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Tyumentseva M, Tyumentsev A, Akimkin V. CRISPR/Cas9 Landscape: Current State and Future Perspectives. Int J Mol Sci 2023; 24:16077. [PMID: 38003266 PMCID: PMC10671331 DOI: 10.3390/ijms242216077] [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: 10/18/2023] [Revised: 11/06/2023] [Accepted: 11/06/2023] [Indexed: 11/26/2023] Open
Abstract
CRISPR (clustered regularly interspaced short palindromic repeats)/Cas9 is a unique genome editing tool that can be easily used in a wide range of applications, including functional genomics, transcriptomics, epigenetics, biotechnology, plant engineering, livestock breeding, gene therapy, diagnostics, and so on. This review is focused on the current CRISPR/Cas9 landscape, e.g., on Cas9 variants with improved properties, on Cas9-derived and fusion proteins, on Cas9 delivery methods, on pre-existing immunity against CRISPR/Cas9 proteins, anti-CRISPR proteins, and their possible roles in CRISPR/Cas9 function improvement. Moreover, this review presents a detailed outline of CRISPR/Cas9-based diagnostics and therapeutic approaches. Finally, the review addresses the future expansion of genome editors' toolbox with Cas9 orthologs and other CRISPR/Cas proteins.
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Affiliation(s)
- Marina Tyumentseva
- Central Research Institute of Epidemiology, Novogireevskaya Str., 3a, 111123 Moscow, Russia; (A.T.); (V.A.)
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Tabassum T, Pietrogrande G, Healy M, Wolvetang EJ. CRISPR-Cas9 Direct Fusions for Improved Genome Editing via Enhanced Homologous Recombination. Int J Mol Sci 2023; 24:14701. [PMID: 37834150 PMCID: PMC10572186 DOI: 10.3390/ijms241914701] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 09/27/2023] [Accepted: 09/27/2023] [Indexed: 10/15/2023] Open
Abstract
DNA repair in mammalian cells involves the coordinated action of a range of complex cellular repair machinery. Our understanding of these DNA repair processes has advanced to the extent that they can be leveraged to improve the efficacy and precision of Cas9-assisted genome editing tools. Here, we review how the fusion of CRISPR-Cas9 to functional domains of proteins that directly or indirectly impact the DNA repair process can enhance genome editing. Such studies have allowed the development of diverse technologies that promote efficient gene knock-in for safer genome engineering practices.
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Affiliation(s)
- Tahmina Tabassum
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St. Lucia, Brisbane, QLD 4072, Australia; (T.T.); (G.P.)
| | - Giovanni Pietrogrande
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St. Lucia, Brisbane, QLD 4072, Australia; (T.T.); (G.P.)
| | - Michael Healy
- Institute for Molecular Biosciences, The University of Queensland, St. Lucia, Brisbane, QLD 4072, Australia;
| | - Ernst J. Wolvetang
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St. Lucia, Brisbane, QLD 4072, Australia; (T.T.); (G.P.)
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Zhang Y, Chen S, Yang L, Zhang Q. Application progress of CRISPR/Cas9 genome-editing technology in edible fungi. Front Microbiol 2023; 14:1169884. [PMID: 37303782 PMCID: PMC10248459 DOI: 10.3389/fmicb.2023.1169884] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Accepted: 04/26/2023] [Indexed: 06/13/2023] Open
Abstract
Edible fungi are not only delicious but are also rich in nutritional and medicinal value, which is highly sought after by consumers. As the edible fungi industry continues to rapidly advance worldwide, particularly in China, the cultivation of superior and innovative edible fungi strains has become increasingly pivotal. Nevertheless, conventional breeding techniques for edible fungi can be arduous and time-consuming. CRISPR/Cas9 (clustered regularly interspaced short palindromic repeats/CRISPR-associated nuclease 9) is a powerful tool for molecular breeding due to its ability to mediate high-efficiency and high-precision genome modification, which has been successfully applied to many kinds of edible fungi. In this review, we briefly summarized the working mechanism of the CRISPR/Cas9 system and highlighted the application progress of CRISPR/Cas9-mediated genome-editing technology in edible fungi, including Agaricus bisporus, Ganoderma lucidum, Flammulina filiformis, Ustilago maydis, Pleurotus eryngii, Pleurotus ostreatus, Coprinopsis cinerea, Schizophyllum commune, Cordyceps militaris, and Shiraia bambusicola. Additionally, we discussed the limitations and challenges encountered using CRISPR/Cas9 technology in edible fungi and provided potential solutions. Finally, the applications of CRISPR/Cas9 system for molecular breeding of edible fungi in the future are explored.
