Frontiers in genome editing最新文献

{"title":"Genome editing for sustainable agriculture in Peru: advances, potential applications and regulation.","authors":"Marilu Mestanza, Angel David Hernández-Amasifuen, Alexandra Jherina Pineda-Lázaro, Dennis Eriksson, Juan Carlos Guerrero-Abad","doi":"10.3389/fgeed.2025.1611040","DOIUrl":"10.3389/fgeed.2025.1611040","url":null,"abstract":"<p><p>Peruvian agriculture is characterize by crops such as potato, maize, rice, asparagus, mango, banana, avocado, cassava, onion, oil palm, chili, papikra, blueberry, coffee, cacao, grapes, quinoa, olive, citrus and others. All of them have challenges in production in their specific agroecosystems under stress due to pests, diseases, salinity, drought, cold among others. Gene editing through CRISPR/Cas is a key tool for addressing critical challenges in agriculture by improving resilience to biotic and abiotic stress, increasing yield and enhancing the nutritional value of the crops. This approach allows precise mutation on site-specific gene at the DNA level, obtaining desirable traits when its function is altered. The CRISPR/Cas system could be used as a transgene-free genome editing tool when the ribonucleoprotein (RNP) acts as a carrier to delivered the CRISPR/Cas components into the plant cell protoplasts, or when the tRNA-like sequence (TLS) motifs are fused to single-guide RNA (sgRNA) and Cas mRNA sequence and expressed in transgenic plants rootstock to produce \"mobile\" CRISPR/Cas components to upper tissue (scion). Those innovations could be a potential approach to strengthen the Peruvian agriculture, food security and gricultural economy, especially in the tropical, Andean and coastal regions. This review article examines the advances and strategies of gene editing, focusing on transgene-free methodologies that could be adopted for research, development and use, and also identifies potential applications in key crops for Peru and analyzes their impact in the productivity and reduction of agrochemicals dependence. Finally, this review highlights the need to establish regulatory policies that strengthen the use of biotechnological precise innovations, ensuring the conservation and valorization of agrobiodiversity for the benefit of Peruvian farmers.</p>","PeriodicalId":73086,"journal":{"name":"Frontiers in genome editing","volume":"7 ","pages":"1611040"},"PeriodicalIF":4.9,"publicationDate":"2025-06-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12258049/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144638867","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A long shelf-life melon created via CRISPR/Cas9 RNP-based <i>in planta</i> genome editing.","authors":"Kentaro Sasaki, Kaoru Urano, Naozumi Mimida, Satoko Nonaka, Hiroshi Ezura, Ryozo Imai","doi":"10.3389/fgeed.2025.1623097","DOIUrl":"10.3389/fgeed.2025.1623097","url":null,"abstract":"<p><p>Genome editing in melon (<i>Cucumis melo</i> L.) remains a significant challenge due to the inefficiencies associated with conventional cell culture-based transformation methods. In the present study, a novel <i>in planta</i> Particle Bombardment (iPB) approach was developed to enable DNA-free genome editing in melon without the need for cell culture. CRISPR/Cas9 ribonucleoproteins (RNPs) were coated onto gold particles and delivered directly into shoot apical meristem tissue, which harbors potential germline cells, via particle bombardment. This method was applied to enhance fruit shelf-life by targeting an ethylene biosynthesis gene (<i>CmACO1</i>). The resulting <i>cmaco1</i> mutant demonstrated a significantly extended shelf-life, attributable to reduced ethylene production during fruit ripening. This delayed ripening phenotype was reversed upon treatment with exogenous ethylene, confirming the functional impact of <i>CmACO1</i> disruption. Because this strategy bypasses cell culture, the iPB-RNP method offers a solution to common limitations in genome editing, such as genotype dependence and somaclonal variation. Consequently, this technique holds substantial promise for advancing commercial melon breeding efforts and may be broadly applicable to other species within the Cucurbitaceae family.</p>","PeriodicalId":73086,"journal":{"name":"Frontiers in genome editing","volume":"7 ","pages":"1623097"},"PeriodicalIF":4.9,"publicationDate":"2025-06-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12213888/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144556081","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Long read sequencing reveals transgene concatemerization and vector sequences integration following AAV-driven electroporation of CRISPR RNP complexes in mouse zygotes.","authors":"Muhammad W Luqman, Piroon Jenjaroenpun, Jessica Spathos, Nikhil Shingte, Mitchell Cummins, Pattaraporn Nimsamer, Lars M Ittner, Thidathip Wongsurawat, Fabien Delerue","doi":"10.3389/fgeed.2025.1582097","DOIUrl":"10.3389/fgeed.2025.1582097","url":null,"abstract":"<p><p>Over the last decade CRISPR gene editing has been successfully used to streamline the generation of animal models for biomedical research purposes. However, one limitation to its use is the potential