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Zhao Y, Li X, Liu C, Jiang C, Guo X, Xu Q, Yin Z, Liu Z, Mu Y. Improving the Efficiency of CRISPR Ribonucleoprotein-Mediated Precise Gene Editing by Small Molecules in Porcine Fibroblasts. Animals (Basel) 2024; 14:719. [PMID: 38473105 DOI: 10.3390/ani14050719] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Revised: 02/21/2024] [Accepted: 02/23/2024] [Indexed: 03/14/2024] Open
Abstract
The aim of this study was to verify whether small molecules can improve the efficiency of precision gene editing using clustered regularly interspaced short palindromic repeats (CRISPR) ribonucleoprotein (RNP) in porcine cells. CRISPR associated 9 (Cas9) protein, small guide RNA (sgRNA), phosphorothioate-modified single-stranded oligonucleotides (ssODN), and different small molecules were used to generate precise nucleotide substitutions at the insulin (INS) gene by homology-directed repair (HDR) in porcine fetal fibroblasts (PFFs). These components were introduced into PFFs via electroporation, followed by polymerase chain reaction (PCR) for the target site. All samples were sequenced and analyzed, and the efficiencies of different small molecules at the target site were compared. The results showed that the optimal concentrations of the small molecules, including L-189, NU7441, SCR7, L755507, RS-1, and Brefeldin A, for in vitro-cultured PFFs' viability were determined. Compared with the control group, the single small molecules including L-189, NU7441, SCR7, L755507, RS-1, and Brefeldin A increased the efficiency of HDR-mediated precise gene editing from 1.71-fold to 2.28-fold, respectively. There are no benefits in using the combination of two small molecules, since none of the combinations improved the precise gene editing efficiency compared to single small molecules. In conclusion, these results suggested that a single small molecule can increase the efficiency of CRISPR RNP-mediated precise gene editing in porcine cells.
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Affiliation(s)
- Yunjing Zhao
- Key Laboratory of Animal Cellular and Genetic Engineering of Heilongjiang Province, Northeast Agricultural University, Harbin 150030, China
- College of Life Science, Northeast Agricultural University, Harbin 150030, China
| | - Xinyu Li
- Key Laboratory of Animal Cellular and Genetic Engineering of Heilongjiang Province, Northeast Agricultural University, Harbin 150030, China
- College of Life Science, Northeast Agricultural University, Harbin 150030, China
| | - Chang Liu
- Key Laboratory of Animal Cellular and Genetic Engineering of Heilongjiang Province, Northeast Agricultural University, Harbin 150030, China
| | - Chaoqian Jiang
- Key Laboratory of Animal Cellular and Genetic Engineering of Heilongjiang Province, Northeast Agricultural University, Harbin 150030, China
| | - Xiaochen Guo
- Key Laboratory of Animal Cellular and Genetic Engineering of Heilongjiang Province, Northeast Agricultural University, Harbin 150030, China
- College of Life Science, Northeast Agricultural University, Harbin 150030, China
| | - Qianqian Xu
- Key Laboratory of Animal Cellular and Genetic Engineering of Heilongjiang Province, Northeast Agricultural University, Harbin 150030, China
- College of Life Science, Northeast Agricultural University, Harbin 150030, China
| | - Zhi Yin
- Key Laboratory of Animal Cellular and Genetic Engineering of Heilongjiang Province, Northeast Agricultural University, Harbin 150030, China
- College of Life Science, Northeast Agricultural University, Harbin 150030, China
| | - Zhonghua Liu
- Key Laboratory of Animal Cellular and Genetic Engineering of Heilongjiang Province, Northeast Agricultural University, Harbin 150030, China
- College of Life Science, Northeast Agricultural University, Harbin 150030, China
| | - Yanshuang Mu
- Key Laboratory of Animal Cellular and Genetic Engineering of Heilongjiang Province, Northeast Agricultural University, Harbin 150030, China
- College of Life Science, Northeast Agricultural University, Harbin 150030, China
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Volodina O, Smirnikhina S. The Future of Gene Therapy: A Review of In Vivo and Ex Vivo Delivery Methods for Genome Editing-Based Therapies. Mol Biotechnol 2024:10.1007/s12033-024-01070-4. [PMID: 38363528 DOI: 10.1007/s12033-024-01070-4] [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: 10/06/2023] [Accepted: 01/08/2024] [Indexed: 02/17/2024]
Abstract
The development of gene therapy based on genome editing has opened up new possibilities for the treatment of human genetic disorders. This field has developed rapidly over the past few decades, some genome editing-based therapies are already in phase 3 clinical trials. However, there are several challenges to be addressed before widespread adoption of gene editing therapy becomes possible. The main obstacles in the development of such therapy are safety and efficiency, so one of the biggest issues is the delivery of genetic constructs to patient cells. Approaches in genetic cargo delivery divide into ex vivo and in vivo, which are suitable for different cases. The ex vivo approach is mainly used to edit blood cells, improve cancer therapy, and treat infectious diseases. To edit cells in organs researches choose in vivo approach. For each approach, there is a fairly large set of methods, but, unfortunately, these methods are not universal in their effectiveness and safety. The focus of this article is to discuss the current status of in vivo and ex vivo delivery methods used in genome editing-based therapy. We will discuss the main methods employed in these approaches and their applications in current gene editing treatments under development.
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Affiliation(s)
- Olga Volodina
- Laboratory of Genome Editing, Research Centre for Medical Genetics, Moscow, 115522, Russia.
| | - Svetlana Smirnikhina
- Laboratory of Genome Editing, Research Centre for Medical Genetics, Moscow, 115522, Russia
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3
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Sá AGA, House JD. Adding pulse flours to cereal-based snacks and bakery products: An overview of free asparagine quantification methods and mitigation strategies of acrylamide formation in foods. Compr Rev Food Sci Food Saf 2024; 23:e13260. [PMID: 38284574 DOI: 10.1111/1541-4337.13260] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Revised: 09/30/2023] [Accepted: 10/13/2023] [Indexed: 01/30/2024]
Abstract
Thermal processing techniques can lead to the formation of heat-induced toxic substances. Acrylamide is one contaminant that has received much scientific attention in recent years, and it is formed essentially during the Maillard reaction when foods rich in carbohydrates, particularly reducing sugars (glucose, fructose), and certain free amino acids, especially asparagine (ASN), are processed at high temperatures (>120°C). The highly variable free ASN concentration in raw materials makes it challenging for food businesses to keep acrylamide content below the European Commission benchmark levels, while avoiding flavor, color, and texture impacts on their products. Free ASN concentrations in crops are affected by environment, genotype, and soil fertilization, which can also influence protein content and amino acid composition. This review aims to provide an overview of free ASN and acrylamide quantification methods and mitigation strategies for acrylamide formation in foods, focusing on adding pulse flours to cereal-based snacks and bakery products. Overall, this review emphasizes the importance of these mitigation strategies in minimizing acrylamide formation in plant-based products and ensuring safer and healthier food options.