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Elhawary NA, AlJahdali IA, Abumansour IS, Elhawary EN, Gaboon N, Dandini M, Madkhali A, Alosaimi W, Alzahrani A, Aljohani F, Melibary EM, Kensara OA. Genetic etiology and clinical challenges of phenylketonuria. Hum Genomics 2022; 16:22. [PMID: 35854334 PMCID: PMC9295449 DOI: 10.1186/s40246-022-00398-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Accepted: 07/08/2022] [Indexed: 02/08/2023] Open
Abstract
This review discusses the epidemiology, pathophysiology, genetic etiology, and management of phenylketonuria (PKU). PKU, an autosomal recessive disease, is an inborn error of phenylalanine (Phe) metabolism caused by pathogenic variants in the phenylalanine hydroxylase (PAH) gene. The prevalence of PKU varies widely among ethnicities and geographic regions, affecting approximately 1 in 24,000 individuals worldwide. Deficiency in the PAH enzyme or, in rare cases, the cofactor tetrahydrobiopterin results in high blood Phe concentrations, causing brain dysfunction. Untreated PKU, also known as PAH deficiency, results in severe and irreversible intellectual disability, epilepsy, behavioral disorders, and clinical features such as acquired microcephaly, seizures, psychological signs, and generalized hypopigmentation of skin (including hair and eyes). Severe phenotypes are classic PKU, and less severe forms of PAH deficiency are moderate PKU, mild PKU, mild hyperphenylalaninaemia (HPA), or benign HPA. Early diagnosis and intervention must start shortly after birth to prevent major cognitive and neurological effects. Dietary treatment, including natural protein restriction and Phe-free supplements, must be used to maintain blood Phe concentrations of 120-360 μmol/L throughout the life span. Additional treatments include the casein glycomacropeptide (GMP), which contains very limited aromatic amino acids and may improve immunological function, and large neutral amino acid (LNAA) supplementation to prevent plasma Phe transport into the brain. The synthetic BH4 analog, sapropterin hydrochloride (i.e., Kuvan®, BioMarin), is another potential treatment that activates residual PAH, thus decreasing Phe concentrations in the blood of PKU patients. Moreover, daily subcutaneous injection of pegylated Phe ammonia-lyase (i.e., pegvaliase; PALYNZIQ®, BioMarin) has promised gene therapy in recent clinical trials, and mRNA approaches are also being studied.
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Affiliation(s)
- Nasser A. Elhawary
- grid.412832.e0000 0000 9137 6644Department of Medical Genetics, College of Medicine, Umm Al-Qura University, P.O. Box 57543, Mecca, 21955 Saudi Arabia
| | - Imad A. AlJahdali
- grid.412832.e0000 0000 9137 6644Department of Community Medicine, College of Medicine, Umm Al-Qura University, P.O. Box 57543, Mecca, 21955 Saudi Arabia
| | - Iman S. Abumansour
- grid.412832.e0000 0000 9137 6644Department of Medical Genetics, College of Medicine, Umm Al-Qura University, P.O. Box 57543, Mecca, 21955 Saudi Arabia
| | - Ezzeldin N. Elhawary
- grid.123047.30000000103590315Faculty of Medicine, MS Genomic Medicine Program, University of Southampton, Southampton General Hospital, Southampton, UK
| | - Nagwa Gaboon
- grid.7269.a0000 0004 0621 1570Department of Clinical Genetics, Faculty of Medicine, Ain Shams University, Cairo, Egypt
| | - Mohammed Dandini
- Department of Laboratory and Blood Bank, Maternity and Children Hospital, Mecca, Saudi Arabia
| | - Abdulelah Madkhali
- grid.415254.30000 0004 1790 7311Department of Pathology and Laboratory Medicine, King Abdulaziz Medical City, Ministry of National Guard Health Affairs, Riyadh, Saudi Arabia
| | - Wafaa Alosaimi
- Department of Hematology, Maternity and Children Hospital, Mecca, Saudi Arabia
| | - Abdulmajeed Alzahrani
- Department of Laboratory and Blood Bank at Maternity and Children Hospital, Mecca, Saudi Arabia
| | - Fawzia Aljohani
- Department of Pediatric Clinics, Maternity and Children Hospital, King Salman Medical City, Madinah, Saudi Arabia
| | - Ehab M. Melibary
- grid.412832.e0000 0000 9137 6644Department of Medical Genetics, College of Medicine, Umm Al-Qura University, P.O. Box 57543, Mecca, 21955 Saudi Arabia
| | - Osama A. Kensara
- grid.412832.e0000 0000 9137 6644Department of Clinical Nutrition, Faculty of Applied Medical Sciences, Umm Al-Qura University, Jeddah, Saudi Arabia
- Department of Biochemistry, Batterjee Medical College, Jeddah, Saudi Arabia
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Shams F, Bayat H, Mohammadian O, Mahboudi S, Vahidnezhad H, Soosanabadi M, Rahimpour A. Advance trends in targeting homology-directed repair for accurate gene editing: An inclusive review of small molecules and modified CRISPR-Cas9 systems. BIOIMPACTS 2022; 12:371-391. [PMID: 35975201 PMCID: PMC9376165 DOI: 10.34172/bi.2022.23871] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Revised: 11/21/2021] [Accepted: 11/21/2021] [Indexed: 11/25/2022]