occurrence of on-target mutations that may be detrimental or otherwise unintended. These bystander mutations are often undetected using conventional genotyping methods. The use of Adeno-Associated Viruses (AAVs) to bring donor templates in zygotes is currently being deployed by transgenic cores around the world to generate knock-ins with large transgenes (i.e., 1-4 kb payloads). Thanks to a high level of efficiency and the relative ease to establish this technique, it recently became a method of choice for transgenic laboratories. However, a thorough analysis of the editing outcomes following this method is yet to be developed. To this end, we generated three different types of integration using AAVs in two different murine genes (i.e., <i>Ace2</i> and <i>Foxg1</i>) and employed Oxford Nanopore Technologies long read sequencing to analyze the outcomes. Using a workflow that includes Cas9 enrichment and adaptive sampling, we showed that unintended on-target mutations, including duplication events and integration of viral sequences (sometimes reported using other workflows) can occur when using AAVs. This work highlights the importance of in-depth validation of the mutant lines generated and informs the uptake of this new method.</p>","PeriodicalId":73086,"journal":{"name":"Frontiers in genome editing","volume":"7 ","pages":"1582097"},"PeriodicalIF":4.9,"publicationDate":"2025-06-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12174137/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144327947","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Recent developments, challenges and opportunities in genome editing for crop science from a societal perspective.","authors":"Srividhya Venkataraman, David Zaruk, Kathleen Hefferon","doi":"10.3389/fgeed.2025.1568072","DOIUrl":"10.3389/fgeed.2025.1568072","url":null,"abstract":"<p><p>Genome editing has presented enormous potential in the fields of medicine and agriculture. Here, we explore the social and regulatory aspects of genome editing from the perspective of food security. We provide recent examples of crop genome editing successes. We discuss the current regulatory framework for genome edited crops in North America and Europe, and present how public perception can influence international policies and trade.</p>","PeriodicalId":73086,"journal":{"name":"Frontiers in genome editing","volume":"7 ","pages":"1568072"},"PeriodicalIF":4.9,"publicationDate":"2025-06-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12170646/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144318812","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Lentiviral CRISPRa/i in the adult prairie vole brain: modulating neuronal gene expression without DNA cleavage.","authors":"Meredith K Loth, Kendall T Mesch, Celine Herrera-Garcia, Liza E Brusman, Zoe R Donaldson","doi":"10.3389/fgeed.2025.1602983","DOIUrl":"10.3389/fgeed.2025.1602983","url":null,"abstract":"<p><p>Prairie voles (<i>Microtus ochrogaster</i>) are a powerful model for studying the neurobiology of social bonding, yet tools for region- and cell type-specific gene regulation remain underdeveloped in this species. Here, we present a lentivirus-mediated CRISPR activation and interference (CRISPRa/i) platform for somatic gene modulation in the prairie vole brain. This system enables non-mutagenic, titratable regulation of gene expression in the adult brain without germline modification. Our dual-vector system includes one construct expressing dCas9-VPR (VP64-p65-Rta) referred to as CRISPRa or dCas9-KRAB-MeCP2 (Kruppel-associated box-methyl CpG binding protein 2), referred to as CRISPRi under a neuron-specific promoter, and a second construct delivering a U6-driven sgRNA (single guide RNA) alongside an elongation factor 1 alpha (EF1α)-driven mCherry reporter. We detail the design, production, and stereotaxic delivery of these tools and demonstrate their application by targeting four genes implicated in social behavior (<i>Oxtr, Avpr1a, Drd1,</i> and <i>Drd2</i>) across two mesolimbic brain regions: the nucleus accumbens and ventral pallidum. Gene expression analyses confirmed robust, bidirectional transcriptional modulation for selected targets, establishing a proof of concept for CRISPRa/i in this non-traditional model. The dual-vector design is readily adaptable to other gene targets, cell types, and brain regions, and can be multiplexed to provide a flexible and scalable framework for investigating gene function in behaviorally relevant circuits. These advances represent the first successful implementation of somatic CRISPRa/i in prairie voles and expand the genetic toolkit available for this species.