1
|
Tavakolidakhrabadi N, Aulicino F, May CJ, Saleem MA, Berger I, Welsh GI. Genome editing and kidney health. Clin Kidney J 2024; 17:sfae119. [PMID: 38766272 PMCID: PMC11099665 DOI: 10.1093/ckj/sfae119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Indexed: 05/22/2024] Open
Abstract
Genome editing technologies, clustered regularly interspaced short palindromic repeats (CRISPR)-Cas in particular, have revolutionized the field of genetic engineering, providing promising avenues for treating various genetic diseases. Chronic kidney disease (CKD), a significant health concern affecting millions of individuals worldwide, can arise from either monogenic or polygenic mutations. With recent advancements in genomic sequencing, valuable insights into disease-causing mutations can be obtained, allowing for the development of new treatments for these genetic disorders. CRISPR-based treatments have emerged as potential therapies, especially for monogenic diseases, offering the ability to correct mutations and eliminate disease phenotypes. Innovations in genome editing have led to enhanced efficiency, specificity and ease of use, surpassing earlier editing tools such as zinc-finger nucleases and transcription activator-like effector nucleases (TALENs). Two prominent advancements in CRISPR-based gene editing are prime editing and base editing. Prime editing allows precise and efficient genome modifications without inducing double-stranded DNA breaks (DSBs), while base editing enables targeted changes to individual nucleotides in both RNA and DNA, promising disease correction in the absence of DSBs. These technologies have the potential to treat genetic kidney diseases through specific correction of disease-causing mutations, such as somatic mutations in PKD1 and PKD2 for polycystic kidney disease; NPHS1, NPHS2 and TRPC6 for focal segmental glomerulosclerosis; COL4A3, COL4A4 and COL4A5 for Alport syndrome; SLC3A1 and SLC7A9 for cystinuria and even VHL for renal cell carcinoma. Apart from editing the DNA sequence, CRISPR-mediated epigenome editing offers a cost-effective method for targeted treatment providing new avenues for therapeutic development, given that epigenetic modifications are associated with the development of various kidney disorders. However, there are challenges to overcome, including developing efficient delivery methods, improving safety and reducing off-target effects. Efforts to improve CRISPR-Cas technologies involve optimizing delivery vectors, employing viral and non-viral approaches and minimizing immunogenicity. With research in animal models providing promising results in rescuing the expression of wild-type podocin in mouse models of nephrotic syndrome and successful clinical trials in the early stages of various disorders, including cancer immunotherapy, there is hope for successful translation of genome editing to kidney diseases.
Collapse
Affiliation(s)
| | - Francesco Aulicino
- BrisSynBio Bristol Synthetic Biology Centre, Biomedical Sciences, School of Biochemistry, Bristol Royal Hospital for Children
| | - Carl J May
- Bristol Renal, University of Bristol, Dorothy Hodgkin Building, Whitson Street, Bristol, UK
| | - Moin A Saleem
- Bristol Renal, University of Bristol, Dorothy Hodgkin Building, Whitson Street, Bristol, UK
- Department of Paediatric Nephrology, Bristol Royal Hospital for Children, Bristol, UK
| | - Imre Berger
- School of Biochemistry, University of Bristol, Bristol, UK
| | - Gavin I Welsh
- Bristol Renal, University of Bristol, Dorothy Hodgkin Building, Whitson Street, Bristol, UK
| |
Collapse
|
2
|
Singh A, Smedley GD, Rose JG, Fredriksen K, Zhang Y, Li L, Yuan SH. A high efficiency precision genome editing method with CRISPR in iPSCs. Sci Rep 2024; 14:9933. [PMID: 38688988 PMCID: PMC11061145 DOI: 10.1038/s41598-024-60766-4] [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: 01/09/2024] [Accepted: 04/26/2024] [Indexed: 05/02/2024] Open
Abstract
The use of genetic engineering to generate point mutations in induced pluripotent stem cells (iPSCs) is essential for studying a specific genetic effect in an isogenic background. We demonstrate that a combination of p53 inhibition and pro-survival small molecules achieves a homologous recombination rate higher than 90% using Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) in human iPSCs. Our protocol reduces the effort and time required to create isogenic lines.
