151
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Puppulin L, Ishikawa J, Sumino A, Marchesi A, Flechsig H, Umeda K, Kodera N, Nishimasu H, Shibata M. Dynamics of Target DNA Binding and Cleavage by Staphylococcus aureus Cas9 as Revealed by High-Speed Atomic Force Microscopy. ACS NANO 2023; 17:4629-4641. [PMID: 36848598 DOI: 10.1021/acsnano.2c10709] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Programmable DNA binding and cleavage by CRISPR-Cas9 has revolutionized the life sciences. However, the off-target cleavage observed in DNA sequences with some homology to the target still represents a major limitation for a more widespread use of Cas9 in biology and medicine. For this reason, complete understanding of the dynamics of DNA binding, interrogation and cleavage by Cas9 is crucial to improve the efficiency of genome editing. Here, we use high-speed atomic force microscopy (HS-AFM) to investigate Staphylococcus aureus Cas9 (SaCas9) and its dynamics of DNA binding and cleavage. Upon binding to single-guide RNA (sgRNA), SaCas9 forms a close bilobed structure that transiently and flexibly adopts also an open configuration. The SaCas9-mediated DNA cleavage is characterized by release of cleaved DNA and immediate dissociation, confirming that SaCas9 operates as a multiple turnover endonuclease. According to present knowledge, the process of searching for target DNA is mainly governed by three-dimensional diffusion. Independent HS-AFM experiments show a potential long-range attractive interaction between SaCas9-sgRNA and its target DNA. The interaction precedes the formation of the stable ternary complex and is observed exclusively in the vicinity of the protospacer-adjacent motif (PAM), up to distances of several nanometers. The direct visualization of the process by sequential topographic images suggests that SaCas9-sgRNA binds to the target sequence first, while the following binding of the PAM is accompanied by local DNA bending and formation of the stable complex. Collectively, our HS-AFM data reveal a potential and unexpected behavior of SaCas9 during the search for DNA targets.
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Affiliation(s)
- Leonardo Puppulin
- WPI Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Kanazawa, Ishikawa 920-1192, Japan
| | - Junichiro Ishikawa
- Structural Biology Division, Research Center for Advanced Science and Technology, The University of Tokyo, Meguro-ku, Tokyo 153-8904, Japan
| | - Ayumi Sumino
- WPI Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Kanazawa, Ishikawa 920-1192, Japan
- Institute for Frontier Science Initiative, Kanazawa University, Kanazawa, Ishikawa 920-1192, Japan
| | - Arin Marchesi
- Department of Experimental and Clinical Medicine, Università Politecnica delle Marche, Via Tronto, 10/A Torrette di Ancona, 60126, Ancona, Italy
| | - Holger Flechsig
- WPI Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Kanazawa, Ishikawa 920-1192, Japan
| | - Kenichi Umeda
- WPI Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Kanazawa, Ishikawa 920-1192, Japan
| | - Noriyuki Kodera
- WPI Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Kanazawa, Ishikawa 920-1192, Japan
| | - Hiroshi Nishimasu
- Structural Biology Division, Research Center for Advanced Science and Technology, The University of Tokyo, Meguro-ku, Tokyo 153-8904, Japan
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, Bunkyo-ku, Tokyo 113-8656, Japan
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
- Inamori Research Institute for Science, Shimogyo-ku, Kyoto 600-8411, Japan
| | - Mikihiro Shibata
- WPI Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Kanazawa, Ishikawa 920-1192, Japan
- Institute for Frontier Science Initiative, Kanazawa University, Kanazawa, Ishikawa 920-1192, Japan
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152
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Rupawate PS, Roylawar P, Khandagale K, Gawande S, Ade AB, Jaiswal DK, Borgave S. Role of gut symbionts of insect pests: A novel target for insect-pest control. Front Microbiol 2023; 14:1146390. [PMID: 36992933 PMCID: PMC10042327 DOI: 10.3389/fmicb.2023.1146390] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Accepted: 02/15/2023] [Indexed: 03/15/2023] Open
Abstract
Insects possess beneficial and nuisance values in the context of the agricultural sector and human life around them. An ensemble of gut symbionts assists insects to adapt to diverse and extreme environments and to occupy every available niche on earth. Microbial symbiosis helps host insects by supplementing necessary diet elements, providing protection from predators and parasitoids through camouflage, modulation of signaling pathway to attain homeostasis and to trigger immunity against pathogens, hijacking plant pathways to circumvent plant defence, acquiring the capability to degrade chemical pesticides, and degradation of harmful pesticides. Therefore, a microbial protection strategy can lead to overpopulation of insect pests, which can drastically reduce crop yield. Some studies have demonstrated increased insect mortality via the destruction of insect gut symbionts; through the use of antibiotics. The review summarizes various roles played by the gut microbiota of insect pests and some studies that have been conducted on pest control by targeting the symbionts. Manipulation or exploitation of the gut symbionts alters the growth and population of the host insects and is consequently a potential target for the development of better pest control strategies. Methods such as modulation of gut symbionts via CRISPR/Cas9, RNAi and the combining of IIT and SIT to increase the insect mortality are further discussed. In the ongoing insect pest management scenario, gut symbionts are proving to be the reliable, eco-friendly and novel approach in the integrated pest management.
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Affiliation(s)
- Pravara S. Rupawate
- Department of Zoology, Sangamner Nagarpalika Arts, D. J. Malpani Commerce and B. N. Sarda Science College (Autonomous), Sangamner, Maharashtra, India
| | - Praveen Roylawar
- Department of Botany, Sangamner Nagarpalika Arts, D. J. Malpani Commerce and B. N. Sarda Science College (Autonomous), Sangamner, Maharashtra, India
| | | | - Suresh Gawande
- ICAR-Directorate of Onion and Garlic Research, Pune, India
| | - Avinash B. Ade
- Department of Botany, Savitribai Phule Pune University, Pune, India
| | - Durgesh Kumar Jaiswal
- Department of Botany, Savitribai Phule Pune University, Pune, India
- *Correspondence: Durgesh Kumar Jaiswal,
| | - Seema Borgave
- Department of Zoology, Sangamner Nagarpalika Arts, D. J. Malpani Commerce and B. N. Sarda Science College (Autonomous), Sangamner, Maharashtra, India
- Seema Borgave,
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153
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Xu Y, Tian N, Shi H, Zhou C, Wang Y, Liang FS. A Split CRISPR/Cas13b System for Conditional RNA Regulation and Editing. J Am Chem Soc 2023; 145:5561-5569. [PMID: 36811465 PMCID: PMC10425183 DOI: 10.1021/jacs.3c01087] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/24/2023]
Abstract
The CRISPR/Cas13b system has been demonstrated as a robust tool for versatile RNA studies and relevant applications. New strategies enabling precise control of Cas13b/dCas13b activities and minimal interference with native RNA activities will further facilitate the understanding and regulation of RNA functions. Here, we engineered a split Cas13b system that can be conditionally activated and deactivated under the induction of abscisic acid (ABA), which achieved the downregulation of endogenous RNAs in dosage- and time-dependent manners. Furthermore, an ABA inducible split dCas13b system was generated to achieve temporally controlled deposition of m6A at specific sites on cellular RNAs through conditional assembly and disassembly of split dCas13b fusion proteins. We also showed that the activities of split Cas13b/dCas13b systems can be modulated by light via using a photoactivatable ABA derivative. Overall, these split Cas13b/dCas13b platforms expand the existing repertoire of the CRISPR and RNA regulation toolkit to achieve targeted manipulation of RNAs in native cellular environments with minimal functional disruption to these endogenous RNAs.
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Affiliation(s)
- Ying Xu
- Department of Chemistry, Case Western Reserve University, 2080 Adelbert Road, Cleveland, OH 44106, USA
| | - Na Tian
- Department of Chemistry, Case Western Reserve University, 2080 Adelbert Road, Cleveland, OH 44106, USA
| | - Huaxia Shi
- Department of Chemistry, Case Western Reserve University, 2080 Adelbert Road, Cleveland, OH 44106, USA
| | - Chenwei Zhou
- Department of Chemistry, Case Western Reserve University, 2080 Adelbert Road, Cleveland, OH 44106, USA
| | - Yufan Wang
- Department of Chemistry, Case Western Reserve University, 2080 Adelbert Road, Cleveland, OH 44106, USA
| | - Fu-Sen Liang
- Department of Chemistry, Case Western Reserve University, 2080 Adelbert Road, Cleveland, OH 44106, USA
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154
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Saeed S, Khan SU, Khan WU, Abdel-Maksoud MA, Mubarak AS, Mohammed MA, Kiani FA, Wahab A, Shah MW, Saleem MH. Genome Editing Technology: A New Frontier for the Treatment and Prevention of Cardiovascular Diseases. Curr Probl Cardiol 2023; 48:101692. [PMID: 36898595 DOI: 10.1016/j.cpcardiol.2023.101692] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Accepted: 03/02/2023] [Indexed: 03/11/2023]
Abstract
Over the past two decades, genome-editing technique has proven to be a robust editing method that revolutionizes the field of biomedicine. At the genetic level, it can be efficiently utilized to generate various disease-resistance models to elucidate the mechanism of human diseases. It also develops an outstanding tool and enables the generation of genetically modified organisms for the treatment and prevention of various diseases. The versatile and novel CRISPR/Cas9 system mitigates the challenges of various GETs such as ZFNs, and TALENs. For this reason, it has become a ground-breaking technology potentially employed to manipulate the desired gene of interest. Interestingly, this system has been broadly utilized due to its tremendous applications for treating and preventing tumors and various rare disorders; however, its applications for treating CVDs remain in infancy. More recently, two newly developed GETs, such as base editing and prime editing, have further broadened the accuracy range to treat CVDs under consideration. Furthermore, recently emerged CRISPR tools have been potentially applied in vivo and in vitro to treat CVDs. To the best of our knowledge, we strongly enlightened the applications of the CRISPR/Cas9 system that opened a new window in the field of cardiovascular research and, in detail, discussed the challenges and limitations of CVDs.
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Affiliation(s)
- Sumbul Saeed
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, P.R, China
| | - Shahid Ullah Khan
- Women Medical and Dental College, Khyber Medical University, Khyber Pakhtunkhwa, Pakistan
| | - Wasim Ullah Khan
- School of Materials Science and Engineering, Sun Yat-sen University, Guangzhou 510275, PR China.
| | - Mostafa A Abdel-Maksoud
- Botany and Microbiology Department, College of Science, King Saud University, Riyadh 11451, Saudi Arabia
| | - Ayman S Mubarak
- Botany and Microbiology Department, College of Science, King Saud University, Riyadh 11451, Saudi Arabia
| | - Mohammed Aufy Mohammed
- Department of Pharmaceutical Sciences, Division of Pharmacology and Toxicology, University of Vienna, Vienna, Austria
| | - Faisal Ayub Kiani
- Department of Clinical Sciences, Faculty of Veterinary Sciences, Bahauddin Zakariya University, Multan, 60800, Pakistan
| | - Abdul Wahab
- Department of Pharmacy, Kohat University of Science and Technology, Kohat, Khyber, Pakhtunkhwa, Pakistan
| | | | - Muhammad Hamzah Saleem
- Office of Academic Research, Office of VP for Research & Graduate Studies, Qatar University, Doha 2713, Qatar
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155
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Fujii T, Inoue N, Nobeyama T, Inoue J, Ogasawara S, Otani Y, Fujii S, Ito C, Fukunaga R. A simple, rapid, and efficient method for generating multigene-knockout culture cells by the CRISPR/Cas9 system. Genes Cells 2023; 28:390-397. [PMID: 36861495 DOI: 10.1111/gtc.13021] [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: 02/07/2023] [Revised: 02/24/2023] [Accepted: 02/25/2023] [Indexed: 03/03/2023]
Abstract
We evaluated the efficacy of simultaneous multiple-gene knockout in human culture cells. By simple co-transfection of HeLa cells with a mixture of pX330-based targeting plasmids together with a puromycin resistance plasmid, followed by transient selection of puromycin-resistant cells, Cas9/single-guide RNA (sgRNA)-transduced polyclonal cell populations were selected and grown. Western blot analyses revealed co-transfection of up to seven targeting plasmids for p38α, p38β, JNK1, JNK2, Mnk1, ERK1, and mLST8 genes, drastically reduced protein expression of these genes in the polyclonal population. Analyses of a randomly isolated group of 25 clones revealed knockout efficiencies for the seven targeted genes ranging between 68% and 100%, and in six clones (24%), all targeted genes were disrupted. Deep sequencing analyses of the individual target sites revealed that, in most cases, Cas9/sgRNA-induced nonhomologous end joining resulted in deletion or insertion of only a few base pairs at the break points. These results demonstrate that simple co-transfection-based simultaneous targeting offers an easy, rapid, and efficient method to generate multiplex gene-knockout cell lines.