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Affiliation(s)
- Amanda G A Sá
- Richardson Centre for Food Technology and Research, Department of Food and Human Nutritional Sciences, University of Manitoba, Winnipeg, Manitoba, Canada
| | - James D House
- Richardson Centre for Food Technology and Research, Department of Food and Human Nutritional Sciences, University of Manitoba, Winnipeg, Manitoba, Canada
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4
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Shahid M, Khan MS, Singh UB. Pesticide-tolerant microbial consortia: Potential candidates for remediation/clean-up of pesticide-contaminated agricultural soil. ENVIRONMENTAL RESEARCH 2023; 236:116724. [PMID: 37500042 DOI: 10.1016/j.envres.2023.116724] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2023] [Revised: 07/16/2023] [Accepted: 07/21/2023] [Indexed: 07/29/2023]
Abstract
Reclamation of pesticide-polluted lands has long been a difficult endeavour. The use of synthetic pesticides could not be restricted due to rising agricultural demand. Pesticide toxicity has become a pressing agronomic problem due to its adverse impact on agroecosystems, agricultural output, and consequently food security and safety. Among different techniques used for the reclamation of pesticide-polluted sites, microbial bioremediation is an eco-friendly approach, which focuses on the application of resilient plant growth promoting rhizobacteria (PGPR) that may transform or degrade chemical pesticides to innocuous forms. Such pesticide-resilient PGPR has demonstrated favourable effects on soil-plant systems, even in pesticide-contaminated environments, by degrading pesticides, providing macro-and micronutrients, and secreting active but variable secondary metabolites like-phytohormones, siderophores, ACC deaminase, etc. This review critically aims to advance mechanistic understanding related to the reduction of phytotoxicity of pesticides via the use of microbe-mediated remediation techniques leading to crop optimization in pesticide-stressed soils. The literature surveyed and data presented herein are extremely useful, offering agronomists-and crop protectionists microbes-assisted remedial strategies for affordably enhancing crop productivity in pesticide-stressed soils.
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Affiliation(s)
- Mohammad Shahid
- Plant-Microbe Interaction and Rhizosphere Biology Lab, ICAR-National Bureau of Agriculturally Important Microorganisms (NBAIM), Kushmaur, Mau Nath Bhanjan, 275103, UP, India; Department of Agricultural Microbiology, Faculty of Agriculture Science, Aligarh Muslim University (A.M.U.), Aligarh, 202001, UP, India.
| | - Mohammad Saghir Khan
- Department of Agricultural Microbiology, Faculty of Agriculture Science, Aligarh Muslim University (A.M.U.), Aligarh, 202001, UP, India
| | - Udai B Singh
- Plant-Microbe Interaction and Rhizosphere Biology Lab, ICAR-National Bureau of Agriculturally Important Microorganisms (NBAIM), Kushmaur, Mau Nath Bhanjan, 275103, UP, India
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5
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Salama II, Sami SM, Salama SI, Abdel-Latif GA, Shaaban FA, Fouad WA, Abdelmohsen AM, Raslan HM. Current and novel modalities for management of chronic hepatitis B infection. World J Hepatol 2023; 15:585-608. [PMID: 37305370 PMCID: PMC10251278 DOI: 10.4254/wjh.v15.i5.585] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/19/2022] [Revised: 03/13/2023] [Accepted: 04/12/2023] [Indexed: 05/24/2023] Open
Abstract
Over 296 million people are estimated to have chronic hepatitis B viral infection (CHB), and it poses unique challenges for elimination. CHB is the result of hepatitis B virus (HBV)-specific immune tolerance and the presence of covalently closed circular DNA as mini chromosome inside the nucleus and the integrated HBV. Serum hepatitis B core-related antigen is the best surrogate marker for intrahepatic covalently closed circular DNA. Functional HBV “cure” is the durable loss of hepatitis B surface antigen (HBsAg), with or without HBsAg seroconversion and undetectable serum HBV DNA after completing a course of treatment. The currently approved therapies are nucleos(t)ide analogues, interferon-alpha, and pegylated-interferon. With these therapies, functional cure can be achieved in < 10% of CHB patients. Any variation to HBV or the host immune system that disrupts the interaction between them can lead to reactivation of HBV. Novel therapies may allow efficient control of CHB. They include direct acting antivirals and immunomodulators. Reduction of the viral antigen load is a crucial factor for success of immune-based therapies. Immunomodulatory therapy may lead to modulation of the host immune system. It may enhance/restore innate immunity against HBV (as toll-like-receptors and cytosolic retinoic acid inducible gene I agonist). Others may induce adaptive immunity as checkpoint inhibitors, therapeutic HBV vaccines including protein (HBsAg/preS and hepatitis B core antigen), monoclonal or bispecific antibodies and genetically engineered T cells to generate chimeric antigen receptor-T or T-cell receptor-T cells and HBV-specific T cells to restore T cell function to efficiently clear HBV. Combined therapy may successfully overcome immune tolerance and lead to HBV control and cure. Immunotherapeutic approaches carry the risk of overshooting immune responses causing uncontrolled liver damage. The safety of any new curative therapies should be measured in relation to the excellent safety of currently approved nucleos(t)ide analogues. Development of novel antiviral and immune modulatory therapies should be associated with new diagnostic assays used to evaluate the effectiveness or to predict response.
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Affiliation(s)
- Iman Ibrahim Salama
- Department of Community Medicine Research, National Research Centre, Giza 12411, Dokki, Egypt
| | - Samia M Sami
- Department of Child Health, National Research Centre, Giza 12411, Dokki, Egypt
| | - Somaia I Salama
- Department of Community Medicine Research, National Research Centre, Giza 12411, Dokki, Egypt
| | - Ghada A Abdel-Latif
- Department of Community Medicine Research, National Research Centre, Giza 12411, Dokki, Egypt
| | - Fatma A Shaaban
- Department of Child Health, National Research Centre, Giza 12411, Dokki, Egypt
| | - Walaa A Fouad
- Department of Community Medicine Research, National Research Centre, Giza 12411, Dokki, Egypt
| | - Aida M Abdelmohsen
- Department of Community Medicine Research, National Research Centre, Giza 12411, Dokki, Egypt
| | - Hala M Raslan
- Department of Internal Medicine, National Research Centre, Giza 12411, Dokki, Egypt
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Shakirova A, Karpov T, Komarova Y, Lepik K. In search of an ideal template for therapeutic genome editing: A review of current developments for structure optimization. Front Genome Ed 2023; 5:1068637. [PMID: 36911237 PMCID: PMC9992834 DOI: 10.3389/fgeed.2023.1068637] [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: 10/13/2022] [Accepted: 02/08/2023] [Indexed: 02/24/2023] Open
Abstract
Gene therapy is a fast developing field of medicine with hundreds of ongoing early-stage clinical trials and numerous preclinical studies. Genome editing (GE) now is an increasingly important technology for achieving stable therapeutic effect in gene correction, with hematopoietic cells representing a key target cell population for developing novel treatments for a number of hereditary diseases, infections and cancer. By introducing a double strand break (DSB) in the defined locus of genomic DNA, GE tools allow to knockout the desired gene or to knock-in the therapeutic gene if provided with an appropriate repair template. Currently, the efficiency of methods for GE-mediated knock-in is limited. Significant efforts were focused on improving the parameters and interaction of GE nuclease proteins. However, emerging data suggests that optimal characteristics of repair templates may play an important role in the knock-in mechanisms. While viral vectors with notable example of AAVs as a donor template carrier remain the mainstay in many preclinical trials, non-viral templates, including plasmid and linear dsDNA, long ssDNA templates, single and double-stranded ODNs, represent a promising alternative. Furthermore, tuning of editing conditions for the chosen template as well as its structure, length, sequence optimization, homology arm (HA) modifications may have paramount importance for achieving highly efficient knock-in with favorable safety profile. This review outlines the current developments in optimization of templates for the GE mediated therapeutic gene correction.