Collapse
Affiliation(s)
- Avinash Singh
- Department of Neurology, University of Minnesota, Twin Cities, Minneapolis, MN, USA
| | - G Dalton Smedley
- Department of Neurology, University of Minnesota, Twin Cities, Minneapolis, MN, USA
| | - Jamee-Grace Rose
- Department of Neurology, University of Minnesota, Twin Cities, Minneapolis, MN, USA
| | - Kristina Fredriksen
- Graduate Program in Neuroscience, University of Minnesota, Twin Cities, Minneapolis, MN, USA
| | - Ying Zhang
- Minnesota Supercomputing Institute, University of Minnesota, Twin Cities, Minneapolis, MN, USA
| | - Ling Li
- Graduate Program in Neuroscience, University of Minnesota, Twin Cities, Minneapolis, MN, USA
- Department of Experimental and Clinical Pharmacology, University of Minnesota, Twin Cities, Minneapolis, MN, USA
| | - Shauna H Yuan
- Department of Neurology, University of Minnesota, Twin Cities, Minneapolis, MN, USA.
- Graduate Program in Neuroscience, University of Minnesota, Twin Cities, Minneapolis, MN, USA.
- Minneapolis Veterans Administration Health Care System, Minneapolis, MN, USA.
| |
Collapse
|
3
|
Hussain W, Yang X, Ullah M, Wang H, Aziz A, Xu F, Asif M, Ullah MW, Wang S. Genetic engineering of bacteriophages: Key concepts, strategies, and applications. Biotechnol Adv 2023; 64:108116. [PMID: 36773707 DOI: 10.1016/j.biotechadv.2023.108116] [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: 10/21/2022] [Revised: 02/03/2023] [Accepted: 02/05/2023] [Indexed: 02/12/2023]
Abstract
Bacteriophages are the most abundant biological entity in the world and hold a tremendous amount of unexplored genetic information. Since their discovery, phages have drawn a great deal of attention from researchers despite their small size. The development of advanced strategies to modify their genomes and produce engineered phages with desired traits has opened new avenues for their applications. This review presents advanced strategies for developing engineered phages and their potential antibacterial applications in phage therapy, disruption of biofilm, delivery of antimicrobials, use of endolysin as an antibacterial agent, and altering the phage host range. Similarly, engineered phages find applications in eukaryotes as a shuttle for delivering genes and drugs to the targeted cells, and are used in the development of vaccines and facilitating tissue engineering. The use of phage display-based specific peptides for vaccine development, diagnostic tools, and targeted drug delivery is also discussed in this review. The engineered phage-mediated industrial food processing and biocontrol, advanced wastewater treatment, phage-based nano-medicines, and their use as a bio-recognition element for the detection of bacterial pathogens are also part of this review. The genetic engineering approaches hold great potential to accelerate translational phages and research. Overall, this review provides a deep understanding of the ingenious knowledge of phage engineering to move them beyond their innate ability for potential applications.
Collapse
Affiliation(s)
- Wajid Hussain
- Advanced Biomaterials & Tissues Engineering Center, College of Life Sciences and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Xiaohan Yang
- Advanced Biomaterials & Tissues Engineering Center, College of Life Sciences and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Mati Ullah
- Department of Biotechnology, College of Life Sciences and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Huan Wang
- Advanced Biomaterials & Tissues Engineering Center, College of Life Sciences and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Ayesha Aziz
- Advanced Biomaterials & Tissues Engineering Center, College of Life Sciences and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Fang Xu
- Huazhong University of Science and Technology Hospital, Wuhan 430074, China
| | - Muhammad Asif
- Hubei Key Laboratory of Plasma Chemistry and Advanced Materials, School of Materials Science and Engineering, Wuhan Institute of Technology, Wuhan 430205, China
| | - Muhammad Wajid Ullah
- Biofuels Institute, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang 212013, China.
| | - Shenqi Wang
- Advanced Biomaterials & Tissues Engineering Center, College of Life Sciences and Technology, Huazhong University of Science and Technology, Wuhan 430074, China.
