{"technology":{"slug":"crispr","name":"CRISPR Gene Editing","description":"CRISPR-Cas9 and related gene editing technologies for precision genome modification. Covers therapeutic applications, agricultural biotech, gene drives, and ethical considerations.","discipline":"Biology / Genetics","icon":"🧬"},"lastUpdated":"2026-04-11T05:58:40.505Z","articleCount":22,"articles":[{"id":"oa-W3112179900","title":"CRISPR-Cas9 Gene Editing for Sickle Cell Disease and β-Thalassemia","authors":"Haydar Frangoul, David Altshuler, Maria Domenica Cappellini, Yi-Shan Chen, Jennifer Domm, Brenda K. Eustace, Juergen Foell, Josu de la Fuente, Stephan A. Grupp, Rupert Handgretinger, Tony W. Ho, Antonis Kattamis, Andrew Kernytsky, Julie Lekstrom-Himes, Amanda M. Li, Franco Locatelli, Markus Y. Mapara, Mariane de Montalembert, Damiano Rondelli, Akshay Sharma, Sujit Sheth, Sandeep Soni, Martin H. Steinberg, Donna A. Wall, Angela Yen, Selim Corbacioglu","journal":"New England Journal of Medicine","pubDate":"2020-12-05","doi":"10.1056/nejmoa2031054","abstract":"Transfusion-dependent β-thalassemia (TDT) and sickle cell disease (SCD) are severe monogenic diseases with severe and potentially life-threatening manifestations. BCL11A is a transcription factor that represses γ-globin expression and fetal hemoglobin in erythroid cells. We performed electroporation of CD34+ hematopoietic stem and progenitor cells obtained from healthy donors, with CRISPR-Cas9 targeting the <i>BCL11A</i> erythroid-specific enhancer. Approximately 80% of the alleles at this locus were modified, with no evidence of off-target editing. After undergoing myeloablation, two patients - one with TDT and the other with SCD - received autologous CD34+ cells edited with CRISPR-Cas9 targeting the same <i>BCL11A</i> enhancer. More than a year later, both patients had high levels of allelic editing in bone marrow and blood, increases in fetal hemoglobin that were distributed pancellularly, transfusion independence, and (in the patient with SCD) elimination of vaso-occlusive episodes. (Funded by CRISPR Therapeutics and Vertex Pharmaceuticals; ClinicalTrials.gov numbers, NCT03655678 for CLIMB THAL-111 and NCT03745287 for CLIMB SCD-121.).","tldr":"","source":"OpenAlex","sourceUrl":"https://openalex.org/W3112179900","citationCount":1769,"isOpenAccess":true,"pdfUrl":"https://www.nejm.org/doi/pdf/10.1056/NEJMoa2031054?articleTools=true"},{"id":"oa-W3177445623","title":"CRISPR-Cas9 In Vivo Gene Editing for Transthyretin Amyloidosis","authors":"Julian D. Gillmore, Ed Gane, Jörg Täubel, Justin Kao, Marianna Fontana, Michael L. Maitland, Jessica Seitzer, Daniel J. O’Connell, Kathryn Walsh, Kristy Wood, Jonathan A. Phillips, Yuanxin Xu, Adam Amaral, Adam P. Boyd, Jeffrey Cehelsky, Mark D. McKee, Andrew Schiermeier, Olivier Harari, Andrew Murphy, Christos A. Kyratsous, Brian Zambrowicz, Randy Soltys, David E. Gutstein, John P. Leonard, Laura Sepp‐Lorenzino, David Lebwohl","journal":"New England Journal of Medicine","pubDate":"2021-06-26","doi":"10.1056/nejmoa2107454","abstract":"In a small group of patients with hereditary ATTR amyloidosis with polyneuropathy, administration of NTLA-2001 was associated with only mild adverse events and led to decreases in serum TTR protein concentrations through targeted knockout of <i>TTR</i>. (Funded by Intellia Therapeutics and Regeneron Pharmaceuticals; ClinicalTrials.gov number, NCT04601051.).","tldr":"","source":"OpenAlex","sourceUrl":"https://openalex.org/W3177445623","citationCount":1572,"isOpenAccess":true,"pdfUrl":"https://www.nejm.org/doi/pdf/10.1056/NEJMoa2107454?articleTools=true"},{"id":"oa-W2141825721","title":"CRISPR/Cas9-mediated gene editing in human tripronuclear zygotes","authors":"Puping Liang, Yanwen Xu, Xiya Zhang, Chenhui Ding, Rui Huang, Zhen Zhang, Jie Lv, Xiaowei Xie, Yuxi Chen, Yujing Li, Ying Sun, Yaofu Bai, Zhou Songyang, Wenbin Ma, Canquan Zhou, Junjiu Huang","journal":"Protein & Cell","pubDate":"2015-04-17","doi":"10.1007/s13238-015-0153-5","abstract":"Genome editing tools such as the clustered regularly interspaced short palindromic repeat (CRISPR)-associated system (Cas) have been widely used to modify genes in model systems including animal zygotes and human cells, and hold tremendous promise for both basic research and clinical applications. To date, a serious knowledge gap remains in our understanding of DNA repair mechanisms in human early embryos, and in the efficiency and potential off-target effects of using technologies such as CRISPR/Cas9 in human pre-implantation embryos. In this report, we used tripronuclear (3PN) zygotes to further investigate CRISPR/Cas9-mediated gene editing in human cells. We found that CRISPR/Cas9 could effectively cleave the endogenous β-globin gene (HBB). However, the efficiency of homologous recombination directed repair (HDR) of HBB was low and the edited embryos were mosaic. Off-target cleavage was also apparent in these 3PN zygotes as revealed by the T7E1 assay and whole-exome sequencing. Furthermore, the endogenous delta-globin gene (HBD), which is homologous to HBB, competed with exogenous donor oligos to act as the repair template, leading to untoward mutations. Our data also indicated that repair of the HBB locus in these embryos occurred preferentially through the non-crossover HDR pathway. Taken together, our work highlights the