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Affiliation(s)
- Alena Shakirova
- RM Gorbacheva Research Institute of Pediatric Oncology, Hematology and Transplantation, Pavlov University, Saint Petersburg, Russia
| | - Timofey Karpov
- RM Gorbacheva Research Institute of Pediatric Oncology, Hematology and Transplantation, Pavlov University, Saint Petersburg, Russia.,Peter the Great St. Petersburg Polytechnic University, Saint Petersburg, Russia
| | - Yaroslava Komarova
- RM Gorbacheva Research Institute of Pediatric Oncology, Hematology and Transplantation, Pavlov University, Saint Petersburg, Russia
| | - Kirill Lepik
- RM Gorbacheva Research Institute of Pediatric Oncology, Hematology and Transplantation, Pavlov University, Saint Petersburg, Russia
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7
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Biotechnological Advances to Improve Abiotic Stress Tolerance in Crops. Int J Mol Sci 2022; 23:ijms231912053. [PMID: 36233352 PMCID: PMC9570234 DOI: 10.3390/ijms231912053] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 10/02/2022] [Accepted: 10/06/2022] [Indexed: 11/16/2022] Open
Abstract
The major challenges that agriculture is facing in the twenty-first century are increasing droughts, water scarcity, flooding, poorer soils, and extreme temperatures due to climate change. However, most crops are not tolerant to extreme climatic environments. The aim in the near future, in a world with hunger and an increasing population, is to breed and/or engineer crops to tolerate abiotic stress with a higher yield. Some crop varieties display a certain degree of tolerance, which has been exploited by plant breeders to develop varieties that thrive under stress conditions. Moreover, a long list of genes involved in abiotic stress tolerance have been identified and characterized by molecular techniques and overexpressed individually in plant transformation experiments. Nevertheless, stress tolerance phenotypes are polygenetic traits, which current genomic tools are dissecting to exploit their use by accelerating genetic introgression using molecular markers or site-directed mutagenesis such as CRISPR-Cas9. In this review, we describe plant mechanisms to sense and tolerate adverse climate conditions and examine and discuss classic and new molecular tools to select and improve abiotic stress tolerance in major crops.
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8
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Advances in CRISPR/Cas9. BIOMED RESEARCH INTERNATIONAL 2022; 2022:9978571. [PMID: 36193328 PMCID: PMC9525763 DOI: 10.1155/2022/9978571] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Revised: 08/09/2022] [Accepted: 08/22/2022] [Indexed: 11/30/2022]
Abstract
CRISPR/Cas9 technology has become the most examined gene editing technology in recent years due to its simple design, yet low cost, high efficiency, and simple operation, which can also achieve simultaneous editing of multiple loci. It can also be carried out without using plasmids, saving lots of troubles caused by plasmids. CRISPR/Cas9 has shown great potential in the study of genes or genomic functions in microorganisms, plants, animals, and human beings. In this review, we will examine the history, structure, and basic mechanisms of the CRISPR/Cas9 system, describe its great value in precision medicine and sgRNA library screening, and dig its great potential in a new field: DNA information storage.
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9
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Talluri S. Engineering and Design of Programmable Genome Editors. J Phys Chem B 2022; 126:5140-5150. [PMID: 35819243 DOI: 10.1021/acs.jpcb.2c03761] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Programmable genome editors are enzymes that can be targeted to a specific location in the genome for making site-specific alterations or deletions. The engineering, design, and development of sequence-specific editors has resulted in a dramatic increase in the precision of editing for nucleotide sequences. These editors can target specific locations in a genome, in vivo. The genome editors are being deployed for the development of genetically modified organisms for agriculture and industry, and for gene therapy of inherited human genetic disorders, cancer, and immunotherapy. Experimental and computational studies of structure, binding, activity, dynamics, and folding, reviewed here, have provided valuable insights that have the potential for increasing the functional efficiency of these gene/genome editors. Biochemical and biophysical studies of the specificities of natural and engineered genome editors reveal that increased binding affinity can be detrimental because of the increase of off-target effects and that the engineering and design of genome editors with higher specificity may require modulation and control of the conformational dynamics.
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Affiliation(s)
- Sekhar Talluri
- Department of Biotechnology, GITAM, Visakhapatnam, India 530045
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10
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Hawsawi YM, Shams A, Theyab A, Siddiqui J, Barnawee M, Abdali WA, Marghalani NA, Alshelali NH, Al-Sayed R, Alzahrani O, Alqahtani A, Alsulaiman AM. The State-of-the-Art of Gene Editing and its Application to Viral Infections and Diseases Including COVID-19. Front Cell Infect Microbiol 2022; 12:869889. [PMID: 35782122 PMCID: PMC9241565 DOI: 10.3389/fcimb.2022.869889] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2022] [Accepted: 05/09/2022] [Indexed: 11/26/2022] Open
Abstract
Gene therapy delivers a promising hope to cure many diseases and defects. The discovery of gene-editing technology fueled the world with valuable tools that have been employed in various domains of science, medicine, and biotechnology. Multiple means of gene editing have been established, including CRISPR/Cas, ZFNs, and TALENs. These strategies are believed to help understand the biological mechanisms of disease progression. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been designated the causative virus for coronavirus disease 2019 (COVID-19) that emerged at the end of 2019. This viral infection is a highly pathogenic and transmissible disease that caused a public health pandemic. As gene editing tools have shown great success in multiple scientific and medical areas, they could eventually contribute to discovering novel therapeutic and diagnostic strategies to battle the COVID-19 pandemic disease. This review aims to briefly highlight the history and some of the recent advancements of gene editing technologies. After that, we will describe various biological features of the CRISPR-Cas9 system and its diverse implications in treating different infectious diseases, both viral and non-viral. Finally, we will present current and future advancements in combating COVID-19 with a potential contribution of the CRISPR system as an antiviral modality in this battle.