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Affiliation(s)
- Toshihiro Fujii
- Department of Biochemistry, Faculty of Pharmacy, Osaka Medical and Pharmaceutical University, Osaka, Japan
| | - Naomi Inoue
- Department of Biochemistry, Faculty of Pharmacy, Osaka Medical and Pharmaceutical University, Osaka, Japan
| | - Takanobu Nobeyama
- Department of Biochemistry, Faculty of Pharmacy, Osaka Medical and Pharmaceutical University, Osaka, Japan
| | - Junko Inoue
- Department of Biochemistry, Faculty of Pharmacy, Osaka Medical and Pharmaceutical University, Osaka, Japan
| | - Shin Ogasawara
- Department of Biochemistry, Faculty of Pharmacy, Osaka Medical and Pharmaceutical University, Osaka, Japan
| | - Yuhei Otani
- Department of Biochemistry, Faculty of Pharmacy, Osaka Medical and Pharmaceutical University, Osaka, Japan
| | - Shinobu Fujii
- Department of Biochemistry, Faculty of Pharmacy, Osaka Medical and Pharmaceutical University, Osaka, Japan
| | - Chihiro Ito
- Department of Biochemistry, Faculty of Pharmacy, Osaka Medical and Pharmaceutical University, Osaka, Japan
| | - Rikiro Fukunaga
- Department of Biochemistry, Faculty of Pharmacy, Osaka Medical and Pharmaceutical University, Osaka, Japan
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156
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Han JY, Seo J, Choi Y, Im W, Ban JJ, Sung JJ. CRISPR-Cas9 mediated genome editing of Huntington's disease neurospheres. Mol Biol Rep 2023; 50:2127-2136. [PMID: 36550260 DOI: 10.1007/s11033-022-08175-6] [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: 04/26/2022] [Accepted: 12/06/2022] [Indexed: 12/24/2022]
Abstract
BACKGROUND Huntington's disease (HD) is a fatal genetic disease caused by polyglutamine aggregation encoded by an expanded CAG repeat in the huntingtin gene (HTT). In this study, we cultured neurospheres derived from R6/2 mice, a representative animal model of HD, as an in vitro model. GuideRNAs were designed to induce large deletion or frameshift indel mutation of CAG expansion. These gRNAs and Cas9 were delivered to the R6/2 neurospheres and disease-related phenotypes were observed. METHODS AND RESULTS Deletion or indel mutation of the CAG repeat was confirmed by PCR, T7E1 assay and sequencing of the edited neurospheres. Edited neurospheres showed decreased polyglutamine aggregation compared with control HD neurospheres. In the edited neurosphere, we confirmed the upregulation of peroxisome proliferator-activated receptor gamma coactivator-1 alpha (PGC-1α) and brain-derived neurotrophic factor (BDNF), whose reduced expressions are closely involved in the disease progression. In addition, flow cytometry result showed an increase in cell viability with an overall decrease in necrotic and apoptotic populations among edited R6/2 neurospheres. Additional siRNA experiments confirmed that the increased viability was decreased through inhibition of PGC-1α or BDNF. CONCLUSION Our study confirmed that CAG repeat of R6/2 mouse-derived neurospheres can be edited through CRISPR-Cas9. Editing of CAG repeat sequence decreases polyglutamine aggregation and cellular apoptosis of HD neurospheres, which may be related to the increased expressions of PGC-1α and BDNF. Our data provide the evidence that CRISPR-Cas9 mediated genome editing has therapeutic potential on HD neuronal cells.
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Affiliation(s)
- Ji Yun Han
- Department of Neurology, Seoul National University Hospital, Seoul National University College of Medicine, 101 Daehak-ro, Jongno-gu, Seoul, 110-744, South Korea
| | - Jaewoo Seo
- Department of Neurology, Seoul National University Hospital, Seoul National University College of Medicine, 101 Daehak-ro, Jongno-gu, Seoul, 110-744, South Korea
| | - Yoori Choi
- Biomedical Research Institute, Seoul National University Hospital, Seoul, South Korea.,Department of Nuclear Medicine, Seoul National University Hospital, Seoul, South Korea
| | - Wooseok Im
- Department of Obstetrics and Gynecology, Gangnam Severance Hospital, Yonsei University College of Medicine, Seoul, South Korea.,Institute of Women's Life Medical Science, Yonsei University College of Medicine, Seoul, South Korea
| | - Jae-Jun Ban
- Department of Neurology, Seoul National University Hospital, Seoul National University College of Medicine, 101 Daehak-ro, Jongno-gu, Seoul, 110-744, South Korea. .,Biomedical Research Institute, Seoul National University Hospital, Seoul, South Korea.
| | - Jung-Joon Sung
- Department of Neurology, Seoul National University Hospital, Seoul National University College of Medicine, 101 Daehak-ro, Jongno-gu, Seoul, 110-744, South Korea. .,Biomedical Research Institute, Seoul National University Hospital, Seoul, South Korea. .,Neuroscience Research Institute, Seoul National University College of Medicine, Seoul, South Korea.
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157
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Yang H, Eremeeva E, Abramov M, Jacquemyn M, Groaz E, Daelemans D, Herdewijn P. CRISPR-Cas9 recognition of enzymatically synthesized base-modified nucleic acids. Nucleic Acids Res 2023; 51:1501-1511. [PMID: 36611237 PMCID: PMC9976875 DOI: 10.1093/nar/gkac1147] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 11/09/2022] [Accepted: 11/17/2022] [Indexed: 01/09/2023] Open
Abstract
An enzymatic method has been successfully established enabling the generation of partially base-modified RNA (previously named RZA) constructs, in which all G residues were replaced by isomorphic fluorescent thienoguanosine (thG) analogs, as well as fully modified RZA featuring thG, 5-bromocytosine, 7-deazaadenine and 5-chlorouracil. The transcriptional efficiency of emissive fully modified RZA was found to benefit from the use of various T7 RNA polymerase variants. Moreover, dthG could be incorporated into PCR products by Taq DNA polymerase together with the other three base-modified nucleotides. Notably, the obtained RNA products containing thG as well as thG together with 5-bromocytosine could function as effectively as natural sgRNAs in an in vitro CRISPR-Cas9 cleavage assay. N1-Methylpseudouridine was also demonstrated to be a faithful non-canonical substitute of uridine to direct Cas9 nuclease cleavage when incorporated in sgRNA. The Cas9 inactivation by 7-deazapurines indicated the importance of the 7-nitrogen atom of purines in both sgRNA and PAM site for achieving efficient Cas9 cleavage. Additional aspects of this study are discussed in relation to the significance of sgRNA-protein and PAM--protein interactions that were not highlighted by the Cas9-sgRNA-DNA complex crystal structure. These findings could expand the impact and therapeutic value of CRISPR-Cas9 and other RNA-based technologies.
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Affiliation(s)
- Hui Yang
- KU Leuven, Department of Pharmaceutical and Pharmacological Sciences, Rega Institute for Medical Research, Medicinal Chemistry, Herestraat 49, Box 1041, 3000 Leuven, Belgium
| | - Elena Eremeeva
- KU Leuven, Department of Pharmaceutical and Pharmacological Sciences, Rega Institute for Medical Research, Medicinal Chemistry, Herestraat 49, Box 1041, 3000 Leuven, Belgium.,Queensland University of Technology, Centre for Agriculture and the Bioeconomy, Molecular Engineering Group, George Street 2, 4000 Brisbane, Queensland, Australia
| | - Mikhail Abramov
- KU Leuven, Department of Pharmaceutical and Pharmacological Sciences, Rega Institute for Medical Research, Medicinal Chemistry, Herestraat 49, Box 1041, 3000 Leuven, Belgium
| | - Maarten Jacquemyn
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, Herestraat 49, Box 1043, 3000 Leuven, Belgium
| | - Elisabetta Groaz
- KU Leuven, Department of Pharmaceutical and Pharmacological Sciences, Rega Institute for Medical Research, Medicinal Chemistry, Herestraat 49, Box 1041, 3000 Leuven, Belgium.,University of Padova, Department of Pharmaceutical and Pharmacological Sciences, Via Marzolo 5, 35131 Padova, Italy
| | - Dirk Daelemans
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, Herestraat 49, Box 1043, 3000 Leuven, Belgium
| | - Piet Herdewijn
- KU Leuven, Department of Pharmaceutical and Pharmacological Sciences, Rega Institute for Medical Research, Medicinal Chemistry, Herestraat 49, Box 1041, 3000 Leuven, Belgium
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158
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Therapeutic strategies for autism: targeting three levels of the central dogma of molecular biology. Transl Psychiatry 2023; 13:58. [PMID: 36792602 PMCID: PMC9931756 DOI: 10.1038/s41398-023-02356-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 02/01/2023] [Accepted: 02/03/2023] [Indexed: 02/17/2023] Open
Abstract
The past decade has yielded much success in the identification of risk genes for Autism Spectrum Disorder (ASD), with many studies implicating loss-of-function (LoF) mutations within these genes. Despite this, no significant clinical advances have been made so far in the development of therapeutics for ASD. Given the role of LoF mutations in ASD etiology, many of the therapeutics in development are designed to rescue the haploinsufficient effect of genes at the transcriptional, translational, and protein levels. This review will discuss the various therapeutic techniques being developed from each level of the central dogma with examples including: CRISPR activation (CRISPRa) and gene replacement at the DNA level, antisense oligonucleotides (ASOs) at the mRNA level, and small-molecule drugs at the protein level, followed by a review of current delivery methods for these therapeutics. Since central nervous system (CNS) penetrance is of utmost importance for ASD therapeutics, it is especially necessary to evaluate delivery methods that have higher efficiency in crossing the blood-brain barrier (BBB).
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159
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Siles L, Gaudó P, Pomares E. High-Efficiency CRISPR/Cas9-Mediated Correction of a Homozygous Mutation in Achromatopsia-Patient-Derived iPSCs. Int J Mol Sci 2023; 24:ijms24043655. [PMID: 36835061 PMCID: PMC9964936 DOI: 10.3390/ijms24043655] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Revised: 02/03/2023] [Accepted: 02/09/2023] [Indexed: 02/15/2023] Open
Abstract
Achromatopsia is an autosomal recessive disorder, in which cone photoreceptors undergo progressive degeneration, causing color blindness and poor visual acuity, among other significant eye affectations. It belongs to a group of inherited retinal dystrophies that currently have no treatment. Although functional improvements have been reported in several ongoing gene therapy studies, more efforts and research should be carried out to enhance their clinical application. In recent years, genome editing has arisen as one of the most promising tools for personalized medicine. In this study, we aimed to correct a homozygous PDE6C pathogenic variant in hiPSCs derived from a patient affected by achromatopsia through CRISPR/Cas9 and TALENs technologies. Here, we demonstrate high efficiency in gene editing by CRISPR/Cas9 but not with TALENs approximation. Despite a few of the edited clones displaying heterozygous on-target defects, the proportion of corrected clones with a potentially restored wild-type PDE6C protein was more than half of the total clones analyzed. In addition, none of them presented off-target aberrations. These results significantly contribute to advances in single-nucleotide gene editing and the development of future strategies for the treatment of achromatopsia.
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Affiliation(s)
- Laura Siles
- Fundació de Recerca de l’Institut de Microcirurgia Ocular, 08035 Barcelona, Spain
- Departament de Genètica, IMO Grupo Miranza, 08035 Barcelona, Spain
| | - Paula Gaudó
- Fundació de Recerca de l’Institut de Microcirurgia Ocular, 08035 Barcelona, Spain
- Departament de Genètica, IMO Grupo Miranza, 08035 Barcelona, Spain
| | - Esther Pomares
- Fundació de Recerca de l’Institut de Microcirurgia Ocular, 08035 Barcelona, Spain
- Departament de Genètica, IMO Grupo Miranza, 08035 Barcelona, Spain
- Correspondence:
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160
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Godbout K, Tremblay JP. Prime Editing for Human Gene Therapy: Where Are We Now? Cells 2023; 12:cells12040536. [PMID: 36831203 PMCID: PMC9954691 DOI: 10.3390/cells12040536] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Revised: 02/06/2023] [Accepted: 02/06/2023] [Indexed: 02/10/2023] Open
Abstract
Gene therapy holds tremendous potential in the treatment of inherited diseases. Unlike traditional medicines, which only treat the symptoms, gene therapy has the potential to cure the disease by addressing the root of the problem: genetic mutations. The discovery of CRISPR/Cas9 in 2012 paved the way for the development of those therapies. Improvement of this system led to the recent development of an outstanding technology called prime editing. This system can introduce targeted insertions, deletions, and all 12 possible base-to-base conversions in the human genome. Since the first publication on prime editing in 2019, groups all around the world have worked on this promising technology to develop a treatment for genetic diseases. To date, prime editing has been attempted in preclinical studies for liver, eye, skin, muscular, and neurodegenerative hereditary diseases, in addition to cystic fibrosis, beta-thalassemia, X-linked severe combined immunodeficiency, and cancer. In this review, we portrayed where we are now on prime editing for human gene therapy and outlined the best strategies for correcting pathogenic mutations by prime editing.
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Affiliation(s)
- Kelly Godbout
- Centre de Recherche du CHU de Québec-Université Laval, Quebec City, QC G1V 4G2, Canada
- Department of Molecular Medicine, Faculty of Medicine, Laval University, Quebec City, QC G1V 0A6, Canada
| | - Jacques P. Tremblay
- Centre de Recherche du CHU de Québec-Université Laval, Quebec City, QC G1V 4G2, Canada
- Department of Molecular Medicine, Faculty of Medicine, Laval University, Quebec City, QC G1V 0A6, Canada
- Correspondence:
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161
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Kamran M, Bhattacharjee R, Das S, Mukherjee S, Ali N. The paradigm of intracellular parasite survival and drug resistance in leishmanial parasite through genome plasticity and epigenetics: Perception and future perspective. Front Cell Infect Microbiol 2023; 13:1001973. [PMID: 36814446 PMCID: PMC9939536 DOI: 10.3389/fcimb.2023.1001973] [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: 07/24/2022] [Accepted: 01/16/2023] [Indexed: 02/09/2023] Open
Abstract
Leishmania is an intracellular, zoonotic, kinetoplastid eukaryote with more than 1.2 million cases all over the world. The leishmanial chromosomes are divided into polymorphic chromosomal ends, conserved central domains, and antigen-encoding genes found in telomere-proximal regions. The genome flexibility of chromosomal ends of the leishmanial parasite is known to cause drug resistance and intracellular survival through the evasion of host defense mechanisms. Therefore, in this review, we discuss the plasticity of Leishmania genome organization which is the primary cause of drug resistance and parasite survival. Moreover, we have not only elucidated the causes of such genome plasticity which includes aneuploidy, epigenetic factors, copy number variation (CNV), and post-translation modification (PTM) but also highlighted their impact on drug resistance and parasite survival.