pressing need to further improve the fidelity and specificity of the CRISPR/Cas9 platform, a prerequisite for any clinical applications of CRSIPR/Cas9-mediated editing.","tldr":"","source":"OpenAlex","sourceUrl":"https://openalex.org/W2141825721","citationCount":1108,"isOpenAccess":true,"pdfUrl":"https://link.springer.com/content/pdf/10.1007/s13238-015-0153-5.pdf"},{"id":"s2-07c69f7ddd34ca8c80618e16981e2fbdb0de6529","title":"CRISPR-Cas9 Gene Editing for Sickle Cell Disease and β-Thalassemia.","authors":"H. Frangoul, D. Altshuler, M. Cappellini, Yi-Shan Chen, J. Domm, Brenda K. Eustace, J. Foell, J. de la Fuente, S. Grupp, R. Handgretinger, Tony Ho, A. Kattamis, A. Kernytsky, J. Lekstrom-Himes, Amanda M Li, F. Locatelli, M. Mapara, M. de Montalembert, D. Rondelli, Akshay Sharma, S. Sheth, S. Soni, M. Steinberg, D. Wall, Angela Yen, S. Corbacioglu","journal":"The New England journal of medicine","pubDate":"2020","doi":"10.1056/NEJMoa2031054","abstract":"Transfusion-dependent β-thalassemia (TDT) and sickle cell disease (SCD) are severe monogenic diseases with severe and potentially life-threatening manifestations. BCL11A is a transcription factor that represses γ-globin expression and fetal hemoglobin in erythroid cells. We performed electroporation of CD34+ hematopoietic stem and progenitor cells obtained from healthy donors, with CRISPR-Cas9 targeting the BCL11A erythroid-specific enhancer. Approximately 80% of the alleles at this locus were modified, with no evidence of off-target editing. After undergoing myeloablation, two patients - one with TDT and the other with SCD - received autologous CD34+ cells edited with CRISPR-Cas9 targeting the same BCL11A enhancer. More than a year later, both patients had high levels of allelic editing in bone marrow and blood, increases in fetal hemoglobin that were distributed pancellularly, transfusion independence, and (in the patient with SCD) elimination of vaso-occlusive episodes. (Funded by CRISPR Therapeutics and Vertex Pharmaceuticals; ClinicalTrials.gov numbers, NCT03655678 for CLIMB THAL-111 and NCT03745287 for CLIMB SCD-121.).","tldr":"Electroporation of CD34+ hematopoietic stem and progenitor cells obtained from healthy donors was performed, with CRISPR-Cas9 targeting the BCL11A erythroid-specific enhancer, and approximately 80% of the alleles at this locus were modified, with no evidence of off-target editing.","source":"Semantic Scholar","sourceUrl":"https://www.semanticscholar.org/paper/07c69f7ddd34ca8c80618e16981e2fbdb0de6529","citationCount":1058,"isOpenAccess":true,"pdfUrl":"https://www.nejm.org/doi/pdf/10.1056/NEJMoa2031054?articleTools=true"},{"id":"s2-5ee44d9fa67f9d3bd423067ca9f01ac4bb4e43c1","title":"Delivery strategies of the CRISPR‐Cas9 gene‐editing system for therapeutic applications","authors":"Chang Liu, Li Zhang, Hao Liu, K. Cheng","journal":"Journal of Controlled Release","pubDate":"2017","doi":"10.1016/j.jconrel.2017.09.012","abstract":"","tldr":"The molecular mechanism and different strategies to edit genes using the CRISPR‐Cas9 system are introduced and the current systems that have been developed to deliver CRISpr‐ Cas9 in vitro and in vivo for various therapeutic purposes are highlighted.","source":"Semantic Scholar","sourceUrl":"https://www.semanticscholar.org/paper/5ee44d9fa67f9d3bd423067ca9f01ac4bb4e43c1","citationCount":485,"isOpenAccess":true,"pdfUrl":"https://europepmc.org/articles/pmc5723556?pdf=render"},{"id":"s2-ee3fc4548be78b7118b82051f44a3e6c4ce8ef78","title":"Off-target effects in CRISPR/Cas9 gene editing","authors":"Congting Guo, Xiaoteng Ma, Fei Gao, Yuxuan Guo","journal":"Frontiers in Bioengineering and Biotechnology","pubDate":"2023","doi":"10.3389/fbioe.2023.1143157","abstract":"Gene editing stands for the methods to precisely make changes to a specific nucleic acid sequence. With the recent development of the clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9 system, gene editing has become efficient, convenient and programmable, leading to promising translational studies and clinical trials for both genetic and non-genetic diseases. A major concern in the applications of the CRISPR/Cas9 system is about its off-target effects, namely the deposition of unexpected, unwanted, or even adverse alterations to the genome. To date, many methods have been developed to nominate or detect the off-target sites of CRISPR/Cas9, which laid the basis for the successful upgrades of CRISPR/Cas9 derivatives with enhanced precision. In this review, we summarize these technological advancements and discuss about the current challenges in the management of off-target effects for future gene therapy.","tldr":"To date, many methods have been developed to nominate or detect the off-target sites of CRISPR/Cas9, which laid the basis for the successful upgrades of CRisPR/ Cas9 derivatives with enhanced precision, and about the current challenges in the management of off- target effects for future gene therapy.","source":"Semantic Scholar","sourceUrl":"https://www.semanticscholar.org/paper/ee3fc4548be78b7118b82051f44a3e6c4ce8ef78","citationCount":402,"isOpenAccess":true,"pdfUrl":"https://www.frontiersin.org/articles/10.3389/fbioe.2023.1143157/pdf"},{"id":"s2-cda0679e86ce8af508a4e5b83b587d4be183cd70","title":"Current applications and future perspective of CRISPR/Cas9 gene editing in cancer","authors":"Si-wei