| |
Collapse
|
4
|
Kershanskaya OI, Yessenbaeva GL, Nelidova DS, Karabekova AN, Sadullaeva ZN. CRISPR/Cas genome editing perspectives for barley breeding. PHYSIOLOGIA PLANTARUM 2022; 174:e13686. [PMID: 35451132 DOI: 10.1111/ppl.13686] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Revised: 02/01/2022] [Accepted: 04/07/2022] [Indexed: 06/14/2023]
Abstract
The CRISPR/Cas9 technology shows potential to improve crop breeding efficiency and antiviral defense. The interest in DNA editing in crops has grown due to the possibility of increasing the resistance of different plants to many viruses. Our aim was to create an elite disease-resistant local barley cultivar using CRISPR/Cas9 biotechnology. For this purpose, we used CRISPR/Cas 9-eIF4E with the eukaryotic translation initiation factor 4E (eIF4E) barley gene to edit the genomes of five local Kazakhstan barley cultivars. After identifying the single guide RNA (sgRNA) target sequences, they were synthesized and cloned into the CRISPR-plant vector before being introduced into barley cells via our own patented Agrobacterium germ-line transformation technique. Barley plants eIF4E-modified were successfully obtained and were resistant to virus infection. Based on our research, the CRISPR/Cas9 system for plant genome editing could be a prospect for applying this breakthrough biotechnology in barley breeding.
Collapse
Affiliation(s)
- Olga I Kershanskaya
- Laboratory of Cell Engineering, Institute of Plant Biology and Biotechnology, Almaty, Kazakhstan
| | - Gulvira L Yessenbaeva
- Laboratory of Cell Engineering, Institute of Plant Biology and Biotechnology, Almaty, Kazakhstan
| | - Darya S Nelidova
- Laboratory of Cell Engineering, Institute of Plant Biology and Biotechnology, Almaty, Kazakhstan
| | - Aizhan N Karabekova
- Laboratory of Cell Engineering, Institute of Plant Biology and Biotechnology, Almaty, Kazakhstan
| | - Zarina N Sadullaeva
- Laboratory of Cell Engineering, Institute of Plant Biology and Biotechnology, Almaty, Kazakhstan
| |
Collapse
|
5
|
Kocher T, Petkovic I, Bischof J, Koller U. Current developments in gene therapy for epidermolysis bullosa. Expert Opin Biol Ther 2022; 22:1137-1150. [PMID: 35235467 DOI: 10.1080/14712598.2022.2049229] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
INTRODUCTION The genodermatosis epidermolysis bullosa (EB) is a monogenetic disease, characterized by severe blister formation on the skin and mucous membranes upon minimal mechanical trauma. Causes for the disease are mutations in genes encoding proteins that are essential for skin integrity. In EB, one of these proteins is either functionally impaired or completely absent. Therefore, the development and improvement of DNA and RNA-based therapeutic approaches for this severe blistering skin disease is mandatory to achieve a treatment option for the patients. AREAS COVERED Currently, there are several forms of DNA/RNA therapies potentially feasible for EB. Whereas some of them are still at the preclinical stage, others are clinically advanced and have already been applied to patients. In particular, this is the case for a cDNA replacement approach successfully applied for a small number of patients with junctional EB. EXPERT OPINION The heterogeneity of EB justifies the development of therapeutic options with distinct modes of action at a DNA or RNA level. Besides, splicing-modulating therapies, based on RNA trans-splicing or short antisense oligonucleotides, especially designer nucleases, have steadily improved in efficiency and safety and thus likely represent the most promising gene therapy tool in the near future.
Collapse
Affiliation(s)
- Thomas Kocher
- EB House Austria, Research Program for Molecular Therapy of Genodermatoses, Department of Dermatology and Allergology, University Hospital of the Paracelsus Medical University Salzburg, 5020 Salzburg, Austria
| | - Igor Petkovic
- EB House Austria, Research Program for Molecular Therapy of Genodermatoses, Department of Dermatology and Allergology, University Hospital of the Paracelsus Medical University Salzburg, 5020 Salzburg, Austria
| | - Johannes Bischof
- EB House Austria, Research Program for Molecular Therapy of Genodermatoses, Department of Dermatology and Allergology, University Hospital of the Paracelsus Medical University Salzburg, 5020 Salzburg, Austria
| | - Ulrich Koller
- EB House Austria, Research Program for Molecular Therapy of Genodermatoses, Department of Dermatology and Allergology, University Hospital of the Paracelsus Medical University Salzburg, 5020 Salzburg, Austria
| |
Collapse
|
6
|
Wimmer T, Bonthu D, Moeschl V, Kleekamp P, Thiel C, Lytvynchuk L, Ellinwood M, Stieger K. A Bioluminescence Resonance Energy Transfer-Based Reporter System: Characterization and Applications. CRISPR J 2021; 4:884-895. [PMID: 34847743 DOI: 10.1089/crispr.2021.0023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Genome editing strategies and DNA repair research need powerful analytical tools. We generated a bioluminescence resonance energy transfer (BRET)-based reporter for the quantification of indel frequencies induced by DNA repair. The BRET reporter, expressed as a single molecule, consists of a mutated Renilla reniformis luciferase domain and a GFP2 domain separated by a shuttle-cloning box for the integration of any given endonuclease target sequence. The luciferase activity acts both as energy donor and as the internal standard, while the loss of GFP2 fluorescence acts as a reporter for the out-of-frame sequence alterations that result from the DNA repair via the non-homologous end joining/microhomology-mediated end joining DNA repair pathways of the endonuclease-mediated DNA double-strand break. This results in a decrease of the fluorescence/luminescence ratio. Employing this reporter in different experimental scenarios, using different cell lines and diseases targeted, we quantified the influence of both protein knockdown of DNA repair pathways as well as guide RNA mismatches on CRISPR-mediated nuclease activity and subsequent repair based on mutagenic repair on the reporter. In conclusion, we demonstrated this BRET-based reporter to be a robust and sensitive analytical tool for assessment of variety of different genome editing-based approaches.