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Affiliation(s)
- Yousef M. Hawsawi
- Research Center, King Faisal Specialist Hospital and Research Center, Jeddah, Saudi Arabia
- College of Medicine, Al-Faisal University, Riyadh, Saudi Arabia
- *Correspondence: Yousef M. Hawsawi, ; Anwar Shams, ;
| | - Anwar Shams
- Department of Pharmacology, College of Medicine, Taif University, Mecca, Saudi Arabia
- *Correspondence: Yousef M. Hawsawi, ; Anwar Shams, ;
| | - Abdulrahman Theyab
- College of Medicine, Al-Faisal University, Riyadh, Saudi Arabia
- Department of Laboratory & Blood Bank, Security Forces Hospital, Mecca, Saudi Arabia
| | - Jumana Siddiqui
- Research Center, King Faisal Specialist Hospital and Research Center, Jeddah, Saudi Arabia
| | - Mawada Barnawee
- Research Center, King Faisal Specialist Hospital and Research Center, Jeddah, Saudi Arabia
| | - Wed A. Abdali
- Research Center, King Faisal Specialist Hospital and Research Center, Jeddah, Saudi Arabia
| | - Nada A. Marghalani
- Research Center, King Faisal Specialist Hospital and Research Center, Jeddah, Saudi Arabia
| | - Nada H. Alshelali
- Research Center, King Faisal Specialist Hospital and Research Center, Jeddah, Saudi Arabia
| | - Rawan Al-Sayed
- Research Center, King Faisal Specialist Hospital and Research Center, Jeddah, Saudi Arabia
| | - Othman Alzahrani
- Department of Biology, Faculty of Science, University of Tabuk, Tabuk, Saudi Arabia
- Genome and Biotechnology Unit, Faculty of Science, University of Tabuk, Tabuk, Saudi Arabia
| | - Alanoud Alqahtani
- Bristol Medical School, Faculty of Health Sciences, University of Bristol, Bristol, United Kingdom
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CRISPR/Cas9 Technique for Temperature, Drought, and Salinity Stress Responses. Curr Issues Mol Biol 2022; 44:2664-2682. [PMID: 35735623 PMCID: PMC9221872 DOI: 10.3390/cimb44060182] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Revised: 06/02/2022] [Accepted: 06/06/2022] [Indexed: 02/07/2023] Open
Abstract
Global warming and climate change have severely affected plant growth and food production. Therefore, minimizing these effects is required for sustainable crop yields. Understanding the molecular mechanisms in response to abiotic stresses and improving agricultural traits to make crops tolerant to abiotic stresses have been going on unceasingly. To generate desirable varieties of crops, traditional and molecular breeding techniques have been tried, but both approaches are time-consuming. Clustered regularly interspaced short palindromic repeat/Cas9 (CRISPR/Cas9) and transcription activator-like effector nucleases (TALENs) are genome-editing technologies that have recently attracted the attention of plant breeders for genetic modification. These technologies are powerful tools in the basic and applied sciences for understanding gene function, as well as in the field of crop breeding. In this review, we focus on the application of genome-editing systems in plants to understand gene function in response to abiotic stresses and to improve tolerance to abiotic stresses, such as temperature, drought, and salinity stresses.
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12
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Lohia A, Sahel DK, Salman M, Singh V, Mariappan I, Mittal A, Chitkara D. Delivery Strategies for CRISPR/Cas Genome editing tool for Retinal Dystrophies: challenges and opportunities. Asian J Pharm Sci 2022; 17:153-176. [PMID: 36320315 PMCID: PMC9614410 DOI: 10.1016/j.ajps.2022.02.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Revised: 11/01/2021] [Accepted: 02/04/2022] [Indexed: 12/12/2022] Open
Abstract
CRISPR/Cas, an adaptive immune system in bacteria, has been adopted as an efficient and precise tool for site-specific gene editing with potential therapeutic opportunities. It has been explored for a variety of applications, including gene modulation, epigenome editing, diagnosis, mRNA editing, etc. It has found applications in retinal dystrophic conditions including progressive cone and cone-rod dystrophies, congenital stationary night blindness, X-linked juvenile retinoschisis, retinitis pigmentosa, age-related macular degeneration, leber's congenital amaurosis, etc. Most of the therapies for retinal dystrophic conditions work by regressing symptoms instead of reversing the gene mutations. CRISPR/Cas9 through indel could impart beneficial effects in the reversal of gene mutations in dystrophic conditions. Recent research has also consolidated on the approaches of using CRISPR systems for retinal dystrophies but their delivery to the posterior part of the eye is a major concern due to high molecular weight, negative charge, and in vivo stability of CRISPR components. Recently, non-viral vectors have gained interest due to their potential in tissue-specific nucleic acid (miRNA/siRNA/CRISPR) delivery. This review highlights the opportunities of retinal dystrophies management using CRISPR/Cas nanomedicine.
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Solayappan M, Azlan A, Khor KZ, Yik MY, Khan M, Yusoff NM, Moses EJ. Utilization of CRISPR-Mediated Tools for Studying Functional Genomics in Hematological Malignancies: An Overview on the Current Perspectives, Challenges, and Clinical Implications. Front Genet 2022; 12:767298. [PMID: 35154242 PMCID: PMC8834884 DOI: 10.3389/fgene.2021.767298] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Accepted: 11/17/2021] [Indexed: 11/26/2022] Open
Abstract
Hematological malignancies (HM) are a group of neoplastic diseases that are usually heterogenous in nature due to the complex underlying genetic aberrations in which collaborating mutations enable cells to evade checkpoints that normally safeguard it against DNA damage and other disruptions of healthy cell growth. Research regarding chromosomal structural rearrangements and alterations, gene mutations, and functionality are currently being carried out to understand the genomics of these abnormalities. It is also becoming more evident that cross talk between the functional changes in transcription and proteins gives the characteristics of the disease although specific mutations may induce unique phenotypes. Functional genomics is vital in this aspect as it measures the complete genetic change in cancerous cells and seeks to integrate the dynamic changes in these networks to elucidate various cancer phenotypes. The advent of CRISPR technology has indeed provided a superfluity of benefits to mankind, as this versatile technology enables DNA editing in the genome. The CRISPR-Cas9 system is a precise genome editing tool, and it has revolutionized methodologies in the field of hematology. Currently, there are various CRISPR systems that are used to perform robust site-specific gene editing to study HM. Furthermore, experimental approaches that are based on CRISPR technology have created promising tools for developing effective hematological therapeutics. Therefore, this review will focus on diverse applications of CRISPR-based gene-editing tools in HM and its potential future trajectory. Collectively, this review will demonstrate the key roles of different CRISPR systems that are being used in HM, and the literature will be a representation of a critical step toward further understanding the biology of HM and the development of potential therapeutic approaches.
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Affiliation(s)
- Maheswaran Solayappan
- Regenerative Medicine Sciences Cluster, Advanced Medical and Dental Institute, Universiti Sains Malaysia, Penang, Malaysia
- Department of Biotechnology, Faculty of Applied Sciences, AIMST University, Bedong, Malaysia
| | - Adam Azlan
- Regenerative Medicine Sciences Cluster, Advanced Medical and Dental Institute, Universiti Sains Malaysia, Penang, Malaysia
- *Correspondence: Emmanuel Jairaj Moses,
| | - Kang Zi Khor
- Regenerative Medicine Sciences Cluster, Advanced Medical and Dental Institute, Universiti Sains Malaysia, Penang, Malaysia
| | - Mot Yee Yik
- Regenerative Medicine Sciences Cluster, Advanced Medical and Dental Institute, Universiti Sains Malaysia, Penang, Malaysia
| | - Matiullah Khan
- Department of Pathology, Faculty of Medicine, AIMST University, Bedong, Malaysia
| | - Narazah Mohd Yusoff
- Regenerative Medicine Sciences Cluster, Advanced Medical and Dental Institute, Universiti Sains Malaysia, Penang, Malaysia
| | - Emmanuel Jairaj Moses
- Regenerative Medicine Sciences Cluster, Advanced Medical and Dental Institute, Universiti Sains Malaysia, Penang, Malaysia
- *Correspondence: Emmanuel Jairaj Moses,
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14
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Díaz-Galicia E, Grünberg R, Arold ST. How to Find the Right RNA-Sensing CRISPR-Cas System for an In Vitro Application. BIOSENSORS 2022; 12:bios12020053. [PMID: 35200314 PMCID: PMC8869480 DOI: 10.3390/bios12020053] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Revised: 01/17/2022] [Accepted: 01/18/2022] [Indexed: 12/26/2022]
Abstract
CRISPR-Cas systems have a great and still largely untapped potential for in vitro applications, in particular, for RNA biosensing. However, there is currently no systematic guide on selecting the most appropriate RNA-targeting CRISPR-Cas system for a given application among thousands of potential candidates. We provide an overview of the currently described Cas effector systems and review existing Cas-based RNA detection methods. We then propose a set of systematic selection criteria for selecting CRISPR-Cas candidates for new applications. Using this approach, we identify four candidates for in vitro RNA.