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Affiliation(s)
| | | | - Sonali Das
- Infectious Diseases and Immunology Division, Indian Institute of Chemical Biology, Kolkata, West Bengal, India
| | - Sohitri Mukherjee
- Infectious Diseases and Immunology Division, Indian Institute of Chemical Biology, Kolkata, West Bengal, India
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162
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Lu Y, Wu F, Xu Y, He C, Luo S, Sun X. Triple functional mild photothermal improves gene editing of PD-L1 for enhanced antitumor immunity. J Control Release 2023; 354:57-68. [PMID: 36581262 DOI: 10.1016/j.jconrel.2022.12.052] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2022] [Revised: 12/23/2022] [Accepted: 12/25/2022] [Indexed: 12/31/2022]
Abstract
Traditional photothermal therapy ablates tumor cells by a high temperature (> 50 °C). Although it has shown good anti-tumor effect in animal models, the potential damages to healthy tissues and the unnecessary inflammatory reactions caused by the high temperature have hindered the clinical transitions of traditional photothermal therapy. In this study, we used polydopamine (PDA) as a mild photothermal material and control the maximum temperature below 45 °C, which not only avoided the side effects caused by a high temperature, but also ablated a fraction of tumor cells and produced tumor antigens. Meanwhile, the near-infrared (NIR) light also served as a "switch" to trigger the release of CRISPR/Cas9 RNP from Fe3O4 nanoparticles (Fe3O4 NPs) after their accumulation to tumor sites via magnetic targeting. The triple functional mild photothermal therapy achieved significant PD-L1 gene knockout efficiency in the tumor-bearing mice, reversed the condition of immunosuppression in the tumor microenvironment, led to a higher level of anti-tumor immune responses and effectively inhibited the growth of melanoma. We anticipate that this triple functional mild photothermal therapy would provide a potential new approach for the treatment of malignant tumors.
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Affiliation(s)
- Yi Lu
- Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry and Sichuan Province, Sichuan Engineering Laboratory for Plant-Sourced Drug and Sichuan Research Center for Drug Precision Industrial Technology, West China School of Pharmacy, Sichuan University, Chengdu 610041, China
| | - Fuhua Wu
- Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry and Sichuan Province, Sichuan Engineering Laboratory for Plant-Sourced Drug and Sichuan Research Center for Drug Precision Industrial Technology, West China School of Pharmacy, Sichuan University, Chengdu 610041, China
| | - Yanhua Xu
- Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry and Sichuan Province, Sichuan Engineering Laboratory for Plant-Sourced Drug and Sichuan Research Center for Drug Precision Industrial Technology, West China School of Pharmacy, Sichuan University, Chengdu 610041, China
| | - Chunting He
- Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry and Sichuan Province, Sichuan Engineering Laboratory for Plant-Sourced Drug and Sichuan Research Center for Drug Precision Industrial Technology, West China School of Pharmacy, Sichuan University, Chengdu 610041, China
| | - Shuang Luo
- Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry and Sichuan Province, Sichuan Engineering Laboratory for Plant-Sourced Drug and Sichuan Research Center for Drug Precision Industrial Technology, West China School of Pharmacy, Sichuan University, Chengdu 610041, China
| | - Xun Sun
- Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry and Sichuan Province, Sichuan Engineering Laboratory for Plant-Sourced Drug and Sichuan Research Center for Drug Precision Industrial Technology, West China School of Pharmacy, Sichuan University, Chengdu 610041, China.
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163
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Wang Y, Wang X, Xie R, Burger JC, Tong Y, Gong S. Overcoming the Blood-Brain Barrier for Gene Therapy via Systemic Administration of GSH-Responsive Silica Nanocapsules. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2023; 35:e2208018. [PMID: 36445243 DOI: 10.1002/adma.202208018] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 10/21/2022] [Indexed: 06/16/2023]
Abstract
CRISPR genome editing can potentially treat the root causes of many genetic diseases, including central nervous system (CNS) disorders. However, the promise of brain-targeted therapeutic genome editing relies on the efficient delivery of biologics bypassing the blood-brain barrier (BBB), which represents a major challenge in the development of CRISPR therapeutics. We created and screened a library of glutathione (GSH)-responsive silica nanocapsules (SNCs) for brain targeted delivery of biologics via systemic administration. In vivo studies demonstrate that systemically delivered SNCs conjugated with glucose and rabies virus glycoprotein peptide under glycemic control can efficiently bypass the intact BBB, enabling brain-wide delivery of various biologics including CRISPR genome editors targeting different genes in both Ai14 reporter mice and wild-type mice. In particular, up to 28% neuron editing via systemic delivery of Cre mRNA in Ai14 mice, up to 6.1% amyloid precursor protein (App) gene editing (resulting in 19.1% reduction in the expression level of intact APP), and up to 3.9% tyrosine hydroxylase (Th) gene editing (resulting in 30.3% reduction in the expression level of TH) in wild-type mice are observed. This versatile SNC nanoplatform may offer a novel strategy for the treatment of CNS disorders including Alzheimer's, Parkinson's, and Huntington's disease.
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Affiliation(s)
- Yuyuan Wang
- Department of Ophthalmology and Visual Sciences, University of Wisconsin-Madison, Madison, WI, 53705, USA
- Department of Biomedical Engineering, University of Wisconsin-Madison, Madison, WI, 53706, USA
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI, 53715, USA
| | - Xiuxiu Wang
- Department of Ophthalmology and Visual Sciences, University of Wisconsin-Madison, Madison, WI, 53705, USA
- Department of Biomedical Engineering, University of Wisconsin-Madison, Madison, WI, 53706, USA
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI, 53715, USA
| | - Ruosen Xie
- Department of Ophthalmology and Visual Sciences, University of Wisconsin-Madison, Madison, WI, 53705, USA
- Department of Biomedical Engineering, University of Wisconsin-Madison, Madison, WI, 53706, USA
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI, 53715, USA
| | - Jacobus C Burger
- Department of Biomedical Engineering, University of Wisconsin-Madison, Madison, WI, 53706, USA
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI, 53715, USA
| | - Yao Tong
- Department of Biomedical Engineering, University of Wisconsin-Madison, Madison, WI, 53706, USA
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI, 53715, USA
| | - Shaoqin Gong
- Department of Ophthalmology and Visual Sciences, University of Wisconsin-Madison, Madison, WI, 53705, USA
- Department of Biomedical Engineering, University of Wisconsin-Madison, Madison, WI, 53706, USA
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI, 53715, USA
- Department of Materials Science and Engineering, University of Wisconsin-Madison, Madison, WI, 53706, USA
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
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164
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Wang H, Wang Y, Luo Z, Lin X, Liu M, Wu F, Shao H, Zhang W. Advances in Off-Target Detection for CRISPR-Based Genome Editing. Hum Gene Ther 2023; 34:112-128. [PMID: 36453226 DOI: 10.1089/hum.2022.198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
The CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats)-based genome editing system exhibits marked potential for both gene editing and gene therapy, and its continuous improvement contributes to its great clinical potential. However, the largest hindrance to its application in clinical practice is the presence of off-target effects (OTEs). Thus, in addition to continuous optimization of the CRISPR system to reduce and eventually eliminate OTEs, further development of unbiased genome-wide detection of OTEs is key for its successful clinical application. This article summarizes detection strategies for OTEs of different CRISPR systems, to provide detailed guidance for the detection of OTEs in CRISPR-based genome editing.
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Affiliation(s)
- Haozheng Wang
- Guangdong Province Key Laboratory of Biotechnology Drug Candidates, Guangdong Pharmaceutical University, Guangzhou, People's Republic of China.,School of Biosciences and Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou, People's Republic of China; and.,Department of Pharmacy, Meizhou People's Hospital, Meizhou, People's Republic of China
| | - Yangmin Wang
- Guangdong Province Key Laboratory of Biotechnology Drug Candidates, Guangdong Pharmaceutical University, Guangzhou, People's Republic of China.,School of Biosciences and Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou, People's Republic of China; and
| | - Zhongtao Luo
- Guangdong Province Key Laboratory of Biotechnology Drug Candidates, Guangdong Pharmaceutical University, Guangzhou, People's Republic of China.,School of Biosciences and Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou, People's Republic of China; and
| | - Xinjian Lin
- Guangdong Province Key Laboratory of Biotechnology Drug Candidates, Guangdong Pharmaceutical University, Guangzhou, People's Republic of China.,School of Biosciences and Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou, People's Republic of China; and
| | - Meilin Liu
- Guangdong Province Key Laboratory of Biotechnology Drug Candidates, Guangdong Pharmaceutical University, Guangzhou, People's Republic of China.,School of Biosciences and Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou, People's Republic of China; and
| | - Fenglin Wu
- Guangdong Province Key Laboratory of Biotechnology Drug Candidates, Guangdong Pharmaceutical University, Guangzhou, People's Republic of China.,School of Biosciences and Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou, People's Republic of China; and
| | - Hongwei Shao
- Guangdong Province Key Laboratory of Biotechnology Drug Candidates, Guangdong Pharmaceutical University, Guangzhou, People's Republic of China.,School of Biosciences and Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou, People's Republic of China; and
| | - Wenfeng Zhang
- Guangdong Province Key Laboratory of Biotechnology Drug Candidates, Guangdong Pharmaceutical University, Guangzhou, People's Republic of China.,School of Biosciences and Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou, People's Republic of China; and
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165
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Kim S, Jeong YK, Cho CS, Lee S, Sohn CH, Kim JH, Jeong Y, Jo DH, Bae S, Lee H. Enhancement of Gene Editing and Base Editing with Therapeutic Ribonucleoproteins through In Vivo Delivery Based on Absorptive Silica Nanoconstruct. Adv Healthc Mater 2023; 12:e2201825. [PMID: 36326169 DOI: 10.1002/adhm.202201825] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Revised: 10/31/2022] [Indexed: 11/06/2022]
Abstract
Key to the widespread and secure application of genome editing tools is the safe and effective delivery of multiple components of ribonucleoproteins (RNPs) into single cells, which remains a biological barrier to their clinical application. To overcome this issue, a robust RNP delivery platform based on a biocompatible sponge-like silica nanoconstruct (SN) for storing and directly delivering therapeutic RNPs, including Cas9 nuclease RNP (Cas9-RNP) and base editor RNP (BE-RNP) is designed. Compared with commercialized material such as lipid-based methods, up to 50-fold gene deletion and 10-fold base substitution efficiency is obtained with a low off-target efficiency by targeting various cells and genes. In particular, gene correction is successfully induced by SN-based delivery through intravenous injection in an in vivo solid-tumor model and through subretinal injection in mouse eye. Moreover, because of its low toxicity and high biodegradability, SN has negligible effect on cellular function of organs. As the engineered SN can overcome practical challenges associated with therapeutic RNP application, it is strongly expected this platform to be a modular RNPs delivery system, facilitating in vivo gene deletion and editing.
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Affiliation(s)
- Seongchan Kim
- Biomaterials Research Center, Biomedical Research Institute, Korea Institute of Science and Technology (KIST), 02792, Seoul, Republic of Korea
| | - You Kyeong Jeong
- Medical Research Center of Genomic Medicine Institute, Seoul National University College of Medicine, 03080, Seoul, Republic of Korea
| | - Chang Sik Cho
- Fight Against Angiogenesis-Related Blindness (FARB) Laboratory, Biomedical Research Institute, Seoul National University Hospital, 03080, Seoul, Republic of Korea
| | - SeokHoon Lee
- Department of Biomedical Sciences, Seoul National University College of Medicine, 03080, Seoul, Republic of Korea
| | - Chang Ho Sohn
- Center for Nanomedicine, Institute for Basic Science, Graduate Program in Nanobiomedical Engineering, Advanced Science Institute, Yonsei University, 03722, Seoul, Republic of Korea
| | - Jeong Hun Kim
- Fight Against Angiogenesis-Related Blindness (FARB) Laboratory, Biomedical Research Institute, Seoul National University Hospital, 03080, Seoul, Republic of Korea.,Department of Ophthalmology and Department of Biomedical Sciences, Seoul National University College of Medicine, 03080, Seoul, Republic of Korea
| | - Youngdo Jeong
- Biomaterials Research Center, Biomedical Research Institute, Korea Institute of Science and Technology (KIST), 02792, Seoul, Republic of Korea
| | - Dong Hyun Jo
- Department of Anatomy and Cell Biology, Seoul National University College of Medicine, 03080, Seoul, Republic of Korea
| | - Sangsu Bae
- Medical Research Center of Genomic Medicine Institute, Seoul National University College of Medicine, 03080, Seoul, Republic of Korea.,Department of Biomedical Sciences, Seoul National University College of Medicine, 03080, Seoul, Republic of Korea
| | - Hyojin Lee
- Biomaterials Research Center, Biomedical Research Institute, Korea Institute of Science and Technology (KIST), 02792, Seoul, Republic of Korea.,Division of Bio-Medical Science & Technology, KIST School - Korea University of Science and Technology (UST), 02792, Seoul, Republic of Korea
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166
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Konu M, Kulmuni J, Viljakainen L. Genetic modification of the ant Lasius niger using CRISPR-Cas9 technology. INSECT MOLECULAR BIOLOGY 2023; 32:11-25. [PMID: 36030521 PMCID: PMC10087202 DOI: 10.1111/imb.12809] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Accepted: 08/22/2022] [Indexed: 06/15/2023]
Abstract
CRISPR-Cas9 has become one of the most prominent gene editing tools available and it has been utilized in various organisms from bacteria to fungi, plants, and animals. In this study, we developed a CRISPR-Cas9 protocol for the black garden ant Lasius niger, a common and easily available study species for lab and field experiments. To create indel mutations using CRISPR-Cas9 in L. niger, we targeted three different locations in a well-studied eye pigmentation gene cinnabar, generating several mutations that disrupt the ommochrome biosynthesis pathway and result in the lack of the pigment and therefore, abnormal eye coloration in adult workers. We also developed a protocol to collect L. niger eggs, inject them with CRISPR-Cas9 construct, and rear the eggs into mature adult workers with the assistance of nursing workers. We demonstrated for the first time in L. niger that CRISPR-Cas9 is an excellent tool to create targeted mutations for this species. Our protocol can be referred to when developing similar studies for other species of ants and eusocial insects.