Collapse
Affiliation(s)
- Tobias Wimmer
- Department of Ophthalmology, Justus-Liebig-University Giessen, Giessen, Germany
| | - Dileep Bonthu
- Department of Ophthalmology, Justus-Liebig-University Giessen, Giessen, Germany
| | - Vincent Moeschl
- Department of Ophthalmology, Justus-Liebig-University Giessen, Giessen, Germany
| | - Philip Kleekamp
- Department of Ophthalmology, Justus-Liebig-University Giessen, Giessen, Germany
| | - Christian Thiel
- Department of Ophthalmology, Justus-Liebig-University Giessen, Giessen, Germany
| | - Lyubomyr Lytvynchuk
- Department of Ophthalmology, Justus-Liebig-University Giessen, Giessen, Germany
| | | | - Knut Stieger
- Department of Ophthalmology, Justus-Liebig-University Giessen, Giessen, Germany
| |
Collapse
|
7
|
Bhardwaj A, Nain V. TALENs-an indispensable tool in the era of CRISPR: a mini review. J Genet Eng Biotechnol 2021; 19:125. [PMID: 34420096 PMCID: PMC8380213 DOI: 10.1186/s43141-021-00225-z] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2021] [Accepted: 08/08/2021] [Indexed: 12/26/2022]
Abstract
BACKGROUND Genome of an organism has always fascinated life scientists. With the discovery of restriction endonucleases, scientists were able to make targeted manipulations (knockouts) in any gene sequence of any organism, by the technique popularly known as genome engineering. Though there is a range of genome editing tools, but this era of genome editing is dominated by the CRISPR/Cas9 tool due to its ease of design and handling. But, when it comes to clinical applications, CRISPR is not usually preferred. In this review, we will elaborate on the structural and functional role of designer nucleases with emphasis on TALENs and CRISPR/Cas9 genome editing system. We will also present the unique features of TALENs and limitations of CRISPRs which makes TALENs a better genome editing tool than CRISPRs. MAIN BODY Genome editing is a robust technology used to make target specific DNA modifications in the genome of any organism. With the discovery of robust programmable endonucleases-based designer gene manipulating tools such as meganucleases (MN), zinc-finger nucleases (ZFNs), transcription activator-like effector nucleases (TALENs), and clustered regularly interspaced short palindromic repeats associated protein (CRISPR/Cas9), the research in this field has experienced a tremendous acceleration giving rise to a modern era of genome editing with better precision and specificity. Though, CRISPR-Cas9 platform has successfully gained more attention in the scientific world, TALENs and ZFNs are unique in their own ways. Apart from high-specificity, TALENs are proven to target the mitochondrial DNA (mito-TALEN), where gRNA of CRISPR is difficult to import. This review talks about genome editing goals fulfilled by TALENs and drawbacks of CRISPRs. CONCLUSIONS This review provides significant insights into the pros and cons of the two most popular genome editing tools TALENs and CRISPRs. This mini review suggests that, TALENs provides novel opportunities in the field of therapeutics being highly specific and sensitive toward DNA modifications. In this article, we will briefly explore the special features of TALENs that makes this tool indispensable in the field of synthetic biology. This mini review provides great perspective in providing true guidance to the researchers working in the field of trait improvement via genome editing.