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Affiliation(s)
- Escarlet Díaz-Galicia
- Computational Bioscience Research Center (CBRC), Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia;
| | - Raik Grünberg
- Computational Bioscience Research Center (CBRC), Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia;
- Correspondence: (R.G.); (S.T.A.)
| | - Stefan T. Arold
- Computational Bioscience Research Center (CBRC), Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia;
- Centre de Biologie Structurale (CBS), INSERM, CNRS, Université de Montpellier, F-34090 Montpellier, France
- Correspondence: (R.G.); (S.T.A.)
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15
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Liao B, Chen X, Zhou X, Zhou Y, Shi Y, Ye X, Liao M, Zhou Z, Cheng L, Ren B. Applications of CRISPR/Cas gene-editing technology in yeast and fungi. Arch Microbiol 2021; 204:79. [DOI: 10.1007/s00203-021-02723-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 11/20/2021] [Accepted: 12/09/2021] [Indexed: 12/12/2022]
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16
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Freitas DF, da Rocha IM, Vieira-da-Motta O, de Paula Santos C. The Role of Melanin in the Biology and Ecology of Nematophagous Fungi. J Chem Ecol 2021; 47:597-613. [PMID: 34232439 DOI: 10.1007/s10886-021-01282-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Revised: 05/03/2021] [Accepted: 05/13/2021] [Indexed: 11/24/2022]
Abstract
Melanin is a heteropolymer formed by the polymerization of phenolic and indolic compounds. It occurs in organisms across all biological kingdoms and has a range different of functions, thus indicating its important evolutionary role. The presence of melanin offers several protective advantages, including against ultraviolet radiation, traumatic damage, oxidative stress, extreme temperatures, and pressure. For many species of fungi, melanin also participates directly in the process of virulence and pathogenicity. These organisms can synthesize melanin in two main ways: using a substrate of endogenous origin, involving 1,8-dihydroxynaphthalene (DHN); alternatively, in an exogenous manner with the addition of L-3, 4-dihydroxyphenylalanine (L-DOPA or levodopa). As melanin is an amorphous and complex substance, its study requires expensive and inaccessible technologies and analyses are often difficult to perform with conventional biochemical techniques. As such, details about its chemical structure are not yet fully understood, particularly for nematophagous fungi that remain poorly studied. Thus, this review presents an overview of the different types of melanin, with an emphasis on fungi, and discusses the role of melanin in the biology and ecology of nematophagous fungi.
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Affiliation(s)
- Deivid França Freitas
- Laboratory of Cellular and Tissue Biology-LBCT, State University of the North Fluminense Darcy Ribeiro-UENF, Av. Alberto Lamego, 2000, Parque Califórnia, Campos dos Goytacazes, RJ, Cep. 28013‑600, Brazil
| | - Izabelli Martins da Rocha
- Laboratory of Cellular and Tissue Biology-LBCT, State University of the North Fluminense Darcy Ribeiro-UENF, Av. Alberto Lamego, 2000, Parque Califórnia, Campos dos Goytacazes, RJ, Cep. 28013‑600, Brazil
| | - Olney Vieira-da-Motta
- Animal Health Laboratory - Infectious Contagious Diseases Sector, State University of North Fluminense Darcy Ribeiro-UENF, Av. Alberto Lamego, 2000, Parque Califórnia, Campos dos Goytacazes, RJ, Cep. 28013‑600, Brazil
| | - Clóvis de Paula Santos
- Laboratory of Cellular and Tissue Biology-LBCT, State University of the North Fluminense Darcy Ribeiro-UENF, Av. Alberto Lamego, 2000, Parque Califórnia, Campos dos Goytacazes, RJ, Cep. 28013‑600, Brazil.
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17
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Borbolla-Jiménez FV, Del Prado-Audelo ML, Cisneros B, Caballero-Florán IH, Leyva-Gómez G, Magaña JJ. New Perspectives of Gene Therapy on Polyglutamine Spinocerebellar Ataxias: From Molecular Targets to Novel Nanovectors. Pharmaceutics 2021; 13:1018. [PMID: 34371710 PMCID: PMC8309146 DOI: 10.3390/pharmaceutics13071018] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Revised: 06/25/2021] [Accepted: 06/29/2021] [Indexed: 01/03/2023] Open
Abstract
Seven of the most frequent spinocerebellar ataxias (SCAs) are caused by a pathological expansion of a cytosine, adenine and guanine (CAG) trinucleotide repeat located in exonic regions of unrelated genes, which in turn leads to the synthesis of polyglutamine (polyQ) proteins. PolyQ proteins are prone to aggregate and form intracellular inclusions, which alter diverse cellular pathways, including transcriptional regulation, protein clearance, calcium homeostasis and apoptosis, ultimately leading to neurodegeneration. At present, treatment for SCAs is limited to symptomatic intervention, and there is no therapeutic approach to prevent or reverse disease progression. This review provides a compilation of the experimental advances obtained in cell-based and animal models toward the development of gene therapy strategies against polyQ SCAs, providing a discussion of their potential application in clinical trials. In the second part, we describe the promising potential of nanotechnology developments to treat polyQ SCA diseases. We describe, in detail, how the design of nanoparticle (NP) systems with different physicochemical and functionalization characteristics has been approached, in order to determine their ability to evade the immune system response and to enhance brain delivery of molecular tools. In the final part of this review, the imminent application of NP-based strategies in clinical trials for the treatment of polyQ SCA diseases is discussed.