Wang, Chao Gao, Yi-Min Zheng, Li Yi, Jia-Cheng Lu, Xiao-yong Huang, Jia-Bin Cai, Peng-fei Zhang, Yuexin Cui, A. Ke","journal":"Molecular Cancer","pubDate":"2022","doi":"10.1186/s12943-022-01518-8","abstract":"Clustered regularly interspaced short palindromic repeats (CRISPR) system provides adaptive immunity against plasmids and phages in prokaryotes. This system inspires the development of a powerful genome engineering tool, the CRISPR/CRISPR-associated nuclease 9 (CRISPR/Cas9) genome editing system. Due to its high efficiency and precision, the CRISPR/Cas9 technique has been employed to explore the functions of cancer-related genes, establish tumor-bearing animal models and probe drug targets, vastly increasing our understanding of cancer genomics. Here, we review current status of CRISPR/Cas9 gene editing technology in oncological research. We first explain the basic principles of CRISPR/Cas9 gene editing and introduce several new CRISPR-based gene editing modes. We next detail the rapid progress of CRISPR screening in revealing tumorigenesis, metastasis, and drug resistance mechanisms. In addition, we introduce CRISPR/Cas9 system delivery vectors and finally demonstrate the potential of CRISPR/Cas9 engineering to enhance the effect of adoptive T cell therapy (ACT) and reduce adverse reactions.","tldr":"The basic principles ofCRISPR/Cas9 gene editing are explained and several new CRISPR-based gene editing modes are introduced, and the rapid progress of CRISpr screening in revealing tumorigenesis, metastasis, and drug resistance mechanisms are detailed.","source":"Semantic Scholar","sourceUrl":"https://www.semanticscholar.org/paper/cda0679e86ce8af508a4e5b83b587d4be183cd70","citationCount":358,"isOpenAccess":true,"pdfUrl":"https://molecular-cancer.biomedcentral.com/track/pdf/10.1186/s12943-022-01518-8"},{"id":"s2-6ed5821eb6473824fab4e21ecffa9e2c3dbe6246","title":"Significant enhancement of fatty acid composition in seeds of the allohexaploid, Camelina sativa, using CRISPR/Cas9 gene editing","authors":"W. Jiang, I. Henry, Peter G. Lynagh, L. Comai, E. Cahoon, D. Weeks","journal":"Plant Biotechnology Journal","pubDate":"2017","doi":"10.1111/pbi.12663","abstract":"Summary The CRISPR/Cas9 nuclease system is a powerful and flexible tool for genome editing, and novel applications of this system are being developed rapidly. Here, we used CRISPR/Cas9 to target the FAD2 gene in Arabidopsis thaliana and in the closely related emerging oil seed plant, Camelina sativa, with the goal of improving seed oil composition. We successfully obtained Camelina seeds in which oleic acid content was increased from 16% to over 50% of the fatty acid composition. These increases were associated with significant decreases in the less desirable polyunsaturated fatty acids, linoleic acid (i.e. a decrease from ~16% to <4%) and linolenic acid (a decrease from ~35% to <10%). These changes result in oils that are superior on multiple levels: they are healthier, more oxidatively stable and better suited for production of certain commercial chemicals, including biofuels. As expected, A. thaliana T2 and T3 generation seeds exhibiting these types of altered fatty acid profiles were homozygous for disrupted FAD2 alleles. In the allohexaploid, Camelina, guide RNAs were designed that simultaneously targeted all three homoeologous FAD2 genes. This strategy that significantly enhanced oil composition in T3 and T4 generation Camelina seeds was associated with a combination of germ‐line mutations and somatic cell mutations in FAD2 genes in each of the three Camelina subgenomes.","tldr":"A CRISPR/Cas9 strategy that significantly enhanced oil composition in T3 and T4 generation Camelina seeds was associated with a combination of germ‐line mutations and somatic cell mutations in FAD2 genes in each of the three Camelina subgenomes.","source":"Semantic Scholar","sourceUrl":"https://www.semanticscholar.org/paper/6ed5821eb6473824fab4e21ecffa9e2c3dbe6246","citationCount":302,"isOpenAccess":true,"pdfUrl":"https://onlinelibrary.wiley.com/doi/pdfdirect/10.1111/pbi.12663"},{"id":"s2-8b9b236b38ce529c71a4f1aae7f3f9fa95216b1f","title":"Elimination of HIV-1 Genomes from Human T-lymphoid Cells by CRISPR/Cas9 Gene Editing","authors":"R. Kamiński, Yilan Chen, Tracy Fischer, E. Tedaldi, A. Napoli, Yonggang Zhang, J. Karn, Wenhui Hu, K. Khalili","journal":"Scientific Reports","pubDate":"2015","doi":"10.1038/srep22555","abstract":"We employed an RNA-guided CRISPR/Cas9 DNA editing system to precisely remove the entire HIV-1 genome spanning between 5′ and 3′ LTRs of integrated HIV-1 proviral DNA copies from latently infected human CD4+ T-cells. Comprehensive assessment of whole-genome sequencing of HIV-1 eradicated cells ruled out any off-target effects by our CRISPR/Cas9 technology that might compromise the integrity of the host genome and further showed no effect on several cell health indices including viability, cell cycle and apoptosis. Persistent co-expression of Cas9 and the specific targeting guide RNAs in HIV-1-eradicated T-cells protected them against new infection by HIV-1. Lentivirus-delivered CRISPR/Cas9 significantly diminished HIV-1 replication in infected primary CD4+ T-cell cultures and drastically reduced viral load in ex vivo culture of CD4+ T-cells obtained from HIV-1 infected patients. Thus, gene