 10, Novosibirsk, Russia, 630090 ; Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Lavrentyev Prosp., 8, Novosibirsk, Russia, 630090 ; Meshalkin Novosibirsk State Research Institute of Circulation Pathology, Ministry of Health of the Russian Federation, Rechkunovskaya Str., 15, Novosibirsk, Russia, 630055 ; Novosibirsk State University, Pirogova Str., 2, Novosibirsk, Russia, 630090
| | - S P Medvedev
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Lavrentyev Prosp., 10, Novosibirsk, Russia, 630090 ; Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Lavrentyev Prosp., 8, Novosibirsk, Russia, 630090 ; Meshalkin Novosibirsk State Research Institute of Circulation Pathology, Ministry of Health of the Russian Federation, Rechkunovskaya Str., 15, Novosibirsk, Russia, 630055 ; Novosibirsk State University, Pirogova Str., 2, Novosibirsk, Russia, 630090
| | - S M Zakian
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Lavrentyev Prosp., 10, Novosibirsk, Russia, 630090 ; Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Lavrentyev Prosp., 8, Novosibirsk, Russia, 630090 ; Meshalkin Novosibirsk State Research Institute of Circulation Pathology, Ministry of Health of the Russian Federation, Rechkunovskaya Str., 15, Novosibirsk, Russia, 630055 ; Novosibirsk State University, Pirogova Str., 2, Novosibirsk, Russia, 630090
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23
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Evans-Galea MV, Pébay A, Dottori M, Corben LA, Ong SH, Lockhart PJ, Delatycki MB. Cell and gene therapy for Friedreich ataxia: progress to date. Hum Gene Ther 2014; 25:684-93. [PMID: 24749505 DOI: 10.1089/hum.2013.180] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Neurodegenerative disorders such as Friedreich ataxia (FRDA) present significant challenges in developing effective therapeutic intervention. Current treatments aim to manage symptoms and thus improve quality of life, but none can cure, nor are proven to slow, the neurodegeneration inherent to this disease. The primary clinical features of FRDA include progressive ataxia and shortened life span, with complications of cardiomyopathy being the major cause of death. FRDA is most commonly caused by an expanded GAA trinucleotide repeat in the first intron of FXN that leads to reduced levels of frataxin, a mitochondrial protein important for iron metabolism. The GAA expansion in FRDA does not alter the coding sequence of FXN. It results in reduced production of structurally normal frataxin, and hence any increase in protein level is expected to be therapeutically beneficial. Recently, there has been increased interest in developing novel therapeutic applications like cell and/or gene therapies, and these cutting-edge applications could provide effective treatment options for FRDA. Importantly, since individuals with FRDA produce frataxin at low levels, increased expression should not elicit an immune response. Here we review the advances to date and highlight the future potential for cell and gene therapy to treat this debilitating disease.
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Affiliation(s)
- Marguerite V Evans-Galea
- 1 Bruce Lefroy Centre for Genetic Health Research, Murdoch Children's Research Institute , Parkville Victoria 3052, Australia
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24
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Gersbach CA, Perez-Pinera P. Activating human genes with zinc finger proteins, transcription activator-like effectors and CRISPR/Cas9 for gene therapy and regenerative medicine. Expert Opin Ther Targets 2014; 18:835-9. [PMID: 24917359 DOI: 10.1517/14728222.2014.913572] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
New technologies have recently been developed to control the expression of human genes in their native genomic context by engineering synthetic transcription factors that can be targeted to any DNA sequence. The ability to precisely regulate any gene as it occurs naturally in the genome provides a means to address a variety of diseases and disorders. This approach also circumvents some of the traditional challenges of gene therapy. In this editorial, we review the technologies that have enabled targeted human gene activation, including the engineering of transcription factors based on zinc finger proteins, transcription activator-like effectors and the CRISPR/Cas9 system. Additionally, we highlight examples in which these methods have been developed for therapeutic applications and discuss challenges and opportunities.
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Affiliation(s)
- Charles A Gersbach
- Duke University, Department of Biomedical Engineering , Room 136 Hudson Hall, Box 90281, Durham, NC 27708-0281 , USA +1 919 613 2147 ; +1 919 668 0795 ;
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25
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Anthony K, More A, Zhang X. Activation of silenced cytokine gene promoters by the synergistic effect of TBP-TALE and VP64-TALE activators. PLoS One 2014; 9:e95790. [PMID: 24755922 PMCID: PMC3995891 DOI: 10.1371/journal.pone.0095790] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2014] [Accepted: 03/29/2014] [Indexed: 11/19/2022] Open
Abstract
Recent work has shown that the combinatorial use of multiple TALE activators can selectively activate certain cellular genes in inaccessible chromatin regions. In this study, we aimed to interrogate the activation potential of TALEs upon transcriptionally silenced immune genes in the context of non-immune cells. We designed a unique strategy, in which a single TALE fused to the TATA-box binding protein (TBP-TALE) is coupled with multiple VP64-TALE activators. We found that our strategy is significantly more potent than multiple TALE activators alone in activating expression of IL-2 and GM-CSF in diverse cell origins in which both genes are otherwise completely silenced. Chromatin analysis revealed that the gene activation was due in part to displacement of a distinctly positioned nucleosome. These studies provide a novel epigenetic mechanism for artificial gene induction and have important implications for targeted cancer immunotherapy, DNA vaccine development, as well as rational design of TALE activators.
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Affiliation(s)
- Kim Anthony
- Department of Biology and Biochemistry, University of Houston, Houston, Texas, United States of America
- Center for Nuclear Receptors and Cell Signaling, University of Houston, Houston, Texas, United States of America
| | - Abhijit More
- Department of Biology and Biochemistry, University of Houston, Houston, Texas, United States of America
| | - Xiaoliu Zhang
- Department of Biology and Biochemistry, University of Houston, Houston, Texas, United States of America
- Center for Nuclear Receptors and Cell Signaling, University of Houston, Houston, Texas, United States of America
- * E-mail:
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