Abstract
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Introduction: Clustered regularly interspaced short palindromic repeat and its associated protein (CRISPR-Cas)-based technologies generate targeted modifications in host genome by inducing site-specific double-strand breaks (DSBs) that can serve as a substrate for homology-directed repair (HDR) in both in vitro and in vivo models. HDR pathway could enhance incorporation of exogenous DNA templates into the CRISPR-Cas9-mediated DSB site. Owing to low rate of HDR pathway, the efficiency of accurate genome editing is diminished. Enhancing the efficiency of HDR can provide fast, easy, and accurate technologies based on CRISPR-Cas9 technologies.
Methods: The current study presents an overview of attempts conducted on the precise genome editing strategies based on small molecules and modified CRISPR-Cas9 systems.
Results: In order to increase HDR rate in targeted cells, several logical strategies have been introduced such as generating CRISPR effector chimeric proteins, anti-CRISPR proteins, modified Cas9 with donor template, and using validated synthetic or natural small molecules for either inhibiting non-homologous end joining (NHEJ), stimulating HDR, or synchronizing cell cycle. Recently, high-throughput screening methods have been applied for identification of small molecules which along with the CRISPR system can regulate precise genome editing through HDR.
Conclusion: The stimulation of HDR components or inhibiting NHEJ can increase the accuracy of CRISPR-Cas-mediated engineering systems. Generating chimeric programmable endonucleases provide this opportunity to direct DNA template close proximity of CRISPR-Cas-mediated DSB. Small molecules and their derivatives can also proficiently block or activate certain DNA repair pathways and bring up novel perspectives for increasing HDR efficiency, especially in human cells. Further, high throughput screening of small molecule libraries could result in more discoveries of promising chemicals that improve HDR efficiency and CRISPR-Cas9 systems.
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Affiliation(s)
- Forough Shams
- Department of Medical Biotechnology, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Hadi Bayat
- Department of Molecular Genetics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
- Department of Tissue Engineering and Applied Cell Sciences, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Omid Mohammadian
- Medical Nano-Technology and Tissue Engineering Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
- Department of Tissue Engineering and Applied Cell Sciences, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Somayeh Mahboudi
- Department of Food Science and Technology, School of Agriculture, Shiraz University, Shiraz, Iran
| | - Hassan Vahidnezhad
- Department of Dermatology and Cutaneous Biology, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA, USA
- Jefferson Institute of Molecular Medicine, Thomas Jefferson University, Philadelphia, PA, USA
| | - Mohsen Soosanabadi
- Department of Medical Genetics, Semnan University of Medical Sciences, Semnan, Iran
| | - Azam Rahimpour
- Medical Nano-Technology and Tissue Engineering Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
- Department of Tissue Engineering and Applied Cell Sciences, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
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Shin JH, Lee J, Jung YK, Kim KS, Jeong J, Choi D. Therapeutic applications of gene editing in chronic liver diseases: an update. BMB Rep 2022. [PMID: 35651324 PMCID: PMC9252892 DOI: 10.5483/bmbrep.2022.55.6.033] [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] [Indexed: 11/23/2022] Open
Abstract
Innovative genome editing techniques developed in recent decades have revolutionized the biomedical research field. Liver is the most favored target organ for genome editing owing to its ability to regenerate. The regenerative capacity of the liver enables ex vivo gene editing in which the mutated gene in hepatocytes isolated from the animal model of genetic disease is repaired. The edited hepatocytes are injected back into the animal to mitigate the disease. Furthermore, the liver is considered as the easiest target organ for gene editing as it absorbs almost all foreign molecules. The mRNA vaccines, which have been developed to manage the COVID-19 pandemic, have provided a novel gene editing strategy using Cas mRNA. A single injection of gene editing components with Cas mRNA is reported to be efficient in the treatment of patients with genetic liver diseases. In this review, we first discuss previously reported gene editing tools and cases managed using them, as well as liver diseases caused by genetic mutations. Next, we summarize the recent successes of ex vivo and in vivo gene editing approaches in ameliorating liver diseases in animals and humans.