Collapse
Affiliation(s)
- Anuradha Bhardwaj
- Department of Biotechnology, Gautam Buddha University, Greater Noida, Uttar Pradesh, 201312, India
| | - Vikrant Nain
- Department of Biotechnology, Gautam Buddha University, Greater Noida, Uttar Pradesh, 201312, India.
| |
Collapse
|
8
|
Anurogo D, Yuli Prasetyo Budi N, Thi Ngo MH, Huang YH, Pawitan JA. Cell and Gene Therapy for Anemia: Hematopoietic Stem Cells and Gene Editing. Int J Mol Sci 2021; 22:ijms22126275. [PMID: 34200975 PMCID: PMC8230702 DOI: 10.3390/ijms22126275] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Revised: 06/06/2021] [Accepted: 06/07/2021] [Indexed: 12/23/2022] Open
Abstract
Hereditary anemia has various manifestations, such as sickle cell disease (SCD), Fanconi anemia, glucose-6-phosphate dehydrogenase deficiency (G6PDD), and thalassemia. The available management strategies for these disorders are still unsatisfactory and do not eliminate the main causes. As genetic aberrations are the main causes of all forms of hereditary anemia, the optimal approach involves repairing the defective gene, possibly through the transplantation of normal hematopoietic stem cells (HSCs) from a normal matching donor or through gene therapy approaches (either in vivo or ex vivo) to correct the patient’s HSCs. To clearly illustrate the importance of cell and gene therapy in hereditary anemia, this paper provides a review of the genetic aberration, epidemiology, clinical features, current management, and cell and gene therapy endeavors related to SCD, thalassemia, Fanconi anemia, and G6PDD. Moreover, we expound the future research direction of HSC derivation from induced pluripotent stem cells (iPSCs), strategies to edit HSCs, gene therapy risk mitigation, and their clinical perspectives. In conclusion, gene-corrected hematopoietic stem cell transplantation has promising outcomes for SCD, Fanconi anemia, and thalassemia, and it may overcome the limitation of the source of allogenic bone marrow transplantation.
Collapse
Affiliation(s)
- Dito Anurogo
- International PhD Program for Cell Therapy and Regeneration Medicine, College of Medicine, Taipei Medical University, Taipei 11031, Taiwan; (D.A.); (N.Y.P.B.); (M.-H.T.N.)
- Department of Biochemistry and Molecular Cell Biology, School of Medicine, College of Medicine, Taipei Medical University, Taipei 11031, Taiwan
- Faculty of Medicine and Health Sciences, Universitas Muhammadiyah Makassar, Makassar 90221, Indonesia
| | - Nova Yuli Prasetyo Budi
- International PhD Program for Cell Therapy and Regeneration Medicine, College of Medicine, Taipei Medical University, Taipei 11031, Taiwan; (D.A.); (N.Y.P.B.); (M.-H.T.N.)
- Department of Biochemistry and Molecular Cell Biology, School of Medicine, College of Medicine, Taipei Medical University, Taipei 11031, Taiwan
| | - Mai-Huong Thi Ngo
- International PhD Program for Cell Therapy and Regeneration Medicine, College of Medicine, Taipei Medical University, Taipei 11031, Taiwan; (D.A.); (N.Y.P.B.); (M.-H.T.N.)
- Department of Biochemistry and Molecular Cell Biology, School of Medicine, College of Medicine, Taipei Medical University, Taipei 11031, Taiwan
| | - Yen-Hua Huang
- International PhD Program for Cell Therapy and Regeneration Medicine, College of Medicine, Taipei Medical University, Taipei 11031, Taiwan; (D.A.); (N.Y.P.B.); (M.-H.T.N.)
- Department of Biochemistry and Molecular Cell Biology, School of Medicine, College of Medicine, Taipei Medical University, Taipei 11031, Taiwan
- Research Center of Cell Therapy and Regeneration Medicine, Taipei Medical University, Taipei 11031, Taiwan
- Graduate Institute of Medical Sciences, College of Medicine, Taipei Medical University, Taipei 11031, Taiwan
- Center for Reproductive Medicine, Taipei Medical University Hospital, Taipei 11031, Taiwan
- Comprehensive Cancer Center, Taipei Medical University, Taipei 11031, Taiwan
- Research Center of Cancer Translational Medicine, Taipei Medical University, Taipei 11031, Taiwan
- PhD Program for Translational Medicine, College of Medical Science and Technology, Taipei Medical University, Taipei 11031, Taiwan
- Correspondence: (Y.-H.H.); (J.A.P.); Tel.: +886-2-2736-1661 (ext. 3150) (Y.-H.H.); +62-812-9535-0097 (J.A.P.)