editing using CRISPR/Cas9 may provide a new therapeutic path for eliminating HIV-1 DNA from CD4+ T-cells and potentially serve as a novel and effective platform toward curing AIDS.","tldr":"Gene editing using CRISPR/Cas9 may provide a new therapeutic path for eliminating HIV-1 DNA from CD4+ T-cells and potentially serve as a novel and effective platform toward curing AIDS.","source":"Semantic Scholar","sourceUrl":"https://www.semanticscholar.org/paper/8b9b236b38ce529c71a4f1aae7f3f9fa95216b1f","citationCount":295,"isOpenAccess":true,"pdfUrl":"https://doi.org/10.1016/s2055-6640(20)31337-6"},{"id":"s2-334a60ae88d3926699991115a8ad4f632c302ed1","title":"A boronic acid–rich dendrimer with robust and unprecedented efficiency for cytosolic protein delivery and CRISPR-Cas9 gene editing","authors":"Chongyi Liu, Tao Wan, Hui Wang, Song Zhang, Y. Ping, Yiyun Cheng","journal":"Science Advances","pubDate":"2019","doi":"10.1126/sciadv.aaw8922","abstract":"We report the rational design of a polymer with unprecedented and robust efficiency for cytosolic delivery of native proteins. Cytosolic protein delivery is of central importance for the development of protein-based biotechnologies and therapeutics; however, efficient intracellular delivery of native proteins remains a challenge. Here, we reported a boronic acid–rich dendrimer with unprecedented efficiency for cytosolic delivery of native proteins. The dendrimer could bind with both negatively and positively charged proteins and efficiently delivered 13 cargo proteins into the cytosol of living cells. All the delivered proteins kept their bioactivities after cytosolic delivery. The dendrimer ensures efficient intracellular delivery of Cas9 protein into various cell lines and showed high efficiency in CRISPR-Cas9 genome editing. The rationally designed boronic acid–rich dendrimer permits the development of an efficient platform with high generality for the delivery of native proteins.","tldr":"The rational design of a polymer with unprecedented and robust efficiency for cytosolic delivery of native proteins and ensures efficient intracellular delivery of Cas9 protein into various cell lines and showed high efficiency in CRISPR-Cas9 genome editing.","source":"Semantic Scholar","sourceUrl":"https://www.semanticscholar.org/paper/334a60ae88d3926699991115a8ad4f632c302ed1","citationCount":293,"isOpenAccess":true,"pdfUrl":"https://advances.sciencemag.org/content/advances/5/6/eaaw8922.full.pdf"},{"id":"oa-W2199356015","title":"In Vivo CRISPR/Cas9 Gene Editing Corrects Retinal Dystrophy in the S334ter-3 Rat Model of Autosomal Dominant Retinitis Pigmentosa","authors":"Benjamin Bakondi, Wenjian Lv, Bin Lü, Melissa K. Jones, Yu-Chun Tsai, Kevin J. Kim, Rachelle Levy, Aslam Abbasi Akhtar, Joshua J. Breunig, Clive N. Svendsen, Shaomei Wang","journal":"Molecular Therapy","pubDate":"2015-12-15","doi":"10.1038/mt.2015.220","abstract":"Reliable genome editing via Clustered Regularly Interspaced Short Palindromic Repeat (CRISPR)/Cas9 may provide a means to correct inherited diseases in patients. As proof of principle, we show that CRISPR/Cas9 can be used in vivo to selectively ablate the rhodopsin gene carrying the dominant S334ter mutation (Rho(S334)) in rats that model severe autosomal dominant retinitis pigmentosa. A single subretinal injection of guide RNA/Cas9 plasmid in combination with electroporation generated allele-specific disruption of Rho(S334), which prevented retinal degeneration and improved visual function.","tldr":"","source":"OpenAlex","sourceUrl":"https://openalex.org/W2199356015","citationCount":290,"isOpenAccess":true,"pdfUrl":"http://www.cell.com/article/S152500161630973X/pdf"},{"id":"oa-W2092493681","title":"Optical Control of CRISPR/Cas9 Gene Editing","authors":"James Hemphill, Erin K. Borchardt, Kalyn A. Brown, Aravind Asokan, Alexander Deiters","journal":"Journal of the American Chemical Society","pubDate":"2015-04-23","doi":"10.1021/ja512664v","abstract":"The CRISPR/Cas9 system has emerged as an important tool in biomedical research for a wide range of applications, with significant potential for genome engineering and gene therapy. In order to achieve conditional control of the CRISPR/Cas9 system, a genetically encoded light-activated Cas9 was engineered through the site-specific installation of a caged lysine amino acid. Several potential lysine residues were identified as viable caging sites that can be modified to optically control Cas9 function, as demonstrated through optical activation and deactivation of both exogenous and endogenous gene function.","tldr":"","source":"OpenAlex","sourceUrl":"https://openalex.org/W2092493681","citationCount":271,"isOpenAccess":false,"pdfUrl":""},{"id":"s2-5d923eebf9f2306e65ee75710a4468189c784dfc","title":"Engineering the next-generation of CAR T-cells with CRISPR-Cas9 gene editing","authors":"Alexander J Dimitri, F. Herbst, J. Fraietta","journal":"Molecular Cancer","pubDate":"2022","doi":"10.1186/s12943-022-01559-z","abstract":"Chimeric Antigen Receptor (CAR) T-cells represent a breakthrough in personalized cancer therapy. In this strategy, synthetic receptors comprised of antigen recognition, signaling, and costimulatory domains are used to reprogram T-cells to target tumor cells for destruction. Despite the success of this approach in refractory B-cell malignancies, optimal potency