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Affiliation(s)
- Ji Hyun Shin
- Department of Surgery, Hanyang University College of Medicine, Seoul 04763, Korea
- HY Indang Institute of Regenerative Medicine and Stem Cell Research, Hanyang University, Seoul 04763, Korea
| | - Jinho Lee
- Department of Surgery, Hanyang University College of Medicine, Seoul 04763, Korea
- HY Indang Institute of Regenerative Medicine and Stem Cell Research, Hanyang University, Seoul 04763, Korea
| | - Yun Kyung Jung
- Department of Surgery, Hanyang University College of Medicine, Seoul 04763, Korea
- HY Indang Institute of Regenerative Medicine and Stem Cell Research, Hanyang University, Seoul 04763, Korea
| | - Kyeong Sik Kim
- Department of Surgery, Hanyang University College of Medicine, Seoul 04763, Korea
| | - Jaemin Jeong
- Department of Surgery, Hanyang University College of Medicine, Seoul 04763, Korea
- HY Indang Institute of Regenerative Medicine and Stem Cell Research, Hanyang University, Seoul 04763, Korea
| | - Dongho Choi
- Department of Surgery, Hanyang University College of Medicine, Seoul 04763, Korea
- HY Indang Institute of Regenerative Medicine and Stem Cell Research, Hanyang University, Seoul 04763, Korea
- Department of HY-KIST Bio-convergence, Hanyang University, Seoul 04763, Korea
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Aoshima T, Kobayashi Y, Takagi H, Iijima K, Sato M, Takabayashi S. Modification of improved-genome editing via oviductal nucleic acids delivery (i-GONAD)-mediated knock-in in rats. BMC Biotechnol 2021; 21:63. [PMID: 34724929 PMCID: PMC8561937 DOI: 10.1186/s12896-021-00723-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Accepted: 10/28/2021] [Indexed: 11/10/2022] Open
Abstract
Background Improved genome-editing via oviductal nucleic acids delivery (i-GONAD) is a new technology that facilitates in situ genome-editing of mammalian zygotes exiting the oviductal lumen. The i-GONAD technology has been developed for use in mice, rats, and hamsters; however, oligonucleotide (ODN)-based knock-in (KI) is more inefficient in rats than mice. To improve the efficiency of i-GONAD in rats we examined KI efficiency using three guide RNAs (gRNA), crRNA1, crRNA2 and crRNA3. These gRNAs recognize different portions of the target locus, but also overlap each other in the target locus. We also examined the effects of commercially available KI -enhancing drugs (including SCR7, L755,507, RS-1, and HDR enhancer) on i-GONAD-mediated KI efficiency. Results The KI efficiency in rat fetuses generated after i-GONAD with crRNA2 and single-stranded ODN was significantly higher (24%) than crRNA1 (5%; p < 0.05) or crRNA3 (0%; p < 0.01). The KI efficiency of i-GONAD with triple gRNAs was 11%. These findings suggest that KI efficiency largely depends on the type of gRNA used. Furthermore, the KI efficiency drugs, SCR7, L755,507 and HDR enhancer, all of which are known to enhance KI efficiency, increased KI efficiency using the i-GONAD with crRNA1 protocol. In contrast, only L755,507 (15 μM) increased KI efficiency using the i-GONAD with crRNA2 protocol. None of them were significantly different. Conclusions We attempted to improve the KI efficiency of i-GONAD in rats. We demonstrated that the choice of gRNA is important for determining KI efficiency and insertion and deletion rates. Some drugs (e.g. SCR7, L755,507 and HDR enhancer) that are known to increase KI efficiency in culture cells were found to be effective in i-GONAD in rats, but their effects were limited. Supplementary Information The online version contains supplementary material available at 10.1186/s12896-021-00723-5.