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Affiliation(s)
- Mauno Konu
- Ecology and Genetics Research UnitUniversity of OuluOuluFinland
| | - Jonna Kulmuni
- Organismal and Evolutionary Research ProgrammeUniversity of HelsinkiHelsinkiFinland
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167
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Sheikh Beig Goharrizi MA, Ghodsi S, Memarjafari MR. Implications of CRISPR-Cas9 Genome Editing Methods in Atherosclerotic Cardiovascular Diseases. Curr Probl Cardiol 2023; 48:101603. [PMID: 36682390 DOI: 10.1016/j.cpcardiol.2023.101603] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Accepted: 01/17/2023] [Indexed: 01/21/2023]
Abstract
Today, new methods have been developed to treat or modify the natural course of cardiovascular diseases (CVDs), including atherosclerosis, by the clustered regularly interspaced short palindromic repeats-CRISPR-associated protein 9 (CRISPR-Cas9) system. Genome-editing tools are CRISPR-related palindromic short iteration systems such as CRISPR-Cas9, a valuable technology for achieving somatic and germinal genomic manipulation in model cells and organisms for various applications, including the creation of deletion alleles. Mutations in genomic deoxyribonucleic acid and new genes' placement have emerged. Based on World Health Organization fact sheets, 17.9 million people die from CVDs each year, an estimated 32% of all deaths worldwide. 85% of all CVD deaths are due to acute coronary events and strokes. This review discusses the applications of CRISPR-Cas9 technology throughout atherosclerotic disease research and the prospects for future in vivo genome editing therapies. We also describe several limitations that must be considered to achieve the full scientific and therapeutic potential of cardiovascular genome editing in the treatment of atherosclerosis.
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Affiliation(s)
| | - Saeed Ghodsi
- Department of Cardiology, Sina Hospital, Tehran University of Medical Sciences, Tehran, Iran
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168
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Sandoz PA, Denhardt-Eriksson RA, Abrami L, Abriata LA, Spreemann G, Maclachlan C, Ho S, Kunz B, Hess K, Knott G, S Mesquita F, Hatzimanikatis V, van der Goot FG. Dynamics of CLIMP-63 S-acylation control ER morphology. Nat Commun 2023; 14:264. [PMID: 36650170 PMCID: PMC9844198 DOI: 10.1038/s41467-023-35921-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Accepted: 01/06/2023] [Indexed: 01/19/2023] Open
Abstract
The complex architecture of the endoplasmic reticulum (ER) comprises distinct dynamic features, many at the nanoscale, that enable the coexistence of the nuclear envelope, regions of dense sheets and a branched tubular network that spans the cytoplasm. A key player in the formation of ER sheets is cytoskeleton-linking membrane protein 63 (CLIMP-63). The mechanisms by which CLIMP-63 coordinates ER structure remain elusive. Here, we address the impact of S-acylation, a reversible post-translational lipid modification, on CLIMP-63 cellular distribution and function. Combining native mass-spectrometry, with kinetic analysis of acylation and deacylation, and data-driven mathematical modelling, we obtain in-depth understanding of the CLIMP-63 life cycle. In the ER, it assembles into trimeric units. These occasionally exit the ER to reach the plasma membrane. However, the majority undergoes S-acylation by ZDHHC6 in the ER where they further assemble into highly stable super-complexes. Using super-resolution microscopy and focused ion beam electron microscopy, we show that CLIMP-63 acylation-deacylation controls the abundance and fenestration of ER sheets. Overall, this study uncovers a dynamic lipid post-translational regulation of ER architecture.
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Affiliation(s)
- Patrick A Sandoz
- Global Health Institute, School of Life Sciences, EPFL, Lausanne, Switzerland
| | | | - Laurence Abrami
- Global Health Institute, School of Life Sciences, EPFL, Lausanne, Switzerland
| | - Luciano A Abriata
- Laboratory for Biomolecular Modelling, Institute of Bioengineering, EPFL and Swiss Institute of Bioinformatics, Lausanne, Switzerland.,Protein Production and Structure Core Facility, School of Life Sciences, EPFL, Lausanne, Switzerland
| | | | | | - Sylvia Ho
- Global Health Institute, School of Life Sciences, EPFL, Lausanne, Switzerland
| | - Béatrice Kunz
- Global Health Institute, School of Life Sciences, EPFL, Lausanne, Switzerland
| | - Kathryn Hess
- Brain Mind Institute, EPFL, Lausanne, Switzerland
| | - Graham Knott
- BioEM Facility, School of Life Sciences, EPFL, Lausanne, Switzerland
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169
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Das J, Kumar S, Mishra DC, Chaturvedi KK, Paul RK, Kairi A. Machine learning in the estimation of CRISPR-Cas9 cleavage sites for plant system. Front Genet 2023; 13:1085332. [PMID: 36699447 PMCID: PMC9868961 DOI: 10.3389/fgene.2022.1085332] [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: 10/31/2022] [Accepted: 12/12/2022] [Indexed: 01/12/2023] Open
Abstract
CRISPR-Cas9 system is one of the recent most used genome editing techniques. Despite having a high capacity to alter the precise target genes and genomic regions that the planned guide RNA (or sgRNA) complements, the off-target effect still exists. But there are already machine learning algorithms for people, animals, and a few plant species. In this paper, an effort has been made to create models based on three machine learning-based techniques [namely, artificial neural networks (ANN), support vector machines (SVM), and random forests (RF)] for the prediction of the CRISPR-Cas9 cleavage sites that will be cleaved by a particular sgRNA. The plant dataset was the sole source of inspiration for all of these machine learning-based algorithms. 70% of the on-target and off-target dataset of various plant species that was gathered was used to train the models. The remaining 30% of the data set was used to evaluate the model's performance using a variety of evaluation metrics, including specificity, sensitivity, accuracy, precision, F1 score, F2 score, and AUC. Based on the aforementioned machine learning techniques, eleven models in all were developed. Comparative analysis of these produced models suggests that the model based on the random forest technique performs better. The accuracy of the Random Forest model is 96.27%, while the AUC value was found to be 99.21%. The SVM-Linear, SVM-Polynomial, SVM-Gaussian, and SVM-Sigmoid models were trained, making a total of six ANN-based models (ANN1-Logistic, ANN1-Tanh, ANN1-ReLU, ANN2-Logistic, ANN2-Tanh, and ANN-ReLU) and Support Vector Machine models (SVM-Linear, SVM-Polynomial, SVM-Gaussian However, the overall performance of Random Forest is better among all other ML techniques. ANN1-ReLU and SVM-Linear model performance were shown to be better among Artificial Neural Network and Support Vector Machine-based models, respectively.
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Affiliation(s)
- Jutan Das
- ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Sanjeev Kumar
- ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India,*Correspondence: Sanjeev Kumar,
| | | | | | - Ranjit Kumar Paul
- ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Amit Kairi
- ICAR-Indian Agricultural Research Institute, New Delhi, India
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170
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Progresses, Challenges, and Prospects of CRISPR/Cas9 Gene-Editing in Glioma Studies. Cancers (Basel) 2023; 15:cancers15020396. [PMID: 36672345 PMCID: PMC9856991 DOI: 10.3390/cancers15020396] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2022] [Revised: 12/19/2022] [Accepted: 12/28/2022] [Indexed: 01/11/2023] Open
Abstract
Glioma refers to a tumor that is derived from brain glial stem cells or progenitor cells and is the most common primary intracranial tumor. Due to its complex cellular components, as well as the aggressiveness and specificity of the pathogenic site of glioma, most patients with malignant glioma have poor prognoses following surgeries, radiotherapies, and chemotherapies. In recent years, an increasing amount of research has focused on the use of CRISPR/Cas9 gene-editing technology in the treatment of glioma. As an emerging gene-editing technology, CRISPR/Cas9 utilizes the expression of certain functional proteins to repair tissues or treat gene-deficient diseases and could be applied to immunotherapies through the expression of antigens, antibodies, or receptors. In addition, some research also utilized CRISPR/Cas9 to establish tumor models so as to study tumor pathogenesis and screen tumor prognostic targets. This paper mainly discusses the roles of CRISPR/Cas9 in the treatment of glioma patients, the exploration of the pathogenesis of neuroglioma, and the screening targets for clinical prognosis. This paper also raises the future research prospects of CRISPR/Cas9 in glioma, as well as the opportunities and challenges that it will face in clinical treatment in the future.
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171
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Functional Analysis of Variants in BRCA1 Using CRISPR Base Editors. Methods Mol Biol 2023; 2606:73-85. [PMID: 36592309 DOI: 10.1007/978-1-0716-2879-9_7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
To date, methods such as fluorescent reporter assays, embryonic stem cell viability assays, and therapeutic drug-based sensitivity assays have been used to evaluate the function of the variants of uncertain significance (VUS) of the BRCA genes. However, these methods have limitations as they are associated with overexpression and do not apply to post-transcriptional regulation. Therefore, there are several VUS whose functions are unclear. Recently, we devised a new way to assess the functionality of variants in BRCA1 via a CRISPR-mediated base editor to overcome these limitations. We precisely introduced the target nucleotide substitution in living cells and identified variants whose functions were not defined. Here, we describe the methods for the functional appraisal of BRCA1 variants using CRISPR-based base editors.
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172
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Song B, Bae S. Introduction and Perspectives of DNA Base Editors. Methods Mol Biol 2023; 2606:3-11. [PMID: 36592303 DOI: 10.1007/978-1-0716-2879-9_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
DNA base editors, one of the CRISPR-based genome editing tools, can induce targeted point mutations at desired sites. Their superiority is based on the fact that they can perform efficient and precise gene editing without generating a DNA double-strand break (DSB) or requiring a donor DNA template. Since they were first developed, significant efforts have been made to improve DNA base editors in order to overcome problems such as off-target edits on DNA/RNA and bystander mutations in editing windows. Here, we provide an overview of DNA base editors with a summary about the history of development of DNA base editors and report on efforts to improve them.
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Affiliation(s)
- Beomjong Song
- Medical Research Center Organization: Seoul National University College of Medicine, Seoul, Republic of Korea.
| | - Sangsu Bae
- Medical Research Center Organization: Seoul National University College of Medicine, Seoul, Republic of Korea.,Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, Republic of Korea.,Department of Biochemistry and Molecular Biology, Seoul National University College of Medicine, Seoul, Republic of Korea
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173
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Li Y, Lian D, Wang J, Zhao Y, Li Y, Liu G, Wu S, Deng S, Du X, Lian Z. MDM2 antagonists promote CRISPR/Cas9-mediated precise genome editing in sheep primary cells. MOLECULAR THERAPY. NUCLEIC ACIDS 2023; 31:309-323. [PMID: 36726409 PMCID: PMC9883270 DOI: 10.1016/j.omtn.2022.12.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/02/2021] [Accepted: 12/31/2022] [Indexed: 01/04/2023]
Abstract
CRISPR-Cas9-mediated genome editing in sheep is of great use in both agricultural and biomedical applications. While targeted gene knockout by CRISPR-Cas9 through non-homologous end joining (NHEJ) has worked efficiently, the knockin efficiency via homology-directed repair (HDR) remains lower, which severely hampers the application of precise genome editing in sheep. Here, in sheep fetal fibroblasts (SFFs), we optimized several key parameters that affect HDR, including homology arm (HA) length and the amount of double-stranded DNA (dsDNA) repair template; we also observed synchronization of SFFs in G2/M phase could increase HDR efficiency. Besides, we identified three potent small molecules, RITA, Nutlin3, and CTX1, inhibitors of p53-MDM2 interaction, that caused activation of the p53 pathway, resulting in distinct G2/M cell-cycle arrest in response to DNA damage and improved CRISPR-Cas9-mediated HDR efficiency by 1.43- to 4.28-fold in SFFs. Furthermore, we demonstrated that genetic knockout of p53 could inhibit HDR in SFFs by suppressing the expression of several key factors involved in the HDR pathway, such as BRCA1 and RAD51. Overall, this study offers an optimized strategy for the usage of dsDNA repair template, more importantly, the application of MDM2 antagonists provides a simple and efficient strategy to promote CRISPR/Cas9-mediated precise genome editing in sheep primary cells.
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Affiliation(s)
- Yan Li
- Beijing Key Laboratory for Animal Genetic Improvement, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China,State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, China,Laboratory Animal Center of the Academy of Military Medical Sciences, Beijing 100071, China,These authors contributed equally
| | - Di Lian
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, China,These authors contributed equally
| | - Jiahao Wang
- Beijing Key Laboratory for Animal Genetic Improvement, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China,Department of Biomedical Engineering, College of Future Technology, Peking University, Beijing 100871, China,These authors contributed equally
| | - Yue Zhao
- Beijing Key Laboratory for Animal Genetic Improvement, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Yao Li
- Beijing Key Laboratory for Animal Genetic Improvement, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Guoshi Liu
- Beijing Key Laboratory for Animal Genetic Improvement, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Sen Wu
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Shoulong Deng
- NHC Key Laboratory of Human Disease Comparative Medicine, Institute of Laboratory Animal Sciences, Chinese Academy of Medical Sciences and Comparative Medicine Center, Peking Union Medical College, Beijing 100021, China,Corresponding author: Shoulong Deng, NHC Key Laboratory of Human Disease Comparative Medicine, Institute of Laboratory Animal Sciences, Chinese Academy of Medical Sciences and Comparative Medicine Center, Peking Union Medical College, 5 Panjiayuannanli, Chaoyang District, Beijing 100021, China.
| | - Xuguang Du
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, China,Corresponding author: Xuguang Du, State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, China.
| | - Zhengxing Lian
- Beijing Key Laboratory for Animal Genetic Improvement, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China,Corresponding author: Zhengxing Lian, Beijing Key Laboratory for Animal Genetic Improvement, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, 2 Mingyuanxilu, Haidian District, Beijing 100193, China. .