of CAR T-cell therapy for many other cancers, particularly solid tumors, has not been achieved. Factors such as T-cell exhaustion, lack of CAR T-cell persistence, cytokine-related toxicities, and bottlenecks in the manufacturing of autologous products have hampered the safety, effectiveness, and availability of this approach. With the ease and accessibility of CRISPR-Cas9-based gene editing, it is possible to address many of these limitations. Accordingly, current research efforts focus on precision engineering of CAR T-cells with conventional CRISPR-Cas9 systems or novel editors that can install desired genetic changes with or without introduction of a double-stranded break (DSB) into the genome. These tools and strategies can be directly applied to targeting negative regulators of T-cell function, directing therapeutic transgenes to specific genomic loci, and generating reproducibly safe and potent allogeneic universal CAR T-cell products for on-demand cancer immunotherapy. This review evaluates several of the ongoing and future directions of combining next-generation CRISPR-Cas9 gene editing with synthetic biology to optimize CAR T-cell therapy for future clinical trials toward the establishment of a new cancer treatment paradigm.","tldr":"This review evaluates several of the ongoing and future directions of combining next-generation CRISPR-Cas9 gene editing with synthetic biology to optimize CAR T-cell therapy for future clinical trials toward the establishment of a new cancer treatment paradigm.","source":"Semantic Scholar","sourceUrl":"https://www.semanticscholar.org/paper/5d923eebf9f2306e65ee75710a4468189c784dfc","citationCount":269,"isOpenAccess":true,"pdfUrl":"https://molecular-cancer.biomedcentral.com/track/pdf/10.1186/s12943-022-01559-z"},{"id":"oa-W2269688815","title":"Outbred genome sequencing and CRISPR/Cas9 gene editing in butterflies","authors":"Xueyan Li, Dingding Fan, Wei Zhang, Guichun Liu, Lu Zhang, Li Zhao, Xiaodong Fang, Lei Chen, Yang Dong, Yuan Chen, Yun Ding, Ruoping Zhao, Mingji Feng, Yabing Zhu, Yue Feng, Xuanting Jiang, Deying Zhu, Zhonghuai Xiang, Xikan Feng, Shuai Cheng Li, Jun Wang, Guojie Zhang, Marcus R. Kronforst, Wen Wang","journal":"Nature Communications","pubDate":"2015-09-10","doi":"10.1038/ncomms9212","abstract":"Butterflies are exceptionally diverse but their potential as an experimental system has been limited by the difficulty of deciphering heterozygous genomes and a lack of genetic manipulation technology. Here we use a hybrid assembly approach to construct high-quality reference genomes for Papilio xuthus (contig and scaffold N50: 492 kb, 3.4 Mb) and Papilio machaon (contig and scaffold N50: 81 kb, 1.15 Mb), highly heterozygous species that differ in host plant affiliations, and adult and larval colour patterns. Integrating comparative genomics and analyses of gene expression yields multiple insights into butterfly evolution, including potential roles of specific genes in recent diversification. To functionally test gene function, we develop an efficient (up to 92.5%) CRISPR/Cas9 gene editing method that yields obvious phenotypes with three genes, Abdominal-B, ebony and frizzled. Our results provide valuable genomic and technological resources for butterflies and unlock their potential as a genetic model system.","tldr":"","source":"OpenAlex","sourceUrl":"https://openalex.org/W2269688815","citationCount":232,"isOpenAccess":true,"pdfUrl":"https://www.nature.com/articles/ncomms9212.pdf"},{"id":"oa-W2783508188","title":"Efficient oligo nucleotide mediated CRISPR-Cas9 gene editing in Aspergilli","authors":"Christina Spuur Nødvig, Jakob Blæsbjerg Hoof, Martin E. Kogle, Zofia Dorota Jarczynska, Jan Lehmbeck, Dorte K. Klitgaard, Uffe Hasbro Mortensen","journal":"Fungal Genetics and Biology","pubDate":"2018-01-08","doi":"10.1016/j.fgb.2018.01.004","abstract":"","tldr":"","source":"OpenAlex","sourceUrl":"https://openalex.org/W2783508188","citationCount":200,"isOpenAccess":true,"pdfUrl":"https://orbit.dtu.dk/en/publications/907485db-a5bd-4e3f-94b7-9062ca1f4560"},{"id":"s2-9a1edb792994e96ebdc1637dfbf365cb6c2d2ba1","title":"Off-target predictions in CRISPR-Cas9 gene editing using deep learning","authors":"Jiecong Lin, Ka-chun Wong","journal":"Bioinformatics","pubDate":"2018","doi":"10.1093/bioinformatics/bty554","abstract":"Motivation The prediction of off‐target mutations in CRISPR‐Cas9 is a hot topic due to its relevance to gene editing research. Existing prediction methods have been developed; however, most of them just calculated scores based on mismatches to the guide sequence in CRISPR‐Cas9. Therefore, the existing prediction methods are unable to scale and improve their performance with the rapid expansion of experimental data in CRISPR‐Cas9. Moreover, the existing methods still cannot satisfy enough precision in off‐target predictions for gene editing at the clinical level. Results To address it, we design and implement two algorithms using deep neural networks to predict off‐target mutations in CRISPR‐Cas9 gene editing (i.e. deep convolutional neural network and deep feedforward neural network). The models were trained and tested on the recently released off‐target dataset, CRISPOR dataset, for performance benchmark. Another off‐target dataset identified by GUIDE‐seq was adopted for additional evaluation. We demonstrate