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Affiliation(s)
- Takuya Aoshima
- Laboratory Animal Facilities and Services, Preeminent Medical Photonics Education and Research Center, Hamamatsu University School of Medicine, 1-20-1 Handayama, Higashi-ku, Hamamatsu, Shizuoka, 431-3192, Japan
| | - Yukari Kobayashi
- Laboratory Animal Facilities and Services, Preeminent Medical Photonics Education and Research Center, Hamamatsu University School of Medicine, 1-20-1 Handayama, Higashi-ku, Hamamatsu, Shizuoka, 431-3192, Japan
| | - Hisayoshi Takagi
- Laboratory Animal Facilities and Services, Preeminent Medical Photonics Education and Research Center, Hamamatsu University School of Medicine, 1-20-1 Handayama, Higashi-ku, Hamamatsu, Shizuoka, 431-3192, Japan
| | - Kenta Iijima
- Laboratory Animal Facilities and Services, Preeminent Medical Photonics Education and Research Center, Hamamatsu University School of Medicine, 1-20-1 Handayama, Higashi-ku, Hamamatsu, Shizuoka, 431-3192, Japan
| | - Masahiro Sato
- Department of Genome Medicine, National Center for Child Health and Development, 2-10-1 Okura, Setagaya, Tokyo, 157-8535, Japan.
| | - Shuji Takabayashi
- Laboratory Animal Facilities and Services, Preeminent Medical Photonics Education and Research Center, Hamamatsu University School of Medicine, 1-20-1 Handayama, Higashi-ku, Hamamatsu, Shizuoka, 431-3192, Japan.
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CRISPR FokI Dead Cas9 System: Principles and Applications in Genome Engineering. Cells 2020; 9:cells9112518. [PMID: 33233344 PMCID: PMC7700487 DOI: 10.3390/cells9112518] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2020] [Revised: 11/05/2020] [Accepted: 11/19/2020] [Indexed: 12/18/2022] Open
Abstract
The identification of the robust clustered regularly interspersed short palindromic repeats (CRISPR) associated endonuclease (Cas9) system gene-editing tool has opened up a wide range of potential therapeutic applications that were restricted by more complex tools, including zinc finger nucleases (ZFNs) and transcription activator-like effector nucleases (TALENs). Nevertheless, the high frequency of CRISPR system off-target activity still limits its applications, and, thus, advanced strategies for highly specific CRISPR/Cas9-mediated genome editing are continuously under development including CRISPR–FokI dead Cas9 (fdCas9). fdCas9 system is derived from linking a FokI endonuclease catalytic domain to an inactive Cas9 protein and requires a pair of guide sgRNAs that bind to the sense and antisense strands of the DNA in a protospacer adjacent motif (PAM)-out orientation, with a defined spacer sequence range around the target site. The dimerization of FokI domains generates DNA double-strand breaks, which activates the DNA repair machinery and results in genomic edit. So far, all the engineered fdCas9 variants have shown promising gene-editing activities in human cells when compared to other platforms. Herein, we review the advantages of all published variants of fdCas9 and their current applications in genome engineering.
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Piccolo P, Rossi A, Brunetti-Pierri N. Liver-directed gene-based therapies for inborn errors of metabolism. Expert Opin Biol Ther 2020; 21:229-240. [PMID: 32880494 DOI: 10.1080/14712598.2020.1817375] [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] [Indexed: 12/14/2022]
Abstract
INTRODUCTION Inborn errors of metabolism include several genetic disorders due to disruption of cellular biochemical reactions. Although individually rare, collectively they are a large and heterogenous group of diseases affecting a significant proportion of patients. Available treatments are often unsatisfactory. Liver-directed gene therapy has potential for treatment of several inborn errors of metabolism. While lentiviral vectors and lipid nanoparticle-mRNA have shown attractive features in preclinical studies and still have to be investigated in humans, adeno-associated virus (AAV) vectors have shown clinical success in both preclinical and clinical trials for in vivo liver-directed gene therapy. AREAS COVERED In this review, we discussed the most relevant clinical applications and the challenges of liver-directed gene-based approaches for therapy of inborn errors of metabolism. EXPERT OPINION Challenges and prospects of clinical gene therapy trials and preclinical studies that are believed to have the greatest potential for clinical translation are presented.