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Affiliation(s)
- Fabiola V. Borbolla-Jiménez
- Laboratorio de Medicina Genómica, Departamento de Genética, Instituto Nacional de Rehabilitación-Luis Guillermo Ibarra Ibarra, Ciudad de México 14389, Mexico;
- Programa de Ciencias Biomédicas, Facultad de Medicina, Universidad Nacional Autónoma de México, Ciudad de México 04510, Mexico
| | - María Luisa Del Prado-Audelo
- Departamento de Bioingeniería, Escuela de Ingeniería y Ciencias, Tecnológico de Monterrey Campus Ciudad de México, Ciudad de México 14380, Mexico;
| | - Bulmaro Cisneros
- Departamento de Genética y Biología Molecular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV), Ciudad de México 07360, Mexico;
| | - Isaac H. Caballero-Florán
- Departamento de Farmacia, Facultad de Química, Universidad Nacional Autónoma de México, Ciudad de México 04510, Mexico;
- Departamento de Farmacia, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV), Ciudad de México 07360, Mexico
| | - Gerardo Leyva-Gómez
- Departamento de Farmacia, Facultad de Química, Universidad Nacional Autónoma de México, Ciudad de México 04510, Mexico;
| | - Jonathan J. Magaña
- Laboratorio de Medicina Genómica, Departamento de Genética, Instituto Nacional de Rehabilitación-Luis Guillermo Ibarra Ibarra, Ciudad de México 14389, Mexico;
- Departamento de Bioingeniería, Escuela de Ingeniería y Ciencias, Tecnológico de Monterrey Campus Ciudad de México, Ciudad de México 14380, Mexico;
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18
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Liu S, Fang SY, An YF. [Gene editing for the treatment of primary immunodeficiency disease]. ZHONGGUO DANG DAI ER KE ZA ZHI = CHINESE JOURNAL OF CONTEMPORARY PEDIATRICS 2021; 23:743-748. [PMID: 34266535 PMCID: PMC8292649 DOI: 10.7499/j.issn.1008-8830.2103150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Accepted: 05/17/2021] [Indexed: 06/13/2023]
Abstract
Gene editing is an advanced technique based on artificial nucleases and can precisely modify genome sequences. It has shown great application prospects in the field of medicine and has provided a new precision therapy for diseases. Primary immunodeficiency disease is a group of diseases caused by single gene mutation and characterized by recurrent and refractory infections, with an extremely high mortality rate. The application of gene editing has brought hope for curing these diseases. This article reviews the development of gene editing technology and briefly introduces the research and application of gene editing technology in primary immunodeficiency disease.
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Affiliation(s)
- Shan Liu
- Department of Rheumatology and Immunology, Children's Hospital of Chongqing Medical University/National Clinical Research Center for Child Health and Disorders/Ministry of Education Key Laboratory of Child Development and Disorders/Chongqing Key Laboratory of Child Infection and Immunity, Chongqing 400014, China
| | - Shu-Yu Fang
- Department of Rheumatology and Immunology, Children's Hospital of Chongqing Medical University/National Clinical Research Center for Child Health and Disorders/Ministry of Education Key Laboratory of Child Development and Disorders/Chongqing Key Laboratory of Child Infection and Immunity, Chongqing 400014, China
| | - Yun-Fei An
- Department of Rheumatology and Immunology, Children's Hospital of Chongqing Medical University/National Clinical Research Center for Child Health and Disorders/Ministry of Education Key Laboratory of Child Development and Disorders/Chongqing Key Laboratory of Child Infection and Immunity, Chongqing 400014, China
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19
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Martín-Fernández JM, Fleischer A, Vallejo-Diez S, Palomino E, Sánchez-Gilabert A, Ruiz R, Bejarano Y, Llinàs P, Gayá A, Bachiller D. New Bicistronic TALENs Greatly Improve Genome Editing. ACTA ACUST UNITED AC 2021; 52:e104. [PMID: 32023363 DOI: 10.1002/cpsc.104] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Genome editing has become one of the most powerful tools in present-day stem cell and regenerative medicine research, but despite its rapid acceptance and widespread use, some elements of the technology still need improvement. In this unit, we present data regarding the use of a new, more efficient type of transcription activator-like effector nuclease (TALEN) for gene editing. Our group has generated bicistronic genes in which classical TALEN coding sequences are linked by 2A elements to different reporter molecules, such as fluorochromes (TALEN-F) or membrane receptors (TALEN-M). This structure results in two proteins transcribed from the same transcript, of which the second (the reporter) can be used as the target for selection by fluorescence-assisted cell sorting (FACS) or magnetic-activated cell sorting (MACS). The application of these new TALEN genes allows a rapid enrichment of cells in which both members of the TALEN pair are active, thus eliminating the need for lengthy selection in culture and laborious characterization of a large number of clones. © 2020 by John Wiley & Sons, Inc. Basic Protocol 1: Generation of new TALENs Basic Protocol 2: Genome editing using TALEN-F Alternate Protocol 1: Generation of TALEN-M Support Protocol 1: mRNA in vitro transcription (IVT) of TALEN-T2A-reporter expression vector Alternate Protocol 2: Editing of primary T cells using TALEN-M Basic Protocol 3: Verifying gene editing Support Protocol 2: Rapid expansion protocol for edited T-cells.
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Affiliation(s)
| | - Aarne Fleischer
- Karuna Good Cells Technologies SL, Vitoria-Gasteiz, Álava, Spain.,Consejo Superior de Investigaciones Científicas (CSIC/IMEDEA), Esporles, Spain
| | - Sara Vallejo-Diez
- Consejo Superior de Investigaciones Científicas (CSIC/IMEDEA), Esporles, Spain
| | - Esther Palomino
- Consejo Superior de Investigaciones Científicas (CSIC/IMEDEA), Esporles, Spain
| | - Almudena Sánchez-Gilabert
- Karuna Good Cells Technologies SL, Vitoria-Gasteiz, Álava, Spain.,Consejo Superior de Investigaciones Científicas (CSIC/IMEDEA), Esporles, Spain
| | - Raúl Ruiz
- Consejo Superior de Investigaciones Científicas (CSIC/IMEDEA), Esporles, Spain
| | - Yazmine Bejarano
- Consejo Superior de Investigaciones Científicas (CSIC/IMEDEA), Esporles, Spain.,Current address: Centro de Investigación del Cáncer, Campus Miguel de Unamuno, Salamanca, Spain
| | - Pere Llinàs
- Consejo Superior de Investigaciones Científicas (CSIC/IMEDEA), Esporles, Spain.,Current address: Josep Carreras Leukaemia Research Institute (IJC), Ctra. de Can Ruti, Camí de les Escoles, Badalona, Spain
| | - Antoni Gayá
- Instituto de Investigación Sanitaria Illes Balears (IDISBA), Fundació Banc de Sang i Teixits de les Illes Balears (FBSTIB), Grupo de Terapia Celular e Ingenieria Tisular, Palma de Mallorca, Spain
| | - Daniel Bachiller
- Consejo Superior de Investigaciones Científicas (CSIC/IMEDEA), Esporles, Spain
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20
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Abstract
CRISPR-Cas systems, widespread in bacteria and archaea, are mainly responsible for adaptive cellular immunity against exogenous DNA (plasmid and phage). However, the latest research shows their involvement in other functions, such as gene expression regulation, DNA repair and virulence. In recent years, they have undergone intensive research as convenient tools for genomic editing, with Cas9 being the most commonly used nuclease. Gene editing may be of interest in biotechnology, medicine (treatment of inherited disorders, cancer, etc.), and in the development of model systems for various genetic diseases. The dCas9 system, based on a modified Cas9 devoid of nuclease activity, called CRISPRi, is widely used to control gene expression in bacteria for new drug biotargets validation and is also promising for therapy of genetic diseases. In addition to direct use for genomic editing in medicine, CRISPR-Cas can also be used in diagnostics, for microorganisms’ genotyping, controlling the spread of drug resistance, or even directly as “smart” antibiotics. This review focuses on the main applications of CRISPR-Cas in medicine, and challenges and perspectives of these approaches.