that convolutional neural network achieves the best performance on CRISPOR dataset, yielding an average classification area under the ROC curve (AUC) of 97.2% under stratified 5‐fold cross‐validation. Interestingly, the deep feedforward neural network can also be competitive at the average AUC of 97.0% under the same setting. We compare the two deep neural network models with the state‐of‐the‐art off‐target prediction methods (i.e. CFD, MIT, CROP‐IT, and CCTop) and three traditional machine learning models (i.e. random forest, gradient boosting trees, and logistic regression) on both datasets in terms of AUC values, demonstrating the competitive edges of the proposed algorithms. Additional analyses are conducted to investigate the underlying reasons from different perspectives. Availability and implementation The example code are available at https://github.com/MichaelLinn/off_target_prediction. The related datasets are available at https://github.com/MichaelLinn/off_target_prediction/tree/master/data.","tldr":"Convolutional neural network achieves the best performance on CRISPOR dataset, yielding an average classification area under the ROC curve (AUC) of 97.2% under stratified 5‐fold cross‐validation, and the deep feedforward neural network can also be competitive at the average AUC of 96.0% under the same setting.","source":"Semantic Scholar","sourceUrl":"https://www.semanticscholar.org/paper/9a1edb792994e96ebdc1637dfbf365cb6c2d2ba1","citationCount":160,"isOpenAccess":true,"pdfUrl":"https://academic.oup.com/bioinformatics/article-pdf/34/17/i656/25702338/bty554.pdf"},{"id":"s2-111a529d67e97e8901c3175310e3ea3ffc1fefb3","title":"Spatiotemporal control of CRISPR/Cas9 gene editing","authors":"Chenya Zhuo, Jiabin Zhang, Jung-Hwan Lee, J. Jiao, Du Cheng, Li Liu, H. Kim, Yu Tao, Mingqiang Li","journal":"Signal Transduction and Targeted Therapy","pubDate":"2021","doi":"10.1038/s41392-021-00645-w","abstract":"The clustered regularly interspaced short palindromic repeats (CRISPR)/associated protein 9 (CRISPR/Cas9) gene editing technology, as a revolutionary breakthrough in genetic engineering, offers a promising platform to improve the treatment of various genetic and infectious diseases because of its simple design and powerful ability to edit different loci simultaneously. However, failure to conduct precise gene editing in specific tissues or cells within a certain time may result in undesirable consequences, such as serious off-target effects, representing a critical challenge for the clinical translation of the technology. Recently, some emerging strategies using genetic regulation, chemical and physical strategies to regulate the activity of CRISPR/Cas9 have shown promising results in the improvement of spatiotemporal controllability. Herein, in this review, we first summarize the latest progress of these advanced strategies involving cell-specific promoters, small-molecule activation and inhibition, bioresponsive delivery carriers, and optical/thermal/ultrasonic/magnetic activation. Next, we highlight the advantages and disadvantages of various strategies and discuss their obstacles and limitations in clinical translation. Finally, we propose viewpoints on directions that can be explored to further improve the spatiotemporal operability of CRISPR/Cas9.","tldr":"This review summarizes the latest progress of these advanced strategies involving cell-specific promoters, small-molecule activation and inhibition, bioresponsive delivery carriers, and optical/thermal/ultrasonic/magnetic activation and proposes viewpoints on directions that can be explored to further improve the spatiotemporal operability of CRISPR/Cas9.","source":"Semantic Scholar","sourceUrl":"https://www.semanticscholar.org/paper/111a529d67e97e8901c3175310e3ea3ffc1fefb3","citationCount":151,"isOpenAccess":true,"pdfUrl":"https://www.nature.com/articles/s41392-021-00645-w.pdf"},{"id":"s2-edcf65933fce7aca9bcf76bb1762dcddda750704","title":"CRISPR/Cas9 gene editing: a new approach for overcoming drug resistance in cancer","authors":"Mostafa Vaghari-Tabari, Parisa Hassanpour, Fatemeh Sadeghsoltani, Faezeh Malakoti, Forough Alemi, D. Qujeq, Z. Asemi, B. Yousefi","journal":"Cellular & Molecular Biology Letters","pubDate":"2022","doi":"10.1186/s11658-022-00348-2","abstract":"The CRISPR/Cas9 system is an RNA-based adaptive immune system in bacteria and archaea. Various studies have shown that it is possible to target a wide range of human genes and treat some human diseases, including cancers, by the CRISPR/Cas9 system. In fact, CRISPR/Cas9 gene editing is one of the most efficient genome manipulation techniques. Studies have shown that CRISPR/Cas9 technology, in addition to having the potential to be used as a new therapeutic approach in the treatment of cancers, can also be used to enhance the effectiveness of existing treatments. Undoubtedly, the issue of drug resistance is one of the main obstacles in the treatment of cancers. Cancer cells resist anticancer drugs by a variety of mechanisms, such as enhancing anticancer drugs efflux, enhancing DNA repair, enhancing stemness, and attenuating apoptosis. Mutations in some proteins of different cellular signaling pathways are associated with these events and drug resistance. Recent studies have shown that the CRISPR/Cas9 technique can be used to target important