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Affiliation(s)
- Pasquale Piccolo
- Telethon Institute of Genetics and Medicine , Pozzuoli, Italy.,Department of Translational Medicine, Federico II University of Naples , Naples, Italy
| | - Alessandro Rossi
- Department of Translational Medicine, Federico II University of Naples , Naples, Italy
| | - Nicola Brunetti-Pierri
- Telethon Institute of Genetics and Medicine , Pozzuoli, Italy.,Department of Translational Medicine, Federico II University of Naples , Naples, Italy
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Sarodaya N, Suresh B, Kim KS, Ramakrishna S. Protein Degradation and the Pathologic Basis of Phenylketonuria and Hereditary Tyrosinemia. Int J Mol Sci 2020; 21:ijms21144996. [PMID: 32679806 PMCID: PMC7404301 DOI: 10.3390/ijms21144996] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Revised: 07/10/2020] [Accepted: 07/13/2020] [Indexed: 12/15/2022] Open
Abstract
A delicate intracellular balance among protein synthesis, folding, and degradation is essential to maintaining protein homeostasis or proteostasis, and it is challenged by genetic and environmental factors. Molecular chaperones and the ubiquitin proteasome system (UPS) play a vital role in proteostasis for normal cellular function. As part of protein quality control, molecular chaperones recognize misfolded proteins and assist in their refolding. Proteins that are beyond repair or refolding undergo degradation, which is largely mediated by the UPS. The importance of protein quality control is becoming ever clearer, but it can also be a disease-causing mechanism. Diseases such as phenylketonuria (PKU) and hereditary tyrosinemia-I (HT1) are caused due to mutations in PAH and FAH gene, resulting in reduced protein stability, misfolding, accelerated degradation, and deficiency in functional proteins. Misfolded or partially unfolded proteins do not necessarily lose their functional activity completely. Thus, partially functional proteins can be rescued from degradation by molecular chaperones and deubiquitinating enzymes (DUBs). Deubiquitination is an important mechanism of the UPS that can reverse the degradation of a substrate protein by covalently removing its attached ubiquitin molecule. In this review, we discuss the importance of molecular chaperones and DUBs in reducing the severity of PKU and HT1 by stabilizing and rescuing mutant proteins.
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Affiliation(s)
- Neha Sarodaya
- Graduate School of Biomedical Science and Engineering, Hanyang University, Seoul 04763, Korea; (N.S.); (B.S.)
| | - Bharathi Suresh
- Graduate School of Biomedical Science and Engineering, Hanyang University, Seoul 04763, Korea; (N.S.); (B.S.)
| | - Kye-Seong Kim
- Graduate School of Biomedical Science and Engineering, Hanyang University, Seoul 04763, Korea; (N.S.); (B.S.)
- College of Medicine, Hanyang University, Seoul 04763, Korea
- Correspondence: (K.-S.K.); or (S.R.)
| | - Suresh Ramakrishna
- Graduate School of Biomedical Science and Engineering, Hanyang University, Seoul 04763, Korea; (N.S.); (B.S.)
- College of Medicine, Hanyang University, Seoul 04763, Korea
- Correspondence: (K.-S.K.); or (S.R.)
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Zhang W, Chen Y, Yang J, Zhang J, Yu J, Wang M, Zhao X, Wei K, Wan X, Xu X, Jiang Y, Chen J, Gao S, Mao Z. A high-throughput small molecule screen identifies farrerol as a potentiator of CRISPR/Cas9-mediated genome editing. eLife 2020; 9:56008. [PMID: 32644042 PMCID: PMC7380943 DOI: 10.7554/elife.56008] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Accepted: 07/08/2020] [Indexed: 12/20/2022] Open
Abstract
Directly modulating the choice between homologous recombination (HR) and non-homologous end joining (NHEJ) - two independent pathways for repairing DNA double-strand breaks (DSBs) - has the potential to improve the efficiency of gene targeting by CRISPR/Cas9. Here, we have developed a rapid and easy-to-score screening approach for identifying small molecules that affect the choice between the two DSB repair pathways. Using this tool, we identified a small molecule, farrerol, that promotes HR but does not affect NHEJ. Further mechanistic studies indicate that farrerol functions through stimulating the recruitment of RAD51 to DSB sites. Importantly, we demonstrated that farrerol effectively promotes precise targeted integration in human cells, mouse cells and mouse embryos at multiple genomic loci. In addition, treating cells with farrerol did not have any obvious negative effect on genomic stability. Moreover, farrerol significantly improved the knock-in efficiency in blastocysts, and the subsequently generated knock-in mice retained the capacity for germline transmission.