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21
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Kerry RG, Das G, Golla U, Del Pilar Rodriguez-Torres M, Shin H, Patra JK. Engineered probiotic and prebiotic nutraceutical supplementations in combating non-communicable disorders: A review. Curr Pharm Biotechnol 2020; 23:72-97. [PMID: 33050862 DOI: 10.2174/1389201021666201013153142] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Revised: 09/15/2020] [Accepted: 09/18/2020] [Indexed: 11/22/2022]
Abstract
Nutritional supplementations are a form of nutrition sources that may help in improving health complexities throughout the life span of a person. Under the umbrella of food supplementations, nutraceuticals are products extracted from edible sources that provide medical benefits along with primary nutritional value, these can be considered as functional foods. These nutraceutical supplementations are also evidenced in altering the commensal gut microbiota and help to prevent or fight against chronic non-communicable degenerative diseases in adults including neurological disorders (Autism Spectrum Disorder [ASD], Parkinson's disease [PD] and Multiple sclerosis [MS]) and metabolic disorder (Type-II Diabetes, Obesity and non-alcoholic fatty liver disease). Even the complexities of preterm babies like extra-uterine growth restriction, necrotizing enterocolitis, infant eczema and allergy (during pregnancy) and bronchopulmonary dysplasia, etc. could also be lessened up by providing proper nutrition. Molecular perceptive of inflammatory and apoptotic modulators regulating the pathogenesis of these health risks, their control and management by probiotics and prebiotics could further emphasize the scientific overview of their utility. The pivotal role of nutraceutical supplementations in regulating or modulating molecular pathways coupled with the above mentioned non-communicable diseases are briefly described. Lastly, an overall introduction to the sophisticated genome-editing techniques and advanced delivery systems in therapeutic activities applicable under these health risks are also emphasized in this paper.
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Affiliation(s)
| | - Gitishree Das
- Research Institute of Biotechnology & Medical Converged Science, Dongguk University-Seoul, Goyangsi 10326. Korea
| | - Upendarrao Golla
- Division of Hematology and Oncology, Penn State College of Medicine, Hershey, PA 17033. United States
| | - Maria Del Pilar Rodriguez-Torres
- Laboratorio de Ondas de Choque (LOCH), Centro de Física Aplicada y Tecnología Avanzada (CFATA), Universidad Nacional Autónoma de México, Campus UNAM Juriquilla Boulevard Juriquilla no. 3001, Santiago de Querétaro, Qro., C.P. 76230. Mexico
| | - HanSeung Shin
- Department of Food Science and Biotechnology, Dongguk University-Seoul, Goyangsi 10326. Korea
| | - Jayanta Kumar Patra
- Research Institute of Biotechnology & Medical Converged Science, Dongguk University-Seoul, Goyangsi 10326. Korea
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22
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Bente H, Mittelsten Scheid O, Donà M. Versatile in vitro assay to recognize Cas9-induced mutations. PLANT DIRECT 2020; 4:e00269. [PMID: 33015536 PMCID: PMC7522499 DOI: 10.1002/pld3.269] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Revised: 08/10/2020] [Accepted: 08/18/2020] [Indexed: 06/11/2023]
Abstract
The discovery of CRISPR/Cas9 has revolutionized molecular biology, and its impact on plant biotechnology and plant breeding cannot be over-estimated. In many plant species, its application for mutagenesis is now a routine procedure--if suitable target sites, sufficient expression of the Cas9 protein, and functioning sgRNAs are combined. sgRNAs differ in their efficiency, depending on parameters that are only poorly understood. Several software tools and experience from growing databases are supporting the design of sgRNAs, but some seemingly perfect sgRNAs turn out to be inefficient or fail entirely, and most data bases stem from work with mammalian cells. Different in vitro assays testing sgRNAs in reconstituted Cas9 complexes are available and useful to reduce the risk of failure, especially in plants when CRISPR/Cas9 application requires modifications within the germ line and laborious transformation protocols. Low sgRNA efficiency and long generation times in plants can also contribute to the workload and costs of screening for the wanted genome edits. Here, we present a protocol in which a simple, initial in vitro test for suitable sgRNAs is modified to accelerate genotyping of Cas9-induced mutations. We demonstrate applicability of our protocol for mutagenesis and mutation screen for specific genes in Arabidopsis, but the principle should be universally suitable to provide a simple, low-cost, and rapid method to identify edited genes also in other plants and other organisms.
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Affiliation(s)
- Heinrich Bente
- Gregor Mendel Institute of Molecular Plant Biology Austrian Academy of Sciences Vienna BioCenter (VBC) Vienna Austria
| | - Ortrun Mittelsten Scheid
- Gregor Mendel Institute of Molecular Plant Biology Austrian Academy of Sciences Vienna BioCenter (VBC) Vienna Austria
| | - Mattia Donà
- Gregor Mendel Institute of Molecular Plant Biology Austrian Academy of Sciences Vienna BioCenter (VBC) Vienna Austria
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23
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Zhang D, Hussain A, Manghwar H, Xie K, Xie S, Zhao S, Larkin RM, Qing P, Jin S, Ding F. Genome editing with the CRISPR-Cas system: an art, ethics and global regulatory perspective. PLANT BIOTECHNOLOGY JOURNAL 2020; 18:1651-1669. [PMID: 32271968 PMCID: PMC7336378 DOI: 10.1111/pbi.13383] [Citation(s) in RCA: 71] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Revised: 02/22/2020] [Accepted: 03/19/2020] [Indexed: 05/18/2023]
Abstract
Over the last three decades, the development of new genome editing techniques, such as ODM, TALENs, ZFNs and the CRISPR-Cas system, has led to significant progress in the field of plant and animal breeding. The CRISPR-Cas system is the most versatile genome editing tool discovered in the history of molecular biology because it can be used to alter diverse genomes (e.g. genomes from both plants and animals) including human genomes with unprecedented ease, accuracy and high efficiency. The recent development and scope of CRISPR-Cas system have raised new regulatory challenges around the world due to moral, ethical, safety and technical concerns associated with its applications in pre-clinical and clinical research, biomedicine and agriculture. Here, we review the art, applications and potential risks of CRISPR-Cas system in genome editing. We also highlight the patent and ethical issues of this technology along with regulatory frameworks established by various nations to regulate CRISPR-Cas-modified organisms/products.