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174
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Isola G. Prospective Advances in Genome Editing Investigation. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2023; 1396:301-313. [DOI: 10.1007/978-981-19-5642-3_19] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
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175
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Efficiency of CRISPR-Cas9 genetic engineering in Escherichia coli BL21 is impaired by lack of Lon protease. J Microbiol Methods 2023; 204:106648. [PMID: 36470413 DOI: 10.1016/j.mimet.2022.106648] [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: 10/24/2022] [Revised: 12/01/2022] [Accepted: 12/01/2022] [Indexed: 12/11/2022]
Abstract
The efficiency with which E.coli BL21 can be modified using CRISPR-Cas9 genetic engineering is several orders of magnitude lower than that of E. coli W3110. We show that the lack of Lon protease is responsible, and demonstrate that restoration of the Lon protease or knock-out of sulA improves CRISPR-Cas9 engineering efficiency of BL21 to levels comparable to E. coli W3110.
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176
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Dreismann AK, Hallam TM, Tam LC, Nguyen CV, Hughes JP, Ellis S, Harris CL. Gene targeting as a therapeutic avenue in diseases mediated by the complement alternative pathway. Immunol Rev 2023; 313:402-419. [PMID: 36369963 PMCID: PMC10099504 DOI: 10.1111/imr.13149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
The complement alternative pathway (AP) is implicated in numerous diseases affecting many organs, ranging from the rare hematological disease paroxysmal nocturnal hemoglobinuria (PNH), to the common blinding disease age-related macular degeneration (AMD). Critically, the AP amplifies any activating trigger driving a downstream inflammatory response; thus, components of the pathway have become targets for drugs of varying modality. Recent validation from clinical trials using drug modalities such as inhibitory antibodies has paved the path for gene targeting of the AP or downstream effectors. Gene targeting in the complement field currently focuses on supplementation or suppression of complement regulators in AMD and PNH, largely because the eye and liver are highly amenable to drug delivery through local (eye) or systemic (liver) routes. Targeting the liver could facilitate treatment of numerous diseases as this organ generates most of the systemic complement pool. This review explains key concepts of RNA and DNA targeting and discusses assets in clinical development for the treatment of diseases driven by the alternative pathway, including the RNA-targeting therapeutics ALN-CC5, ARO-C3, and IONIS-FB-LRX, and the gene therapies GT005 and HMR59. These therapies are but the spearhead of potential drug candidates that might revolutionize the field in coming years.
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177
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Visser B, Le Lann C, Hahn DA, Lammers M, Nieberding CM, Alborn HT, Enriquez T, Scheifler M, Harvey JA, Ellers J. Many parasitoids lack adult fat accumulation, despite fatty acid synthesis: A discussion of concepts and considerations for future research. CURRENT RESEARCH IN INSECT SCIENCE 2023; 3:100055. [PMID: 37124650 PMCID: PMC10139962 DOI: 10.1016/j.cris.2023.100055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Revised: 03/27/2023] [Accepted: 03/28/2023] [Indexed: 05/03/2023]
Abstract
Fat reserves, specifically the accumulation of triacylglycerols, are a major energy source and play a key role for life histories. Fat accumulation is a conserved metabolic pattern across most insects, yet in most parasitoid species adults do not gain fat mass, even when nutrients are readily available and provided ad libitum. This extraordinary physiological phenotype has evolved repeatedly in phylogenetically dispersed parasitoid species. This poses a conundrum because it could lead to significant constraints on energy allocation toward key adult functions such as survival and reproduction. Recent work on the underlying genetic and biochemical mechanisms has spurred a debate on fat accumulation versus fat production, because of incongruent interpretation of results obtained using different methodologies. This debate is in part due to semantics, highlighting the need for a synthetic perspective on fat accumulation that reconciles previous debates and provides new insights and terminology. In this paper, we propose updated, unambiguous terminology for future research in the field, including "fatty acid synthesis" and "lack of adult fat accumulation", and describe the distinct metabolic pathways involved in the complex process of lipogenesis. We then discuss the benefits and drawbacks of the main methods available to measure fatty acid synthesis and adult fat accumulation. Most importantly, gravimetric/colorimetric and isotope tracking methods give complementary information, provided that they are applied with appropriate controls and interpreted correctly. We also compiled a comprehensive list of fat accumulation studies performed during the last 25 years. We present avenues for future research that combine chemistry, ecology, and evolution into an integrative approach, which we think is needed to understand the dynamics of fat accumulation in parasitoids.
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Affiliation(s)
- Bertanne Visser
- Evolution and Ecophysiology Group, Department of Functional and Evolutionary Entomology, Gembloux Agro-Bio Tech, University of Liège, Gembloux, Belgium
- Corresponding author.
| | - Cécile Le Lann
- CNRS, ECOBIO (écosystèmes, Biodiversité, Évolution) – UMR, Université de Rennes, 6553, France
| | - Daniel A. Hahn
- Department of Entomology and Nematology, The University of Florida, USA
| | - Mark Lammers
- Institute for Evolution and Biodiversity, University of Münster, Germany
| | | | - Hans T. Alborn
- United States Department of Agriculture, Chemistry Research Unit, Gainesville, USA
| | - Thomas Enriquez
- Evolution and Ecophysiology Group, Department of Functional and Evolutionary Entomology, Gembloux Agro-Bio Tech, University of Liège, Gembloux, Belgium
| | - Mathilde Scheifler
- Evolution and Ecophysiology Group, Department of Functional and Evolutionary Entomology, Gembloux Agro-Bio Tech, University of Liège, Gembloux, Belgium
| | - Jeffrey A. Harvey
- Department of Terrestrial Ecology, Netherlands Institute of Ecology, the Netherlands
- Amsterdam Institute for Life and Environment, Vrije Universiteit Amsterdam, the Netherlands
| | - Jacintha Ellers
- Amsterdam Institute for Life and Environment, Vrije Universiteit Amsterdam, the Netherlands
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178
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Totorikaguena L, Olabarrieta E. CRISPR/Cas9 as a Simple Technique for the Generation of Murine Knockout Models for Neuropsychiatric Diseases. Methods Mol Biol 2023; 2687:45-55. [PMID: 37464161 DOI: 10.1007/978-1-0716-3307-6_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] [Indexed: 07/20/2023]
Abstract
The development of schizophrenia-like rodent models is still a major challenge for the study of this mental disorder. Schizophrenia and other neuropsychiatric disorders are thought to be triggered by multiple factors, and furthermore, the genetic component of schizophrenia is highly complex. The edition of one single gene for mimicking some of the symptoms of the disorder could cause unintended mutations that could influence animal's behavior making it difficult to study. Since 2013, CRISPR-Cas gene-editing technology has been a great improvement in the specificity of transgenic model generation because of its speed, efficiency, cost, and apparent ease. This protocol describes a simple method to generate a knockout mouse model using CRISPR technology, which can be applied to any gene presumably involved in the development of schizophrenia and other neuropsychiatric disorders.
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Affiliation(s)
- Lide Totorikaguena
- Department of Physiology, Medicine and Nursing Faculty, University of the Basque Country UPV/EHU, Leioa, Spain
| | - Estibaliz Olabarrieta
- Department of Pharmacology, Medicine and Nursing Faculty, University of the Basque Country UPV/EHU, Leioa, Spain.
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179
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Paiva IM, Damasceno S, Cunha TM. CRISPR Libraries and Whole-Genome Screening to Identify Essential Factors for Viral Infections. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2023; 1429:157-172. [PMID: 37486521 DOI: 10.1007/978-3-031-33325-5_9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/25/2023]
Abstract
The CRISPR-Cas9 system has revolutionized genetics and offers a simple and inexpensive way of generating perturbation that results in gene repression, activation, or editing. The advances in this technique make possible the development of CRISPR libraries which consist of a set of sgRNAs to cause perturbations in several genes in the same cell population. The use of libraries raised the CRISPR-Cas9 technique to a genomic scale and provides a powerful approach for identifying previously unknown molecular mechanisms and pathways involved in a specific phenotype or biological process. More specifically, the CRISPRko libraries (set of sgRNAs for gene knockout) and their high-throughput screenings are widely used in research with viral agents, and it was enlarged even more with the COVID-19 pandemic. With this chapter, we aim to point out how this tool helps in understanding virus-host relationships, such as the mechanisms of virus entry into the cell, the essential factors for its replication, and the cellular pathways involved in the response against the pathogen. The chapter also provided some practical considerations for each step of an experimentation using these tools that include choosing the library and screening type, the target cell, the viral strain, the library amplification and guaranteeing its coverage, the strategies for the gene screening pipeline by bioinformatics, and finally, target validation. To conclude, it was presented a table reviewing the last updates in the research for antiviral therapies using CRISPR libraries.
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Affiliation(s)
- Isadora Marques Paiva
- Center for Research in Inflammatory Diseases (CRID), Ribeirao Preto Medical School, University of Sao Paulo, Ribeirão Preto, SP, Brazil
| | - Samara Damasceno
- Center for Research in Inflammatory Diseases (CRID), Ribeirao Preto Medical School, University of Sao Paulo, Ribeirão Preto, SP, Brazil
| | - Thiago Mattar Cunha
- Center for Research in Inflammatory Diseases (CRID), Ribeirao Preto Medical School, University of Sao Paulo, Ribeirão Preto, SP, Brazil.
- Department of Pharmacology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, SP, Brazil.
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180
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Liao J, Wu Y. Gene Editing in Hematopoietic Stem Cells. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2023; 1442:177-199. [PMID: 38228965 DOI: 10.1007/978-981-99-7471-9_11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/18/2024]
Abstract
Hematopoietic stem cells (HSCs) can be isolated and collected from the body, genetically modified, and expanded ex vivo. The invention of innovative and powerful gene editing tools has provided researchers with great convenience in genetically modifying a wide range of cells, including hematopoietic stem and progenitor cells (HSPCs). In addition to being used to modify genes to study the functional role that specific genes play in the hematopoietic system, the application of gene editing platforms in HSCs is largely focused on the development of cell-based gene editing therapies to treat diseases such as immune deficiency disorders and inherited blood disorders. Here, we review the application of gene editing tools in HSPCs. In particular, we provide a broad overview of the development of gene editing tools, multiple strategies for the application of gene editing tools in HSPCs, and exciting clinical advances in HSPC gene editing therapies. We also outline the various challenges integral to clinical translation of HSPC gene editing and provide the possible corresponding solutions.
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Affiliation(s)
- Jiaoyang Liao
- Shanghai Frontiers Science Center of Genome Editing and Cell Therapy, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, China
| | - Yuxuan Wu
- Shanghai Frontiers Science Center of Genome Editing and Cell Therapy, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, China.
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181
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Tripathi S, Khatri P, Fatima Z, Pandey RP, Hameed S. A Landscape of CRISPR/Cas Technique for Emerging Viral Disease Diagnostics and Therapeutics: Progress and Prospects. Pathogens 2022; 12:pathogens12010056. [PMID: 36678404 PMCID: PMC9863163 DOI: 10.3390/pathogens12010056] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Revised: 12/22/2022] [Accepted: 12/25/2022] [Indexed: 12/31/2022] Open
Abstract
Viral diseases have emerged as a serious threat to humanity and as a leading cause of morbidity worldwide. Many viral diagnostic methods and antiviral therapies have been developed over time, but we are still a long way from treating certain infections caused by viruses. Acquired immunodeficiency syndrome (AIDS) is one of the challenges where current medical science advancements fall short. As a result, new diagnostic and treatment options are desperately needed. The CRISPR/Cas9 system has recently been proposed as a potential therapeutic approach for viral disease treatment. CRISPR/Cas9 is a specialised, effective, and adaptive gene-editing technique that can be used to modify, delete, or correct specific DNA sequences. It has evolved into an advanced, configurable nuclease-based single or multiple gene-editing tool with a wide range of applications. It is widely preferred simply because its operational procedures are simple, inexpensive, and extremely efficient. Exploration of infectious virus genomes is required for a comprehensive study of infectious viruses. Herein, we have discussed the historical timeline-based advancement of CRISPR, CRISPR/Cas9 as a gene-editing technology, the structure of CRISPR, and CRISPR as a diagnostic tool for studying emerging viral infections. Additionally, utilizing CRISPR/Cas9 technology to fight viral infections in plants, CRISPR-based diagnostics of viruses, pros, and cons, and bioethical issues of CRISPR/Cas9-based genomic modification are discussed.
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Affiliation(s)
- Shyam Tripathi
- Centre for Drug Design Discovery and Development (C4D), SRM University, Delhi-NCR, Rajiv Gandhi Education City, Sonepat 131029, India
| | - Purnima Khatri
- Centre for Drug Design Discovery and Development (C4D), SRM University, Delhi-NCR, Rajiv Gandhi Education City, Sonepat 131029, India
- Department of Microbiology, SRM University, Delhi-NCR, Rajiv Gandhi Education City, Sonepat 131029, India
| | - Zeeshan Fatima
- Department of Medical Laboratory Sciences, College of Applied Medical Sciences, University of Bisha, Bisha 61922, Saudi Arabia
- Amity Institute of Biotechnology, Amity University Haryana, Gurugram 122413, India
| | - Ramendra Pati Pandey
- Centre for Drug Design Discovery and Development (C4D), SRM University, Delhi-NCR, Rajiv Gandhi Education City, Sonepat 131029, India
- Department of Microbiology, SRM University, Delhi-NCR, Rajiv Gandhi Education City, Sonepat 131029, India
- Correspondence: (R.P.P.); (S.H.)
| | - Saif Hameed
- Amity Institute of Biotechnology, Amity University Haryana, Gurugram 122413, India
- Correspondence: (R.P.P.); (S.H.)