| | - Jeanne Adiwinata Pawitan
- Department of Histology, Faculty of Medicine, Universitas Indonesia, Jakarta 10430, Indonesia
- Stem Cell Medical Technology Integrated Service Unit, Cipto Mangunkusumo Central Hospital, Faculty of Medicine, Universitas Indonesia, Jakarta 10430, Indonesia
- Stem Cell and Tissue Engineering Research Center, Indonesia Medical Education and Research Institute (IMERI), Faculty of Medicine, Universitas Indonesia, Jakarta 10430, Indonesia
- Correspondence: (Y.-H.H.); (J.A.P.); Tel.: +886-2-2736-1661 (ext. 3150) (Y.-H.H.); +62-812-9535-0097 (J.A.P.)
| |
Collapse
|
9
|
Bloh K, Kanchana R, Bialk P, Banas K, Zhang Z, Yoo BC, Kmiec EB. Deconvolution of Complex DNA Repair (DECODR): Establishing a Novel Deconvolution Algorithm for Comprehensive Analysis of CRISPR-Edited Sanger Sequencing Data. CRISPR J 2021; 4:120-131. [PMID: 33571043 PMCID: PMC7898406 DOI: 10.1089/crispr.2020.0022] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
During CRISPR-directed gene editing, multiple gene repair mechanisms interact to produce a wide and largely unpredictable variety of sequence changes across an edited population of cells. Shortcomings inherent to previously available proposal-based insertion and deletion (indel) analysis software necessitated the development of a more comprehensive tool that could detect a larger range and variety of indels while maintaining the ease of use of tools currently available. To that end, we developed Deconvolution of Complex DNA Repair (DECODR). DECODR can detect indels formed from single or multi-guide CRISPR experiments without a limit on indel size. The software is accurate in determining the identities and positions of inserted and deleted bases in DNA extracts from both clonally expanded and bulk cell populations. The accurate identification and output of any potential indel allows for DECODR analysis to be executed in experiments utilizing potentially any configuration of donor DNA sequences, CRISPR-Cas, and endogenous DNA repair pathways.
Collapse
Affiliation(s)
- Kevin Bloh
- Gene Editing Institute, Helen F. Graham Cancer Center and Research Institute, ChristianaCare, Newark, Delaware, USA
- Department of Medical and Molecular Sciences, College of Health Sciences University of Delaware, Newark, Delaware, USA
| | - Rohan Kanchana
- Gene Editing Institute, Helen F. Graham Cancer Center and Research Institute, ChristianaCare, Newark, Delaware, USA
| | - Pawel Bialk
- Gene Editing Institute, Helen F. Graham Cancer Center and Research Institute, ChristianaCare, Newark, Delaware, USA
| | - Kelly Banas
- Gene Editing Institute, Helen F. Graham Cancer Center and Research Institute, ChristianaCare, Newark, Delaware, USA
- Department of Medical and Molecular Sciences, College of Health Sciences University of Delaware, Newark, Delaware, USA
| | - Zugui Zhang
- Value Institute, ChristianaCare, Newark, Delaware, USA
| | - Byung-Chun Yoo
- Gene Editing Institute, Helen F. Graham Cancer Center and Research Institute, ChristianaCare, Newark, Delaware, USA
| | - Eric B. Kmiec
- Gene Editing Institute, Helen F. Graham Cancer Center and Research Institute, ChristianaCare, Newark, Delaware, USA
- Department of Medical and Molecular Sciences, College of Health Sciences University of Delaware, Newark, Delaware, USA
| |
Collapse
|
10
|
Abstract
BACKGROUND Development of efficient strategies has always been one of the great perspectives for biotechnologists. During the last decade, genome editing of different organisms has been a fast advancing field and therefore has received a lot of attention from various researchers comprehensively reviewing latest achievements and offering opinions on future directions. This review presents a brief history, basic principles, advantages and disadvantages, as well as various aspects of each genome editing technology including the modes, applications, and challenges that face delivery of gene editing components. MAIN BODY Genetic modification techniques cover a wide range of studies, including the generation of transgenic animals, functional analysis of genes, model development for diseases, or drug development. The delivery of certain proteins such as monoclonal antibodies, enzymes, and growth hormones has been suffering from several obstacles because of their large size. These difficulties encouraged scientists to explore alternative approaches, leading to the progress in gene editing. The distinguished efforts and enormous experimentation have now been able to introduce methodologies that can change the genetic constitution of the living cell. The genome editing strategies have evolved during the last three decades, and nowadays, four types of "programmable" nucleases are available in this field: meganucleases, zinc finger nucleases, transcription activator-like effector nucleases, and the clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR associated protein 9 (Cas9) (CRISPR/Cas-9) system. Each group has its own characteristics necessary for researchers to select the most suitable method for gene editing tool for a range of applications. Genome engineering/editing technology will revolutionize the creation of precisely manipulated genomes of cells or organisms in order to modify a specific characteristic. Of the potential applications are those in human health and agriculture. Introducing constructs into target cells or organisms is the key step in genome engineering. CONCLUSIONS Despite the success already achieved, the genome editing techniques are still suffering certain difficulties. Challenges must be overcome before the full potential of genome editing can be realized.