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Affiliation(s)
- Debin Zhang
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanChina
- College of Public AdministrationHuazhong Agricultural UniversityWuhanChina
| | - Amjad Hussain
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanChina
| | - Hakim Manghwar
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanChina
| | - Kabin Xie
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanChina
| | - Shengsong Xie
- Key Laboratory of Agricultural Animal Genetics, Breeding and ReproductionMinistry of EducationWuhanChina
| | - Shuhong Zhao
- Key Laboratory of Agricultural Animal Genetics, Breeding and ReproductionMinistry of EducationWuhanChina
| | - Robert M. Larkin
- Key Laboratory of Horticultural Plant BiologyMinistry of EducationCollege of Horticulture and Forestry SciencesHuazhong Agricultural UniversityWuhanChina
| | - Ping Qing
- College of Public AdministrationHuazhong Agricultural UniversityWuhanChina
| | - Shuangxia Jin
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanChina
| | - Fang Ding
- Hubei Key Laboratory of Plant PathologyCollege of Plant Sciences and TechnologyHuazhong Agricultural UniversityWuhanChina
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24
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Almeida MJ, Matos A. Designer Nucleases: Gene-Editing Therapies using CCR5 as an Emerging Target in HIV. Curr HIV Res 2020; 17:306-323. [PMID: 31652113 DOI: 10.2174/1570162x17666191025112918] [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: 09/09/2019] [Revised: 10/16/2019] [Accepted: 10/18/2019] [Indexed: 02/08/2023]
Abstract
Acquired Immunodeficiency Syndrome (AIDS), caused by the Human Immunodeficiency Virus (HIV), is a life-threatening disorder that persists worldwide as a severe health problem. Since it was linked with the HIV attachment process, the Chemokine receptor, CCR5, has been at the development leading edge of several gene-based therapies. Given the shortcomings of the current antiretroviral treatment procedure and the non-availability of a licensed vaccine, the aptitude to modify complex genomes with Designer Nucleases has had a noteworthy impact on biotechnology. Over the last years, ZFN, TALEN and CRISPR/Cas9 gene-editing technology have appeared as a promising solution that mimics the naturally occurring CCR5/Δ32 mutation and permanently guarantees the absence of CCR5-expression on the surface of HIV target-cells, leading to a continuous resistance to the virus entry and, ultimately, proving that cellular immunization from infection could be, in fact, a conceivable therapeutic approach to finally achieve the long-awaited functional cure of HIV.
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Affiliation(s)
- Maria João Almeida
- Laboratory of Microbiology, Faculty of Pharmacy, University of Coimbra, Coimbra, Portugal
| | - Ana Matos
- Laboratory of Microbiology, Faculty of Pharmacy, University of Coimbra, Coimbra, Portugal.,Research Centre on Chemical Processes Engineering and Forest Products (CIEPQF), Faculty of Pharmacy, University of Coimbra, Coimbra, Portugal
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25
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Abstract
PURPOSE OF REVIEW We review the ways in which stem cells are used in psychiatric disease research, including the related advances in gene editing and directed cell differentiation. RECENT FINDINGS The recent development of induced pluripotent stem cell (iPSC) technologies has created new possibilities for the study of psychiatric disease. iPSCs can be derived from patients or controls and differentiated to an array of neuronal and non-neuronal cell types. Their genomes can be edited as desired, and they can be assessed for a variety of phenotypes. This makes them especially interesting for studying genetic variation, which is particularly useful today now that our knowledge on the genetics of psychiatric disease is quickly expanding. The recent advances in cell engineering have led to powerful new methods for studying psychiatric illness including schizophrenia, bipolar disorder, and autism. There is a wide array of possible applications as illustrated by the many examples from the literature, most of which are cited here.
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Affiliation(s)
- Debamitra Das
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Kyra Feuer
- Predoctoral Training Program in Human Genetics, Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Marah Wahbeh
- Predoctoral Training Program in Human Genetics, Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Dimitrios Avramopoulos
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
- Department of Psychiatry, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
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26
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Bacterial non-specific nucleases of the phospholipase D superfamily and their biotechnological potential. Appl Microbiol Biotechnol 2020; 104:3293-3304. [PMID: 32086594 DOI: 10.1007/s00253-020-10459-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Revised: 02/03/2020] [Accepted: 02/10/2020] [Indexed: 12/19/2022]
Abstract
Bacterial non-specific nucleases are ubiquitously distributed and involved in numerous intra- and extracellular processes. Although all nucleases share the basic chemistry for the hydrolysis of phosphodiester bonds in nucleic acid molecules, the catalysis comprises diverse modes of action, which offers great potential for versatile biotechnological applications. A major criterium for their differentiation is substrate specificity. Specific endonucleases are widely used as restriction enzymes in molecular biology approaches, whereas the main applications of non-specific nucleases (NSNs) are the removal of nucleic acids from crude extracts in industrial downstream processing and the prevention of cell clumping in microfabricated channels. In nature, the predominant role of NSNs is the acquisition of nutrient sources such as nucleotides and phosphates. The number of extensively characterized NSNs and available structures is limited. Moreover, their applicability is mostly challenged by the presence of metal chelators that impede the hydrolysis of nucleic acids in a metal ion-dependent manner. However, a few metal ion-independent NSNs that tolerate the presence of metal chelators have been characterized in recent years with none being commercially available to date. The classification and biotechnological potential of bacterial NSNs with a special focus on metal ion-independent nucleases are presented and discussed.Key Points • Bacterial phospholipases (PLD-family) exhibit nucleolytic activity. • Bacterial nucleases of the PLD-family are metal ion-independent. • NSNs can be used in downstream processing approaches.
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27
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Niewiadomska-Cimicka A, Trottier Y. Molecular Targets and Therapeutic Strategies in Spinocerebellar Ataxia Type 7. Neurotherapeutics 2019; 16:1074-1096. [PMID: 31432449 PMCID: PMC6985300 DOI: 10.1007/s13311-019-00778-5] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Spinocerebellar ataxia type 7 (SCA7) is a rare autosomal dominant neurodegenerative disorder characterized by progressive neuronal loss in the cerebellum, brainstem, and retina, leading to cerebellar ataxia and blindness as major symptoms. SCA7 is due to the expansion of a CAG triplet repeat that is translated into a polyglutamine tract in ATXN7. Larger SCA7 expansions are associated with earlier onset of symptoms and more severe and rapid disease progression. Here, we summarize the pathological and genetic aspects of SCA7, compile the current knowledge about ATXN7 functions, and then focus on recent advances in understanding the pathogenesis and in developing biomarkers and therapeutic strategies. ATXN7 is a bona fide subunit of the multiprotein SAGA complex, a transcriptional coactivator harboring chromatin remodeling activities, and plays a role in the differentiation of photoreceptors and Purkinje neurons, two highly vulnerable neuronal cell types in SCA7. Polyglutamine expansion in ATXN7 causes its misfolding and intranuclear accumulation, leading to changes in interactions with native partners and/or partners sequestration in insoluble nuclear inclusions. Studies of cellular and animal models of SCA7 have been crucial to unveil pathomechanistic aspects of the disease, including gene deregulation, mitochondrial and metabolic dysfunctions, cell and non-cell autonomous protein toxicity, loss of neuronal identity, and cell death mechanisms. However, a better understanding of the principal molecular mechanisms by which mutant ATXN7 elicits neurotoxicity, and how interconnected pathogenic cascades lead to neurodegeneration is needed for the development of effective therapies. At present, therapeutic strategies using nucleic acid-based molecules to silence mutant ATXN7 gene expression are under development for SCA7.
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Affiliation(s)
- Anna Niewiadomska-Cimicka
- Institute of Genetic and Molecular and Cellular Biology (IGBMC), Centre National de la Recherche Scientifique (UMR7104), Institut National de la Santé et de la Recherche Médicale (U1258), University of Strasbourg, Illkirch, France
| | - Yvon Trottier
- Institute of Genetic and Molecular and Cellular Biology (IGBMC), Centre National de la Recherche Scientifique (UMR7104), Institut National de la Santé et de la Recherche Médicale (U1258), University of Strasbourg, Illkirch, France.
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