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182
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Sari-Ak D, Alomari O, Shomali RA, Lim J, Thimiri Govinda Raj DB. Advances in CRISPR-Cas9 for the Baculovirus Vector System: A Systematic Review. Viruses 2022; 15:54. [PMID: 36680093 PMCID: PMC9864449 DOI: 10.3390/v15010054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Revised: 12/20/2022] [Accepted: 12/21/2022] [Indexed: 12/28/2022] Open
Abstract
The baculovirus expression vector systems (BEVS) have been widely used for the recombinant production of proteins in insect cells and with high insert capacity. However, baculovirus does not replicate in mammalian cells; thus, the BacMam system, a heterogenous expression system that can infect certain mammalian cells, was developed. Since then, the BacMam system has enabled transgene expression via mammalian-specific promoters in human cells, and later, the MultiBacMam system enabled multi-protein expression in mammalian cells. In this review, we will cover the continual development of the BEVS in combination with CRPISPR-Cas technologies to drive genome-editing in mammalian cells. Additionally, we highlight the use of CRISPR-Cas in glycoengineering to potentially produce a new class of glycoprotein medicines in insect cells. Moreover, we anticipate CRISPR-Cas9 to play a crucial role in the development of protein expression systems, gene therapy, and advancing genome engineering applications in the future.
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Affiliation(s)
- Duygu Sari-Ak
- Department of Medical Biology, Hamidiye International School of Medicine, University of Health Sciences, 34668 Istanbul, Turkey
| | - Omar Alomari
- Hamidiye International School of Medicine, University of Health Sciences, 34668 Istanbul, Turkey; (O.A.); (R.A.S.)
| | - Raghad Al Shomali
- Hamidiye International School of Medicine, University of Health Sciences, 34668 Istanbul, Turkey; (O.A.); (R.A.S.)
| | - Jackwee Lim
- Singapore Immunology Network, A*STAR, 8a Biomedical Grove, Singapore 138648, Singapore;
| | - Deepak B. Thimiri Govinda Raj
- Synthetic Nanobiotechnology and Biomachines Group, Synthetic Biology and Precision Medicine Centre, Next Generation Health Cluster, Council for Scientific and Industrial Research (CSIR), Pretoria 0001, South Africa;
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183
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Saber Sichani A, Ranjbar M, Baneshi M, Torabi Zadeh F, Fallahi J. A Review on Advanced CRISPR-Based Genome-Editing Tools: Base Editing and Prime Editing. Mol Biotechnol 2022; 65:849-860. [DOI: 10.1007/s12033-022-00639-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Accepted: 12/04/2022] [Indexed: 12/24/2022]
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184
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Madina MH, Santhanam P, Asselin Y, Jaswal R, Bélanger RR. Progress and Challenges in Elucidating the Functional Role of Effectors in the Soybean- Phytophthora sojae Interaction. J Fungi (Basel) 2022; 9:jof9010012. [PMID: 36675833 PMCID: PMC9866111 DOI: 10.3390/jof9010012] [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: 11/25/2022] [Revised: 12/16/2022] [Accepted: 12/19/2022] [Indexed: 12/24/2022] Open
Abstract
Phytophthora sojae, the agent responsible for stem and root rot, is one of the most damaging plant pathogens of soybean. To establish a compatible-interaction, P. sojae secretes a wide array of effector proteins into the host cell. These effectors have been shown to act either in the apoplastic area or the cytoplasm of the cell to manipulate the host cellular processes in favor of the development of the pathogen. Deciphering effector-plant interactions is important for understanding the role of P. sojae effectors in disease progression and developing approaches to prevent infection. Here, we review the subcellular localization, the host proteins, and the processes associated with P. sojae effectors. We also discuss the emerging topic of effectors in the context of effector-resistance genes interaction, as well as model systems and recent developments in resources and techniques that may provide a better understanding of the soybean-P. sojae interaction.
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185
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Deng H, Liang X, Liu J, Zheng X, Fan TP, Cai Y. Advances and perspectives on perylenequinone biosynthesis. Front Microbiol 2022; 13:1070110. [PMID: 36605511 PMCID: PMC9808054 DOI: 10.3389/fmicb.2022.1070110] [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: 10/14/2022] [Accepted: 11/21/2022] [Indexed: 12/24/2022] Open
Abstract
Under illumination, the fungal secondary metabolites, perylenequinones (PQs) react with molecular oxygen to generate reactive oxygen species (ROS), which, in excess can damage cellular macromolecules and trigger apoptosis. Based on this property, PQs have been widely used as photosensitizers and applied in pharmaceuticals, which has stimulated research into the discovery of new PQs and the elucidation of their biosynthetic pathways. The PQs-associated literature covering from April 1967 to September 2022 is reviewed in three sections: (1) the sources, structural diversity, and biological activities of microbial PQs; (2) elucidation of PQ biosynthetic pathways, associated genes, and mechanisms of regulation; and (3) advances in pathway engineering and future potential strategies to modify cellular metabolism and improve PQ production.
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Affiliation(s)
- Huaxiang Deng
- Center for Synthetic Biochemistry, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China,The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, China,*Correspondence: Huaxiang Deng,
| | - Xinxin Liang
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, China
| | - Jinbin Liu
- School of Marine and Bioengineering, Yancheng Institute of Technology, Yancheng, Jiangsu, China
| | - Xiaohui Zheng
- College of Life Sciences, Northwest University, Xi’an, Shanxi, China
| | - Tai-Ping Fan
- Department of Pharmacology, University of Cambridge, Cambridge, United Kingdom
| | - Yujie Cai
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, China,Yujie Cai,
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186
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Apolónio JD, Dias JS, Fernandes MT, Komosa M, Lipman T, Zhang CH, Leão R, Lee D, Nunes NM, Maia AT, Morera JL, Vicioso L, Tabori U, Castelo-Branco P. THOR is a targetable epigenetic biomarker with clinical implications in breast cancer. Clin Epigenetics 2022; 14:178. [PMID: 36529814 PMCID: PMC9759897 DOI: 10.1186/s13148-022-01396-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2022] [Accepted: 12/02/2022] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND Breast cancer (BC) is the most frequently diagnosed cancer and a leading cause of death among women worldwide. Early BC is potentially curable, but the mortality rates still observed among BC patients demonstrate the urgent need of novel and more effective diagnostic and therapeutic options. Limitless self-renewal is a hallmark of cancer, governed by telomere maintenance. In around 95% of BC cases, this process is achieved by telomerase reactivation through upregulation of the human telomerase reverse transcriptase (hTERT). The hypermethylation of a specific region within the hTERT promoter, termed TERT hypermethylated oncological region (THOR) has been associated with increased hTERT expression in cancer. However, its biological role and clinical potential in BC have never been studied to the best of our knowledge. Therefore, we aimed to investigate the role of THOR as a biomarker and explore the functional impact of THOR methylation status in hTERT upregulation in BC. RESULTS THOR methylation status in BC was assessed by pyrosequencing on discovery and validation cohorts. We found that THOR is significantly hypermethylated in malignant breast tissue when compared to benign tissue (40.23% vs. 12.81%, P < 0.0001), differentiating malignant tumor from normal tissue from the earliest stage of disease. Using a reporter assay, the addition of unmethylated THOR significantly reduced luciferase activity by an average 1.8-fold when compared to the hTERT core promoter alone (P < 0.01). To further investigate its biological impact on hTERT transcription, targeted THOR demethylation was performed using novel technology based on CRISPR-dCas9 system and significant THOR demethylation was achieved. Cells previously demethylated on THOR region did not develop a histologic cancer phenotype in in vivo assays. Additional studies are required to validate these observations and to unravel the causality between THOR hypermethylation and hTERT upregulation in BC. CONCLUSIONS THOR hypermethylation is an important epigenetic mark in breast tumorigenesis, representing a promising biomarker and therapeutic target in BC. We revealed that THOR acts as a repressive regulatory element of hTERT and that its hypermethylation is a relevant mechanism for hTERT upregulation in BC.
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Affiliation(s)
- Joana Dias Apolónio
- grid.7157.40000 0000 9693 350XFaculty of Medicine and Biomedical Sciences (FMCB), University of Algarve, Gambelas Campus, Bld. 2, 8005-139 Faro, Portugal ,grid.7157.40000 0000 9693 350XAlgarve Biomedical Center Research Institute (ABC-RI), University of Algarve, Gambelas Campus, 8005-139 Faro, Portugal ,grid.7157.40000 0000 9693 350XAlgarve Biomedical Center (ABC), University of Algarve, Gambelas Campus, 8005-139 Faro, Portugal ,grid.42327.300000 0004 0473 9646Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON Canada
| | - João S. Dias
- University Hospital Center of Algarve, Faro, Portugal
| | - Mónica Teotónio Fernandes
- grid.7157.40000 0000 9693 350XAlgarve Biomedical Center Research Institute (ABC-RI), University of Algarve, Gambelas Campus, 8005-139 Faro, Portugal ,grid.7157.40000 0000 9693 350XAlgarve Biomedical Center (ABC), University of Algarve, Gambelas Campus, 8005-139 Faro, Portugal ,grid.7157.40000 0000 9693 350XEscola Superior de Saúde (ESSUAlg), Universidade Do Algarve, Faro, Portugal
| | - Martin Komosa
- grid.42327.300000 0004 0473 9646Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON Canada ,grid.17063.330000 0001 2157 2938Arthur and Sonia Labatt Brain Tumor Research Center, The Hospital for Sick Children, University of Toronto, Toronto, ON Canada
| | - Tatiana Lipman
- grid.42327.300000 0004 0473 9646Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON Canada ,grid.17063.330000 0001 2157 2938Arthur and Sonia Labatt Brain Tumor Research Center, The Hospital for Sick Children, University of Toronto, Toronto, ON Canada
| | - Cindy H. Zhang
- grid.42327.300000 0004 0473 9646Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON Canada ,grid.17063.330000 0001 2157 2938Arthur and Sonia Labatt Brain Tumor Research Center, The Hospital for Sick Children, University of Toronto, Toronto, ON Canada
| | - Ricardo Leão
- grid.8051.c0000 0000 9511 4342Faculty of Medicine, University of Coimbra, Coimbra, Portugal
| | - Donghyun Lee
- grid.42327.300000 0004 0473 9646Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON Canada ,grid.17063.330000 0001 2157 2938Arthur and Sonia Labatt Brain Tumor Research Center, The Hospital for Sick Children, University of Toronto, Toronto, ON Canada
| | - Nuno Miguel Nunes
- grid.42327.300000 0004 0473 9646Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON Canada ,grid.17063.330000 0001 2157 2938Arthur and Sonia Labatt Brain Tumor Research Center, The Hospital for Sick Children, University of Toronto, Toronto, ON Canada
| | - Ana-Teresa Maia
- grid.7157.40000 0000 9693 350XFaculty of Medicine and Biomedical Sciences (FMCB), University of Algarve, Gambelas Campus, Bld. 2, 8005-139 Faro, Portugal ,grid.7157.40000 0000 9693 350XAlgarve Biomedical Center (ABC), University of Algarve, Gambelas Campus, 8005-139 Faro, Portugal ,grid.7157.40000 0000 9693 350XCenter for Research in Health Technologies and Information Systems (CINTESIS@RISE), University of Algarve, Gambelas Campus, 8005-139 Faro, Portugal
| | | | - Luis Vicioso
- grid.10215.370000 0001 2298 7828Faculty of Medicine, Department of Histology and Pathological Anatomy, University of Malaga, Malaga, Spain
| | - Uri Tabori
- grid.42327.300000 0004 0473 9646Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON Canada ,grid.17063.330000 0001 2157 2938Arthur and Sonia Labatt Brain Tumor Research Center, The Hospital for Sick Children, University of Toronto, Toronto, ON Canada ,grid.42327.300000 0004 0473 9646Division of Hematology/Oncology, The Hospital for Sick Children, Toronto, ON Canada
| | - Pedro Castelo-Branco
- grid.7157.40000 0000 9693 350XFaculty of Medicine and Biomedical Sciences (FMCB), University of Algarve, Gambelas Campus, Bld. 2, 8005-139 Faro, Portugal ,grid.7157.40000 0000 9693 350XAlgarve Biomedical Center Research Institute (ABC-RI), University of Algarve, Gambelas Campus, 8005-139 Faro, Portugal ,grid.7157.40000 0000 9693 350XAlgarve Biomedical Center (ABC), University of Algarve, Gambelas Campus, 8005-139 Faro, Portugal ,grid.421010.60000 0004 0453 9636Champalimaud Research Program, Champalimaud Centre for the Unknown, Lisbon, Portugal
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187
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Gu S, Zhang J, Li L, Zhong J. Repurposing the Endogenous CRISPR-Cas9 System for High-Efficiency Genome Editing in Lacticaseibacillus paracasei. ACS Synth Biol 2022; 11:4031-4042. [PMID: 36414383 DOI: 10.1021/acssynbio.2c00374] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Lactobacilli such as Lacticaseibacillus (Lcb) paracasei are generally regarded as safe and health-promoting microbes, and have been widely applied in food and pharmaceutical industries. However, the genetic bases of their beneficial properties were mostly uncertain because of the lack of effective genetic manipulation tools. The type II CRISPR-Cas9 system is the largest family present in lactobacilli, but none of them yet have been developed for genetic modifications. Here, we establish the first endogenous CRISPR-Cas9 genome-editing system in lactobacilli. With a validated protospacer adjacent motif (PAM) and customized single guide RNA (sgRNA) expression cassette, the native CRISPR-Cas9 system was reprogrammed to achieve gene deletion and chromosomal insertion at over 90% efficiency, as well as nucleotide substitution at ≥50% efficiency. We also effectively accomplished deletions of large genomic fragments (5-10 kb) and simultaneous deletion of multiple genes at distal loci, both of which are the first cases in lactobacilli when either endogenous or exogenous CRISPR-Cas systems were employed. In addition, we designed a controllable plasmid-targeting sgRNA expression module and integrated it into the editing plasmid. The all-in-one vector realized gene deletion and plasmid curing at high efficiency (>90%). Collectively, the present study develops a convenient and precise genetic tool in Lcb. paracasei and contributes to the genetics and engineering of lactobacilli.