genes involved in these mechanisms, thereby increasing the effectiveness of anticancer drugs. In this review article, studies related to the applications of this technique in overcoming drug resistance in cancer cells will be reviewed. In addition, we will give a brief overview of the limitations of the CRISP/Cas9 gene-editing technique.","tldr":"Studies related to the applications of this technique in overcoming drug resistance in cancer cells will be reviewed and a brief overview of the limitations of the CRISP/Cas9 gene-editing technique is given.","source":"Semantic Scholar","sourceUrl":"https://www.semanticscholar.org/paper/edcf65933fce7aca9bcf76bb1762dcddda750704","citationCount":103,"isOpenAccess":true,"pdfUrl":"https://cmbl.biomedcentral.com/counter/pdf/10.1186/s11658-022-00348-2"},{"id":"s2-2ec33a956fd6f8ee3ef3be4e3324da62b5e00375","title":"Revolutionizing cancer treatment: enhancing CAR-T cell therapy with CRISPR/Cas9 gene editing technology","authors":"Ruiyu Tao, Xiaopeng Han, Xue Bai, Jianping Yu, Youwei Ma, Weikai Chen, Dawei Zhang, Zhengkai Li","journal":"Frontiers in Immunology","pubDate":"2024","doi":"10.3389/fimmu.2024.1354825","abstract":"CAR-T cell therapy, a novel immunotherapy, has made significant breakthroughs in clinical practice, particularly in treating B-cell-associated leukemia and lymphoma. However, it still faces challenges such as poor persistence, limited proliferation capacity, high manufacturing costs, and suboptimal efficacy. CRISPR/Cas system, an efficient and simple method for precise gene editing, offers new possibilities for optimizing CAR-T cells. It can increase the function of CAR-T cells and reduce manufacturing costs. The combination of CRISPR/Cas9 technology and CAR-T cell therapy may promote the development of this therapy and provide more effective and personalized treatment for cancer patients. Meanwhile, the safety issues surrounding the application of this technology in CAR-T cells require further research and evaluation. Future research should focus on improving the accuracy and safety of CRISPR/Cas9 technology to facilitate the better development and application of CAR-T cell therapy. This review focuses on the application of CRISPR/Cas9 technology in CAR-T cell therapy, including eliminating the inhibitory effect of immune checkpoints, enhancing the ability of CAR-T cells to resist exhaustion, assisting in the construction of universal CAR-T cells, reducing the manufacturing costs of CAR-T cells, and the security problems faced. The objective is to show the revolutionary role of CRISPR/Cas9 technology in CAR-T cell therapy for researchers.","tldr":"This review focuses on the application of CRISPR/Cas9 technology in CAR-T cell therapy, including eliminating the inhibitory effect of immune checkpoints, enhancing the ability of CAR-T cells to resist exhaustion, assisting in the construction of universal CAR-T cells, reducing the manufacturing costs of CAR-T cells, and the security problems faced.","source":"Semantic Scholar","sourceUrl":"https://www.semanticscholar.org/paper/2ec33a956fd6f8ee3ef3be4e3324da62b5e00375","citationCount":66,"isOpenAccess":true,"pdfUrl":"https://www.frontiersin.org/journals/immunology/articles/10.3389/fimmu.2024.1354825/pdf"},{"id":"s2-2777c265653e7b1ad7a36fd5d00c0e9590527407","title":"Recent advances in the delivery and applications of nonviral CRISPR/Cas9 gene editing","authors":"Frazer H. Sinclair, Anjuman A. Begum, Charles C. Dai, I. Toth, P. Moyle","journal":"Drug Delivery and Translational Research","pubDate":"2023","doi":"10.1007/s13346-023-01320-z","abstract":"The CRISPR (clustered regularly interspaced short palindromic repeats)/Cas9 genome editing system has been a major technological breakthrough that has brought revolutionary changes to genome editing for therapeutic and diagnostic purposes and precision medicine. With the advent of the CRISPR/Cas9 system, one of the critical limiting factors has been the safe and efficient delivery of this system to cells or tissues of interest. Several approaches have been investigated to find delivery systems that can attain tissue-targeted delivery, lowering the chances of off-target editing. While viral vectors have shown promise for in vitro, in vivo and ex vivo delivery of CRISPR/Cas9, their further clinical applications have been restricted due to shortcomings including limited cargo packaging capacity, difficulties with large-scale production, immunogenicity and insertional mutagenesis. Rapid progress in nonviral delivery vectors, including the use of lipid, polymer, peptides, and inorganic nanoparticle-based delivery systems, has established nonviral delivery approaches as a viable alternative to viral vectors. This review will introduce the molecular mechanisms of the CRISPR/Cas9 gene editing system, current strategies for delivering CRISPR/Cas9-based tools, an overview of strategies for overcoming off-target genome editing, and approaches for improving genome targeting and tissue targeting. We will also highlight current developments and recent clinical trials for the delivery of CRISPR/Cas9. Finally, future directions for overcoming the limitations and adaptation of this technology for clinical trials will be discussed. Graphical Abstract","tldr":"The molecular mechanisms of the CRISpr/Cas9 gene editing system are introduced, current