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Affiliation(s)
- Weina Zhang
- Clinical and Translational Research Center of Shanghai First Maternity & Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Yu Chen
- Clinical and Translational Research Center of Shanghai First Maternity & Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Jiaqing Yang
- Clinical and Translational Research Center of Shanghai First Maternity & Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Jing Zhang
- Clinical and Translational Research Center of Shanghai First Maternity & Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Jiayu Yu
- Clinical and Translational Research Center of Shanghai First Maternity & Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Mengting Wang
- Clinical and Translational Research Center of Shanghai First Maternity & Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Xiaodong Zhao
- Clinical and Translational Research Center of Shanghai First Maternity & Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Ke Wei
- Clinical and Translational Research Center of Shanghai First Maternity & Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Xiaoping Wan
- Clinical and Translational Research Center of Shanghai First Maternity & Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Xiaojun Xu
- State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, China
| | - Ying Jiang
- Clinical and Translational Research Center of Shanghai First Maternity & Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Jiayu Chen
- Clinical and Translational Research Center of Shanghai First Maternity & Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Shaorong Gao
- Clinical and Translational Research Center of Shanghai First Maternity & Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Zhiyong Mao
- Clinical and Translational Research Center of Shanghai First Maternity & Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai, China.,Tsingtao Advanced Research Institute, Tongji University, Qingdao, China
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12
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Lamas‐Toranzo I, Martínez‐Moro A, O´Callaghan E, Millán‐Blanca G, Sánchez J, Lonergan P, Bermejo‐Álvarez P. RS-1 enhances CRISPR-mediated targeted knock-in in bovine embryos. Mol Reprod Dev 2020; 87:542-549. [PMID: 32227559 PMCID: PMC7496720 DOI: 10.1002/mrd.23341] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2020] [Revised: 03/08/2020] [Accepted: 03/11/2020] [Indexed: 12/15/2022]
Abstract
Targeted knock-in (KI) can be achieved in embryos by clustered regularly interspaced short palindromic repeats (CRISPR)-assisted homology directed repair (HDR). However, HDR efficiency is constrained by the competition of nonhomologous end joining. The objective of this study was to explore whether CRISPR-assisted targeted KI rates can be improved in bovine embryos by exposure to the HDR enhancer RS-1. In vitro produced zygotes were injected with CRISPR components (300 ng/µl Cas9 messenger RNA and 100 ng/µl single guide RNA against a noncoding region) and a single-stranded DNA (ssDNA) repair template (100 ng/µl). ssDNA template contained a 6 bp XbaI site insert, allowing targeted KI detection by restriction analysis, flanked by 50 bp homology arms. Following microinjection, zygotes were exposed to 0, 3.75, or 7.5 µM RS-1 for 24 hr. No differences were noted between groups in terms of development or genome edition rates. However, targeted KI rates were doubled in the group exposed to 7.5 µM RS-1 compared to the others (52.8% vs. 25% and 23.1%, for 7.5, 0, and 3.75 µM, respectively). In conclusion, transient exposure to 7.5 µM RS-1 enhances targeted KI rates resulting in approximately half of the embryos containing the intended mutation, hence allowing direct KI generation in embryos.
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Affiliation(s)
| | - A. Martínez‐Moro
- Animal Reproduction DepartmentINIAMadridSpain
- ProcreatecMadridSpain
| | - E. O´Callaghan
- School of Agriculture and Food ScienceUniversity College DublinDublinIreland
| | | | - J.M. Sánchez
- School of Agriculture and Food ScienceUniversity College DublinDublinIreland
| | - P. Lonergan
- School of Agriculture and Food ScienceUniversity College DublinDublinIreland
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13
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Trevisan M, Masi G, Palù G. Genome editing technologies to treat rare liver diseases. Transl Gastroenterol Hepatol 2020; 5:23. [PMID: 32258527 DOI: 10.21037/tgh.2019.10.10] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Accepted: 10/18/2019] [Indexed: 12/13/2022] Open
Abstract
Liver has a central role in protein and lipid metabolism, and diseases involving hepatocytes have often repercussions on multiple organs and systems. Hepatic disorders are frequently characterized by production of defective or non-functional proteins, and traditional gene therapy approaches have been attempted for years to restore adequate protein levels through delivery of transgenes. Recently, many different genome editing platforms have been developed aimed at correcting at DNA level the defects underlying the diseases. In this Review we discuss the latest applications of these tools applied to develop therapeutic strategies for rare liver disorders, in particular updating the literature with the most recent strategies relying on base editors technology.