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Affiliation(s)
- Shujie Gu
- University of Chinese Academy of Sciences, Beijing 100039, China.,State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Jie Zhang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Lili Li
- University of Chinese Academy of Sciences, Beijing 100039, China.,State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Jin Zhong
- University of Chinese Academy of Sciences, Beijing 100039, China.,State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
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188
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Xu CL, Ruan MZ, Ragi SD, Tsang SH. CRISPR Off-Target Analysis Platforms. Methods Mol Biol 2022; 2560:279-285. [PMID: 36481904 DOI: 10.1007/978-1-0716-2651-1_26] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The clustered regularly interspaced short palindromic repeats (CRISPR)-Caspase9 (Cas9) system provides a programmable technology that may be used to edit the eukaryotic genome and epigenome. CRISPR/Cas9 includes a guide RNA targeted to a gene of interest which hybridizes to a nucleotide sequence next to a protospacer-adjacent motif (PAM) which guides the Cas9 endonucleases to the target site for cleavage via double-strand breaks. A caveat of the CRISPR/Cas9 system is the creation of off-target double-strand breaks (DSBs) which may result in anomalous insertions, deletions, and translocations. Thus, assays for the sensitive detection and analysis of off-target editing are critical. Here, we describe currently available CRISPR technologies, CRISPR applications, and current analysis platforms to detect off-target effects including genome-wide, unbiased identification of DSBs enabled by sequencing (GUIDE-Seq), high-throughput genomic translocation sequencing (HTGTS), breaks labeling, enrichments on streptavidin and next-generation sequencing (BLESS), and in vitro nuclease-digested genome sequencing (Digenome-seq).
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Affiliation(s)
- Christine L Xu
- Stanford University School of Medicine, Stanford, CA, USA
| | - Merry Zhechao Ruan
- Department of Ophthalmology, New York-Presbyterian Hospital, New York, NY, USA
| | - Sara D Ragi
- Warren Alpert Medical School at Brown University, Providence, RI, USA
| | - Stephen H Tsang
- Departments of Ophthalmology, Pathology & Cell Biology, Graduate Programs in Nutritional & Metabolic Biology and Neurobiology & Behavior, Columbia Stem Cell Initiative, New York, NY, USA.
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189
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Farooq Z, Nouman Riaz M, Farooq MS, Li Y, Wang H, Ahmad M, Tu J, Ma C, Dai C, Wen J, Shen J, Fu T, Yang S, Wang B, Yi B. Induction of Male Sterility by Targeted Mutation of a Restorer-of-Fertility Gene with CRISPR/Cas9-Mediated Genome Editing in Brassica napus L. PLANTS (BASEL, SWITZERLAND) 2022; 11:3501. [PMID: 36559613 PMCID: PMC9785856 DOI: 10.3390/plants11243501] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Revised: 11/14/2022] [Accepted: 11/29/2022] [Indexed: 06/17/2023]
Abstract
Brassica napus L. (canola, oil seed rape) is one of the world's most important oil seed crops. In the last four decades, the discovery of cytoplasmic male-sterility (CMS) systems and the restoration of fertility (Rf) genes in B. napus has improved the crop traits by heterosis. The homologs of Rf genes, known as the restoration of fertility-like (RFL) genes, have also gained importance because of their similarities with Rf genes. Such as a high non-synonymous/synonymous codon replacement ratio (dN/dS), autonomous gene duplications, and a possible engrossment in fertility restoration. B. napus contains 53 RFL genes on chromosomes A9 and C8. Our research aims to study the function of BnaRFL11 in fertility restoration using the CRISPR/Cas9 genome editing technique. A total of 88/108 (81.48%) T0 lines, and for T1, 110/145 (75%) lines carried T-DNA insertions. Stable mutations were detected in the T0 and T1 generations, with an average allelic mutation transmission rate of 81%. We used CRISPR-P software to detect off-target 50 plants sequenced from the T0 generation that showed no off-target mutation, signifying that if the designed sgRNA is specific for the target, the off-target effects are negligible. We also concluded that the mutagenic competence of the designed sgRNAs mediated by U6-26 and U6-29 ranged widely from 31% to 96%. The phenotypic analysis of bnarfl11 revealed defects in the floral structure, leaf size, branch number, and seed production. We discovered a significant difference between the sterile line and fertile line flower development after using a stereomicroscope and scanning electron microscope. The pollen visibility test showed that the pollen grain had utterly degenerated. The cytological observations of homozygous mutant plants showed an anther abortion stage similar to nap-CMS, with a Orf222, Orf139, Ap3, and nad5c gene upregulation. The bnarfl11 shows vegetative defects, including fewer branches and a reduced leaf size, suggesting that PPR-encoding genes are essential for the plants' vegetative and reproductive growth. Our results demonstrated that BnaRFL11 has a possible role in fertility restoration. The current study's findings suggest that CRISPR/Cas9 mutations may divulge the functions of genes in polyploid species and provide agronomically desirable traits through a targeted mutation.
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Affiliation(s)
- Zunaira Farooq
- National Key Laboratory of Crop Genetic Improvement, National Center of Rapeseed Improvement, Huazhong Agricultural University, Wuhan 430070, China
- Soybean Research Institute, National Center for Soybean Improvement, Key Laboratory of Biology and Genetic Improvement of Soybean (General Ministry of Agriculture), Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing 210095, China
| | - Muhammad Nouman Riaz
- National Key Laboratory of Crop Genetic Improvement, National Center of Rapeseed Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Muhammad Shoaib Farooq
- National Key Laboratory of Crop Genetic Improvement, National Center of Rapeseed Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Yifan Li
- National Key Laboratory of Crop Genetic Improvement, National Center of Rapeseed Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Huadong Wang
- National Key Laboratory of Crop Genetic Improvement, National Center of Rapeseed Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Mayra Ahmad
- National Key Laboratory of Crop Genetic Improvement, National Center of Rapeseed Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Jinxing Tu
- National Key Laboratory of Crop Genetic Improvement, National Center of Rapeseed Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Chaozhi Ma
- National Key Laboratory of Crop Genetic Improvement, National Center of Rapeseed Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Cheng Dai
- National Key Laboratory of Crop Genetic Improvement, National Center of Rapeseed Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Jing Wen
- National Key Laboratory of Crop Genetic Improvement, National Center of Rapeseed Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Jinxiong Shen
- National Key Laboratory of Crop Genetic Improvement, National Center of Rapeseed Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Tingdong Fu
- National Key Laboratory of Crop Genetic Improvement, National Center of Rapeseed Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Shouping Yang
- Soybean Research Institute, National Center for Soybean Improvement, Key Laboratory of Biology and Genetic Improvement of Soybean (General Ministry of Agriculture), Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing 210095, China
| | - Benqi Wang
- Wuhan Vegetable Research Institute, Wuhan Academy of Agricultural Science and Technology, Wuhan 430065, China
| | - Bin Yi
- National Key Laboratory of Crop Genetic Improvement, National Center of Rapeseed Improvement, Huazhong Agricultural University, Wuhan 430070, China
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190
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Challenges in Gene Therapy for Somatic Reverted Mosaicism in X-Linked Combined Immunodeficiency by CRISPR/Cas9 and Prime Editing. Genes (Basel) 2022; 13:genes13122348. [PMID: 36553615 PMCID: PMC9777626 DOI: 10.3390/genes13122348] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Revised: 12/02/2022] [Accepted: 12/10/2022] [Indexed: 12/15/2022] Open
Abstract
X-linked severe combined immunodeficiency (X-SCID) is a primary immunodeficiency that is caused by mutations in the interleukin-2 receptor gamma (IL2RG) gene. Some patients present atypical X-SCID with mild clinical symptoms due to somatic revertant mosaicism. CRISPR/Cas9 and prime editing are two advanced genome editing tools that paved the way for treating immune deficiency diseases. Prime editing overcomes the limitations of the CRISPR/Cas9 system, as it does not need to induce double-strand breaks (DSBs) or exogenous donor DNA templates to modify the genome. Here, we applied CRISPR/Cas9 with single-stranded oligodeoxynucleotides (ssODNs) and prime editing methods to generate an in vitro model of the disease in K-562 cells and healthy donors' T cells for the c. 458T>C point mutation in the IL2RG gene, which also resulted in a useful way to optimize the gene correction approach for subsequent experiments in patients' cells. Both methods proved to be successful and were able to induce the mutation of up to 31% of treated K-562 cells and 26% of treated T cells. We also applied similar strategies to correct the IL2RG c. 458T>C mutation in patient T cells that carry the mutation with revertant somatic mosaicism. However, both methods failed to increase the frequency of the wild-type sequence in the mosaic T cells of patients due to limited in vitro proliferation of mutant cells and the presence of somatic reversion. To the best of our knowledge, this is the first attempt to treat mosaic cells from atypical X-SCID patients employing CRISPR/Cas9 and prime editing. We showed that prime editing can be applied to the formation of specific-point IL2RG mutations without inducing nonspecific on-target modifications. We hypothesize that the feasibility of the nucleotide substitution of the IL2RG gene using gene therapy, especially prime editing, could provide an alternative strategy to treat X-SCID patients without revertant mutations, and further technological improvements need to be developed to correct somatic mosaicism mutations.
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191
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New Therapeutics for Extracellular Vesicles: Delivering CRISPR for Cancer Treatment. Int J Mol Sci 2022; 23:ijms232415758. [PMID: 36555398 PMCID: PMC9779094 DOI: 10.3390/ijms232415758] [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: 10/30/2022] [Revised: 12/01/2022] [Accepted: 12/07/2022] [Indexed: 12/14/2022] Open
Abstract
Cancers are defined by genetic defects, which underlines the prospect of using gene therapy in patient care. During the past decade, CRISPR technology has rapidly evolved into a powerful gene editing tool with high fidelity and precision. However, one of the impediments slowing down the clinical translation of CRISPR-based gene therapy concerns the lack of ideal delivery vectors. Extracellular vesicles (EVs) are nano-sized membrane sacs naturally released from nearly all types of cells. Although EVs are secreted for bio-information conveyance among cells or tissues, they have been recognized as superior vectors for drug or gene delivery. Recently, emerging evidence has spotlighted EVs in CRISPR delivery towards cancer treatment. In this review, we briefly introduce the biology and function of the CRISPR system and follow this with a summary of current delivery methods for CRISPR applications. We emphasize the recent progress in EV-mediated CRISPR editing for various cancer types and target genes. The reported strategies for constructing EV-CRISPR vectors, as well as their limitations, are discussed in detail. The review aims to throw light on the clinical potential of engineered EVs and encourage the expansion of our available toolkit to defeat cancer.
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192
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Zhang W, Mu Y, Dong K, Zhang L, Yan B, Hu H, Liao Y, Zhao R, Shu W, Ye Z, Lu Y, Wan C, Sun Q, Li L, Wang H, Xiao X. PAM-independent ultra-specific activation of CRISPR-Cas12a via sticky-end dsDNA. Nucleic Acids Res 2022; 50:12674-12688. [PMID: 36484104 PMCID: PMC9825152 DOI: 10.1093/nar/gkac1144] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2022] [Revised: 11/04/2022] [Accepted: 11/18/2022] [Indexed: 12/13/2022] Open
Abstract
Although CRISPR-Cas12a [clustered regularly interspaced short palindromic repeats (CRISPR)-CRISPR-associated protein 12a] combining pre-amplification technology has the advantage of high sensitivity in biosensing, its generality and specificity are insufficient, which greatly restrains its application range. Here, we discovered a new targeting substrate for LbaCas12a (Lachnospiraceae bacterium Cas12a), namely double-stranded DNA (dsDNA) with a sticky-end region (PAM-SE+ dsDNA). We discovered that CRISPR-Cas12a had special enzymatic properties for this substrate DNA, including the ability to recognize and cleave it without needing a protospacer adjacent motif (PAM) sequence and a high sensitivity to single-base mismatches in that substrate. Further mechanism studies revealed that guide RNA (gRNA) formed a triple-stranded flap structure with the substrate dsDNA. We also discovered the property of low-temperature activation of CRISPR-Cas12a and, by coupling with the unique DNA hybridization kinetics at low temperature, we constructed a complete workflow for low-abundance point mutation detection in real samples, which was fast, convenient and free of single-stranded DNA (ssDNA) transformation. The detection limits were 0.005-0.01% for synthesized strands and 0.01-0.05% for plasmid genomic DNA, and the mutation abundances provided by our system for 28 clinical samples were in accordance with next-generation sequencing results. We believe that our work not only reveals novel information about the target recognition mechanism of the CRISPR-Cas12a system, but also greatly broadens its application scenarios.
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Affiliation(s)
| | | | - Kejun Dong
- Department of Obstetrics and Gynecology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430000, China
| | - Lei Zhang
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Bei Yan
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Hao Hu
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Yangwei Liao
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Rong Zhao
- Department of Obstetrics and Gynecology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430000, China
| | - Wan Shu
- Department of Obstetrics and Gynecology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430000, China
| | - Zhengxin Ye
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Yaping Lu
- Sinopharm Genomics Technology Co., Ltd, Wuhan 430000, China
| | - Chong Wan
- Precision Medicine Center, Yangtze Delta Region Institute of Tsinghua University, Jiaxing 314006, China
| | - Qiangqiang Sun
- Life Health Care Clinical Laboratories, Beijing 100000, China
| | - Longjie Li
- Correspondence may also be addressed to Longjie Li.
| | - Hongbo Wang
- Correspondence may also be addressed to Hongbo Wang.
| | - Xianjin Xiao
- To whom correspondence should be addressed. Tel: +86 027 8369 2651; Fax: +86 027 8369 2651;
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193
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Fecal Microbiota Transplantation and Other Gut Microbiota Manipulation Strategies. Microorganisms 2022; 10:microorganisms10122424. [PMID: 36557677 PMCID: PMC9781458 DOI: 10.3390/microorganisms10122424] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 12/02/2022] [Accepted: 12/05/2022] [Indexed: 12/13/2022] Open
Abstract
The gut microbiota is composed of bacteria, archaea, phages, and protozoa. It is now well known that their mutual interactions and metabolism influence host organism pathophysiology. Over the years, there has been growing interest in the composition of the gut microbiota and intervention strategies in order to modulate it. Characterizing the gut microbial populations represents the first step to clarifying the impact on the health/illness equilibrium, and then developing potential tools suited for each clinical disorder. In this review, we discuss the current gut microbiota manipulation strategies available and their clinical applications in personalized medicine. Among them, FMT represents the most widely explored therapeutic tools as recent guidelines and standardization protocols, not only for intestinal disorders. On the other hand, the use of prebiotics and probiotics has evidence of encouraging findings on their safety, patient compliance, and inter-individual effectiveness. In recent years, avant-garde approaches have emerged, including engineered bacterial strains, phage therapy, and genome editing (CRISPR-Cas9), which require further investigation through clinical trials.