strategies for delivering CRISPR/ Cas9-based tools, an overview of strategies for overcoming off-target genome editing, and approaches for improving genome targeting and tissue targeting are highlighted.","source":"Semantic Scholar","sourceUrl":"https://www.semanticscholar.org/paper/2777c265653e7b1ad7a36fd5d00c0e9590527407","citationCount":60,"isOpenAccess":true,"pdfUrl":"https://link.springer.com/content/pdf/10.1007/s13346-023-01320-z.pdf"},{"id":"s2-78d72b039aedbb2dc73612f94139b0562e9703fb","title":"CRISPR–Cas9 Gene Editing: Curing Genetic Diseases by Inherited Epigenetic Modifications","authors":"Nikhil Deep Kolanu","journal":"Global Medical Genetics","pubDate":"2024","doi":"10.1055/s-0044-1785234","abstract":"Abstract Introduction  CRISPR–Cas9 gene editing, leveraging bacterial defense mechanisms, offers precise DNA modifications, holding promise in curing genetic diseases. This review critically assesses its potential, analyzing evidence on therapeutic applications, challenges, and future prospects. Examining diverse genetic disorders, it evaluates efficacy, safety, and limitations, emphasizing the need for a thorough understanding among medical professionals and researchers. Acknowledging its transformative impact, a systematic review is crucial for informed decision-making, responsible utilization, and guiding future research to unlock CRISPR–Cas9's full potential in realizing the cure for genetic diseases. Methods  A comprehensive literature search across PubMed, Scopus, and the Web of Science identified studies applying CRISPR–Cas9 gene editing for genetic diseases, following the Preferred Reporting Items for Systematic Reviews and Meta-Analyses guidelines. Inclusion criteria covered in vitro and in vivo models targeting various genetic diseases with reported outcomes on disease modification or potential cure. Quality assessment revealed a generally moderate to high risk of bias. Heterogeneity prevented quantitative meta-analysis, prompting a narrative synthesis of findings. Discussion  CRISPR–Cas9 enables precise gene editing, correcting disease-causing mutations and offering hope for previously incurable genetic conditions. Leveraging inherited epigenetic modifications, it not only fixes mutations but also restores normal gene function and controls gene expression. The transformative potential of CRISPR–Cas9 holds promise for personalized treatments, improving therapeutic outcomes, but ethical considerations and safety concerns must be rigorously addressed to ensure responsible and safe application, especially in germline editing with potential long-term implications.","tldr":"The transformative potential of CRISPR–Cas9 holds promise for personalized treatments, improving therapeutic outcomes, but ethical considerations and safety concerns must be rigorously addressed to ensure responsible and safe application, especially in germline editing with potential long-term implications.","source":"Semantic Scholar","sourceUrl":"https://www.semanticscholar.org/paper/78d72b039aedbb2dc73612f94139b0562e9703fb","citationCount":55,"isOpenAccess":true,"pdfUrl":"http://www.thieme-connect.de/products/ejournals/pdf/10.1055/s-0044-1785234.pdf"},{"id":"s2-509c7892c1946cd2a3ae9c7e0b0f123abda1c393","title":"Engineered Nanomaterials to Potentiate CRISPR/Cas9 Gene Editing for Cancer Therapy","authors":"Ke Yi, Huimin Kong, Yeh-Hsing Lao, Di Li, Rachel L. Mintz, T. Fang, Guojun Chen, Yu Tao, Mingqiang Li, Jianxun Ding","journal":"Advanced Materials","pubDate":"2023","doi":"10.1002/adma.202300665","abstract":"Clustered regularly interspaced short palindromic repeats/associated protein 9 (CRISPR/Cas9) gene‐editing technology shows promise for manipulating single or multiple tumor‐associated genes and engineering immune cells to treat cancers. Currently, most gene‐editing strategies rely on viral delivery; yet, while being efficient, many limitations, mainly from safety and packaging capacity considerations, hinder the use of viral CRISPR vectors in cancer therapy. In contrast, recent advances in non‐viral CRISPR/Cas9 nanoformulations have paved the way for better cancer gene editing, as these nanoformulations can be engineered to improve safety, efficiency, and specificity through optimizing the packaging capacity, pharmacokinetics, and targetability. In this review, the advance in non‐viral CRISPR delivery is highlighted, and there is a discussion on how these approaches can be potentially used to treat cancers in addressing the aforementioned limitations, followed by the perspectives in designing a proper CRISPR/Cas9‐based cancer nanomedicine system with translational potential.","tldr":"The advance in non‐viral CRISPR delivery is highlighted, and there is a discussion on how these approaches can be potentially used to treat cancers in addressing the aforementioned limitations, followed by the perspectives in designing a proper CRISPR/Cas9‐based cancer nanomedicine system with translational potential.","source":"Semantic Scholar","sourceUrl":"https://www.semanticscholar.org/paper/509c7892c1946cd2a3ae9c7e0b0f123abda1c393","citationCount":53,"isOpenAccess":false,"pdfUrl":""}],"links":{"web":"https://science-database.com/technology/crispr","llms_txt":"https://science-database.com/technology/crispr/llms.txt","api":"https://science-database.com/api/v1/technology/crispr"}}