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Affiliation(s)
- Marta Trevisan
- Department of Molecular Medicine, University of Padova, Padova, Italy
| | - Giulia Masi
- Department of Molecular Medicine, University of Padova, Padova, Italy
| | - Giorgio Palù
- Department of Molecular Medicine, University of Padova, Padova, Italy
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14
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Rozov SM, Permyakova NV, Deineko EV. The Problem of the Low Rates of CRISPR/Cas9-Mediated Knock-ins in Plants: Approaches and Solutions. Int J Mol Sci 2019; 20:E3371. [PMID: 31323994 PMCID: PMC6651222 DOI: 10.3390/ijms20133371] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Revised: 06/28/2019] [Accepted: 07/05/2019] [Indexed: 11/16/2022] Open
Abstract
The main number of genome editing events in plant objects obtained during the last decade with the help of specific nucleases zinc finger (ZFN), transcription activator-like effector nucleases (TALEN), and clustered regularly interspaced short palindromic repeats (CRISPR)/Cas are the microindels causing frameshift and subsequent gene knock-out. The knock-ins of genes or their parts, i.e., the insertion of them into a target genome region, are between one and two orders of magnitude less frequent. First and foremost, this is associated with the specific features of the repair systems of higher eukaryotes and the availability of the donor template in accessible proximity during double-strand break (DSB) repair. This review briefs the main repair pathways in plants according to the aspect of their involvement in genome editing. The main methods for increasing the frequency of knock-ins are summarized both along the homologous recombination pathway and non-homologous end joining, which can be used for plant objects.
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Affiliation(s)
- Serge M Rozov
- Institute of Cytology and Genetics, Siberian Branch, Russian Academy of Sciences, Novosibirsk 630090, Russia.
| | - Natalya V Permyakova
- Institute of Cytology and Genetics, Siberian Branch, Russian Academy of Sciences, Novosibirsk 630090, Russia
| | - Elena V Deineko
- Institute of Cytology and Genetics, Siberian Branch, Russian Academy of Sciences, Novosibirsk 630090, Russia
- Department of Plant Physiology and Biotechnology, Tomsk State University, Tomsk 634050, Russia
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15
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Smirnikhina SA, Anuchina AA, Lavrov AV. Ways of improving precise knock-in by genome-editing technologies. Hum Genet 2018; 138:1-19. [DOI: 10.1007/s00439-018-1953-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Accepted: 10/29/2018] [Indexed: 02/07/2023]
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16
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Production of human recombinant phenylalanine hydroxylase in Lactobacillus plantarum for gastrointestinal delivery. Eur J Pharm Sci 2017; 109:48-55. [DOI: 10.1016/j.ejps.2017.07.033] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2017] [Revised: 07/24/2017] [Accepted: 07/28/2017] [Indexed: 01/08/2023]
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17
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Cebrian-Serrano A, Davies B. CRISPR-Cas orthologues and variants: optimizing the repertoire, specificity and delivery of genome engineering tools. Mamm Genome 2017; 28:247-261. [PMID: 28634692 PMCID: PMC5569134 DOI: 10.1007/s00335-017-9697-4] [Citation(s) in RCA: 83] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Accepted: 05/26/2017] [Indexed: 12/17/2022]
Abstract
Robust and cost-effective genome editing in a diverse array of cells and model organisms is now possible thanks to the discovery of the RNA-guided endonucleases of the CRISPR-Cas system. The commonly used Cas9 of Streptococcus pyogenes shows high levels of activity but, depending on the application, has been associated with some shortcomings. Firstly, the enzyme has been shown to cause mutagenesis at genomic sequences resembling the target sequence. Secondly, the stringent requirement for a specific motif adjacent to the selected target site can limit the target range of this enzyme. Lastly, the physical size of Cas9 challenges the efficient delivery of genomic engineering tools based on this enzyme as viral particles for potential therapeutic applications. Related and parallel strategies have been employed to address these issues. Taking advantage of the wealth of structural information that is becoming available for CRISPR-Cas effector proteins, Cas9 has been redesigned by mutagenizing key residues contributing to activity and target recognition. The protein has also been shortened and redesigned into component subunits in an attempt to facilitate its efficient delivery. Furthermore, the CRISPR-Cas toolbox has been expanded by exploring the properties of Cas9 orthologues and other related effector proteins from diverse bacterial species, some of which exhibit different target site specificities and reduced molecular size. It is hoped that the improvements in accuracy, target range and efficiency of delivery will facilitate the therapeutic application of these site-specific nucleases.
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Affiliation(s)
| | - Benjamin Davies
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK.
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