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194
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Comprehensive computational analysis of epigenetic descriptors affecting CRISPR-Cas9 off-target activity. BMC Genomics 2022; 23:805. [PMID: 36474180 PMCID: PMC9724382 DOI: 10.1186/s12864-022-09012-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Accepted: 10/17/2022] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND A common issue in CRISPR-Cas9 genome editing is off-target activity, which prevents the widespread use of CRISPR-Cas9 in medical applications. Among other factors, primary chromatin structure and epigenetics may influence off-target activity. METHODS In this work, we utilize crisprSQL, an off-target database, to analyze the effect of 19 epigenetic descriptors on CRISPR-Cas9 off-target activity. Termed as 19 epigenetic features/scores, they consist of 6 experimental epigenetic and 13 computed nucleosome organization-related features. In terms of novel features, 15 of the epigenetic scores are newly considered. The 15 newly considered scores consist of 13 freshly computed nucleosome occupancy/positioning scores and 2 experimental features (MNase and DRIP). The other 4 existing scores are experimental features (CTCF, DNase I, H3K4me3, RRBS) commonly used in deep learning models for off-target activity prediction. For data curation, MNase was aggregated from existing experimental nucleosome occupancy data. Based on the sequence context information available in crisprSQL, we also computed nucleosome occupancy/positioning scores for off-target sites. RESULTS To investigate the relationship between the 19 epigenetic features and off-target activity, we first conducted Spearman and Pearson correlation analysis. Such analysis shows that some computed scores derived from training-based models and training-free algorithms outperform all experimental epigenetic features. Next, we evaluated the contribution of all epigenetic features in two successful machine/deep learning models which predict off-target activity. We found that some computed scores, unlike all 6 experimental features, significantly contribute to the predictions of both models. As a practical research contribution, we make the off-target dataset containing all 19 epigenetic features available to the research community. CONCLUSIONS Our comprehensive computational analysis helps the CRISPR-Cas9 community better understand the relationship between epigenetic features and CRISPR-Cas9 off-target activity.
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195
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Wang D, Fan X, Li M, Liu T, Lu P, Wang G, Li Y, Han J, Zhao J. Prime Editing in Mammals: The Next Generation of Precision Genome Editing. CRISPR J 2022; 5:746-768. [PMID: 36512351 DOI: 10.1089/crispr.2022.0084] [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: 12/15/2022] Open
Abstract
The recently established prime editor (PE) system is regarded as next-generation gene-editing technology. This methodology can install any base-to-base change as well as insertions and deletions without the requirement for double-stranded break formation or donor DNA templates; thus, it offers more targeting flexibility and greater editing precision than conventional CRISPR-Cas systems or base editors. In this study, we introduce the basic principles of PE and then review its most recent progress in terms of editing versatility, specificity, and efficiency in mammals. Next, we summarize key considerations regarding the selection of PE variants, prime editing guide RNA (pegRNA) design rules, and the efficiency and accuracy evaluation of PE. Finally, we highlight and discuss how PE can assist in a wide range of biological studies and how it can be applied to make precise genomic corrections in animal models, which paves the way for curing human diseases.
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Affiliation(s)
- Dawei Wang
- Department of Endocrinology, Shandong Provincial Hospital, Shandong University, Jinan, China; Central Hospital Affiliated to Shandong First Medical University, Jinan, China
- Department of Endocrinology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China; Central Hospital Affiliated to Shandong First Medical University, Jinan, China
- Shandong Engineering Research Center of Stem Cell and Gene Therapy for Endocrine and Metabolic Diseases, Jinan, China; Central Hospital Affiliated to Shandong First Medical University, Jinan, China
- Shandong Key Laboratory of Endocrinology and Lipid Metabolism, Jinan, China; and Central Hospital Affiliated to Shandong First Medical University, Jinan, China
| | - Xiude Fan
- Department of Endocrinology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China; Central Hospital Affiliated to Shandong First Medical University, Jinan, China
- Shandong Engineering Research Center of Stem Cell and Gene Therapy for Endocrine and Metabolic Diseases, Jinan, China; Central Hospital Affiliated to Shandong First Medical University, Jinan, China
- Shandong Key Laboratory of Endocrinology and Lipid Metabolism, Jinan, China; and Central Hospital Affiliated to Shandong First Medical University, Jinan, China
| | - Mengzhu Li
- Department of Endocrinology, Shandong Provincial Hospital, Shandong University, Jinan, China; Central Hospital Affiliated to Shandong First Medical University, Jinan, China
- Department of Endocrinology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China; Central Hospital Affiliated to Shandong First Medical University, Jinan, China
- Shandong Engineering Research Center of Stem Cell and Gene Therapy for Endocrine and Metabolic Diseases, Jinan, China; Central Hospital Affiliated to Shandong First Medical University, Jinan, China
- Shandong Key Laboratory of Endocrinology and Lipid Metabolism, Jinan, China; and Central Hospital Affiliated to Shandong First Medical University, Jinan, China
| | - Tianbo Liu
- Department of Endocrinology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China; Central Hospital Affiliated to Shandong First Medical University, Jinan, China
- Shandong Engineering Research Center of Stem Cell and Gene Therapy for Endocrine and Metabolic Diseases, Jinan, China; Central Hospital Affiliated to Shandong First Medical University, Jinan, China
- Shandong Key Laboratory of Endocrinology and Lipid Metabolism, Jinan, China; and Central Hospital Affiliated to Shandong First Medical University, Jinan, China
| | - Peng Lu
- Department of Endocrinology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China; Central Hospital Affiliated to Shandong First Medical University, Jinan, China
- Shandong Engineering Research Center of Stem Cell and Gene Therapy for Endocrine and Metabolic Diseases, Jinan, China; Central Hospital Affiliated to Shandong First Medical University, Jinan, China
- Shandong Key Laboratory of Endocrinology and Lipid Metabolism, Jinan, China; and Central Hospital Affiliated to Shandong First Medical University, Jinan, China
| | - Guangxin Wang
- Shandong Innovation Center of Intelligent Diagnosis, Central Hospital Affiliated to Shandong First Medical University, Jinan, China
| | - Yuan Li
- Department of Endocrinology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China; Central Hospital Affiliated to Shandong First Medical University, Jinan, China
- Shandong Engineering Research Center of Stem Cell and Gene Therapy for Endocrine and Metabolic Diseases, Jinan, China; Central Hospital Affiliated to Shandong First Medical University, Jinan, China
- Shandong Key Laboratory of Endocrinology and Lipid Metabolism, Jinan, China; and Central Hospital Affiliated to Shandong First Medical University, Jinan, China
| | - JunMing Han
- Department of Endocrinology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China; Central Hospital Affiliated to Shandong First Medical University, Jinan, China
- Shandong Engineering Research Center of Stem Cell and Gene Therapy for Endocrine and Metabolic Diseases, Jinan, China; Central Hospital Affiliated to Shandong First Medical University, Jinan, China
- Shandong Key Laboratory of Endocrinology and Lipid Metabolism, Jinan, China; and Central Hospital Affiliated to Shandong First Medical University, Jinan, China
| | - JiaJun Zhao
- Department of Endocrinology, Shandong Provincial Hospital, Shandong University, Jinan, China; Central Hospital Affiliated to Shandong First Medical University, Jinan, China
- Department of Endocrinology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China; Central Hospital Affiliated to Shandong First Medical University, Jinan, China
- Shandong Engineering Research Center of Stem Cell and Gene Therapy for Endocrine and Metabolic Diseases, Jinan, China; Central Hospital Affiliated to Shandong First Medical University, Jinan, China
- Shandong Key Laboratory of Endocrinology and Lipid Metabolism, Jinan, China; and Central Hospital Affiliated to Shandong First Medical University, Jinan, China
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196
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Design and synthesis of DNA hydrogel based on EXPAR and CRISPR/Cas14a for ultrasensitive detection of creatine kinase MB. Biosens Bioelectron 2022; 218:114792. [DOI: 10.1016/j.bios.2022.114792] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Accepted: 10/06/2022] [Indexed: 11/20/2022]
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197
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Zhao Y, Zhang M, Yang D. Bioinformatics approaches to analyzing CRISPR screen data: from dropout screens to single-cell CRISPR screens. QUANTITATIVE BIOLOGY 2022; 10:307-320. [PMID: 36937794 PMCID: PMC10019185] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/21/2023]
Abstract
Background Pooled CRISPR screen is a promising tool in drug targets or essential genes identification with the utilization of three different systems including CRISPR knockout (CRISPRko), CRISPR interference (CRISPRi) and CRISPR activation (CRISPRa). Aside from continuous improvements in technology, more and more bioinformatics methods have been developed to analyze the data obtained by CRISPR screens which facilitate better understanding of physiological effects. Results Here, we provide an overview on the application of CRISPR screens and bioinformatics approaches to analyzing different types of CRISPR screen data. We also discuss mechanisms and underlying challenges for the analysis of dropout screens, sorting-based screens and single-cell screens. Conclusion Different analysis approaches should be chosen based on the design of screens. This review will help community to better design novel algorithms and provide suggestions for wet-lab researchers to choose from different analysis methods.
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Affiliation(s)
- Yueshan Zhao
- Center for Pharmacogenetics, Department of Pharmaceutical Sciences, University of Pittsburgh, Pittsburgh PA 15261, USA
| | - Min Zhang
- Center for Pharmacogenetics, Department of Pharmaceutical Sciences, University of Pittsburgh, Pittsburgh PA 15261, USA
| | - Da Yang
- Center for Pharmacogenetics, Department of Pharmaceutical Sciences, University of Pittsburgh, Pittsburgh PA 15261, USA
- UPMC Hillman Cancer Institute, University of Pittsburgh, Pittsburgh, PA 15261, USA
- Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, PA 15261, USA
- Correspondence:
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Chen BC, Lin HY. Deletion of NTH1 and HSP12 increases the freeze–thaw resistance of baker’s yeast in bread dough. Microb Cell Fact 2022; 21:149. [PMID: 35879798 PMCID: PMC9310457 DOI: 10.1186/s12934-022-01876-4] [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: 04/26/2022] [Accepted: 07/07/2022] [Indexed: 11/15/2022] Open
Abstract
Background The intracellular molecule trehalose in Saccharomyces cerevisiae may have a major protective function under extreme environmental conditions. NTH1 is one gene which expresses trehalase to degrade trehalose. Small heat shock protein 12 (HSP12 expressed) plays a role in protecting membranes and enhancing freezing stress tolerance. Results An optimized S. cerevisiae CRISPR-Cpf1 genome-editing system was constructed. Multiplex genome editing using a single crRNA array was shown to be functional. NTH1 or/and HSP12 knockout in S. cerevisiae enhanced the freezing stress tolerance and improved the leavening ability after freezing and thawing. Conclusions Deleting NTH1 in the combination with deleting HSP12 would strengthen the freezing tolerance and protect the cell viability from high rates of death in longer-term freezing. It provides valuable insights for breeding novel S. cerevisiae strains for the baking industry through a more precise, speedy, and economic genome-editing system.
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Cha JY, Ahn G, Jeong SY, Shin GI, Ali I, Ji MG, Alimzhan A, Lee SY, Kim MG, Kim WY. Nucleoredoxin 1 positively regulates heat stress tolerance by enhancing the transcription of antioxidants and heat-shock proteins in tomato. Biochem Biophys Res Commun 2022; 635:12-18. [DOI: 10.1016/j.bbrc.2022.10.033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Accepted: 10/07/2022] [Indexed: 11/28/2022]
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Wang S, Guo M, Zhu Y, Lin Z, Huang Z. Cryo-EM structure of the type III-E CRISPR-Cas effector gRAMP in complex with TPR-CHAT. Cell Res 2022; 32:1128-1131. [PMID: 36280712 PMCID: PMC9715532 DOI: 10.1038/s41422-022-00738-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2022] [Accepted: 10/07/2022] [Indexed: 01/31/2023] Open
Affiliation(s)
- Shuo Wang
- HIT Center for Life Sciences, School of Life Science and Technology, Harbin Institute of Technology, Harbin, Heilongjiang, China
| | - Minghui Guo
- HIT Center for Life Sciences, School of Life Science and Technology, Harbin Institute of Technology, Harbin, Heilongjiang, China
| | - Yuwei Zhu
- HIT Center for Life Sciences, School of Life Science and Technology, Harbin Institute of Technology, Harbin, Heilongjiang, China
| | - Zhiying Lin
- HIT Center for Life Sciences, School of Life Science and Technology, Harbin Institute of Technology, Harbin, Heilongjiang, China
| | - Zhiwei Huang
- HIT Center for Life Sciences, School of Life Science and Technology, Harbin Institute of Technology, Harbin, Heilongjiang, China.
- Westlake Center for Genome Editing, Westlake Laboratory of Life Sciences and Biomedicine, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China.
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