Collapse
Affiliation(s)
- Ahmad M Khalil
- Department of Biological Sciences, Yarmouk University, Irbid, Jordan.
| |
Collapse
|
11
|
Abstract
BACKGROUND Development of efficient strategies has always been one of the great perspectives for biotechnologists. During the last decade, genome editing of different organisms has been a fast advancing field and therefore has received a lot of attention from various researchers comprehensively reviewing latest achievements and offering opinions on future directions. This review presents a brief history, basic principles, advantages and disadvantages, as well as various aspects of each genome editing technology including the modes, applications, and challenges that face delivery of gene editing components. MAIN BODY Genetic modification techniques cover a wide range of studies, including the generation of transgenic animals, functional analysis of genes, model development for diseases, or drug development. The delivery of certain proteins such as monoclonal antibodies, enzymes, and growth hormones has been suffering from several obstacles because of their large size. These difficulties encouraged scientists to explore alternative approaches, leading to the progress in gene editing. The distinguished efforts and enormous experimentation have now been able to introduce methodologies that can change the genetic constitution of the living cell. The genome editing strategies have evolved during the last three decades, and nowadays, four types of "programmable" nucleases are available in this field: meganucleases, zinc finger nucleases, transcription activator-like effector nucleases, and the clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR associated protein 9 (Cas9) (CRISPR/Cas-9) system. Each group has its own characteristics necessary for researchers to select the most suitable method for gene editing tool for a range of applications. Genome engineering/editing technology will revolutionize the creation of precisely manipulated genomes of cells or organisms in order to modify a specific characteristic. Of the potential applications are those in human health and agriculture. Introducing constructs into target cells or organisms is the key step in genome engineering. CONCLUSIONS Despite the success already achieved, the genome editing techniques are still suffering certain difficulties. Challenges must be overcome before the full potential of genome editing can be realized.
Collapse
Affiliation(s)
- Ahmad M Khalil
- Department of Biological Sciences, Yarmouk University, Irbid, Jordan.
| |
Collapse
|
12
|
Redesigning small ruminant genomes with CRISPR toolkit: Overview and perspectives. Theriogenology 2020; 147:25-33. [PMID: 32086048 DOI: 10.1016/j.theriogenology.2020.02.015] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Revised: 01/24/2020] [Accepted: 02/08/2020] [Indexed: 12/11/2022]
Abstract
Genetic modification is a rapidly developing field in which numerous significant breakthroughs have been achieved. Over the last few decades, genetic modification has evolved from insertional transgenesis to gene targeting and editing and, more recently, to base and prime editing using CRISPR-derived systems. Currently, CRISPR-based genome editing systems are showing great potential for generating gene-edited offspring with defined genetic characteristics. Domestic small ruminants (sheep and goats) have shown great potential as large animal models for genome engineering. Ovine and caprine genomes have been engineered using CRISPR-based systems for numerous purposes. These include generating superior agricultural breeds, expression of therapeutic agents in mammary glands, and developing animal models to be used in the study of human genetic disorders and regenerative medicine. The creation of these models has been facilitated by the continuous emergence and development of genetic modification tools. In this review, we provide an overview on how CRISPR-based systems have been used in the generation of gene-edited small ruminants through the two main pathways (embryonic microinjection and somatic cell nuclear transfer) and highlight the ovine and caprine genes that have been targeted via knockout, knockin, HDR-mediated point mutation, and base editing approaches, as well as the aims of these specific manipulations.
Collapse
|