</p>","PeriodicalId":73086,"journal":{"name":"Frontiers in genome editing","volume":"7 ","pages":"1602983"},"PeriodicalIF":4.9,"publicationDate":"2025-05-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12162470/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144303834","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Editorial: Plant breeding innovations-CRISPR as a powerful weapon for agricultural crops.","authors":"Basavantraya N Devanna, Yugander Arra, Maganti Sheshu Madhav","doi":"10.3389/fgeed.2025.1623540","DOIUrl":"10.3389/fgeed.2025.1623540","url":null,"abstract":"","PeriodicalId":73086,"journal":{"name":"Frontiers in genome editing","volume":"7 ","pages":"1623540"},"PeriodicalIF":4.9,"publicationDate":"2025-05-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12137227/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144236103","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Base editors in zebrafish: a new era for functional genomics and disease modeling.","authors":"Yuwen Liu, Chao Li, Yiren Qiu, Sihong Chen, Yijun Luo, Donghua Xiong, Jun Zhao, Jianmin Ye, Xuegeng Wang, Wei Qin, Fang Liang","doi":"10.3389/fgeed.2025.1598887","DOIUrl":"10.3389/fgeed.2025.1598887","url":null,"abstract":"<p><p>Base editing has revolutionized genome engineering by enabling precise single-nucleotide modifications without inducing double-strand breaks. As a powerful and efficient gene-editing tool, base editors (BEs) have been widely applied in various model organisms, including zebrafish (<i>Danio rerio</i>), to facilitate functional genomic studies and disease modeling. Zebrafish, with its genetic similarity to humans and rapid development, provides an excellent platform for testing and optimizing emerging base editing technologies. This review comprehensively explores the advancements of cytosine and adenine base editors in zebrafish, highlighting recent developments that enhance efficiency, specificity, and editing scope. We discuss novel base editor variants tailored for zebrafish applications, improvements in delivery strategies, and methodologies to minimize off-target effects. Furthermore, we compare base editing with other precision genome-editing technologies, such as prime editing and homology-directed repair, to underscore its advantages in achieving targeted mutations with high fidelity. By evaluating the expanding role of base editing in zebrafish, this review provides valuable insights into its potential for translational research, genetic disease modeling, and future therapeutic applications.</p>","PeriodicalId":73086,"journal":{"name":"Frontiers in genome editing","volume":"7 ","pages":"1598887"},"PeriodicalIF":4.9,"publicationDate":"2025-05-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12133889/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144227852","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genome editing in grain legumes for food security.","authors":"Joshua Yeboah Asiamah, Sakina Haruna Mahdi, Kusum R Tamang, Christian Bryan Carson, Prabesh Koirala, Emily Anne Reed, Aaron Tettey Asare, Anu Augustine, Milind B Ratnaparkhe, Kailash C Bansal, Babu Valliyodan","doi":"10.3389/fgeed.2025.1572292","DOIUrl":"10.3389/fgeed.2025.1572292","url":null,"abstract":"<p><p>Throughout history, leguminous crops have contributed significantly to the human diet. Grain legumes have long been identified as a valuable nutritional source for humans. However, their significance extends beyond nutrition to global food security, reducing reliance on chemical fertilizers, improving soil health and increasing resilience to climate change. Recognizing their vital importance in nutrition and agricultural production, scientists have worked persistently to uncover new genetic traits in legumes, resulting in enhanced yields, improved nutritional value and increased stress tolerance. Recently, the availability of genomic resources for new traits in grain legume plants has greatly increased, laying the groundwork for the adoption of advanced breeding technologies. Gene editing has shown significant potential to improve crop outcomes. This review critically examines the latest developments in gene-editing techniques specific to major grain legumes, focusing on their application in enhancing legume crops with significant agronomic characteristics. The article also shows the potential advantages associated with these advancements. Over the years, advancements in technologies such as Transcription Activator-Like Effector Nucleases (TALENs), Zinc Finger Nucleases (ZFNs), Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR/Cas9), and the more recent Prime Editing technique have significantly contributed to genetic enhancements. These innovations have improved nutritional and market traits, boosted farming incomes, and increased the accessibility of affordable nutritious food, particularly in developing nations. Studies show that CRISPR/Cas9 is the most extensively applied gene editing technology in grain legumes. The advent of this technology has transformed genetic modification by offering exceptional precision and efficiency. This progress has enabled the creation of grain legumes that are more resistant to climate change and enhanced with improved nutritional content. Our research highlights that soybeans have been the primary focus of CRISPR/Cas9 gene editing efforts, surpassing any other grain legume, unlocking significant potential for innovation and improvement. This article presents a scientometric analysis of bibliographic data from the Web of Science using VOSviewer. It highlights global research trends, emphasizing China's leading role in international collaborations, the prominence of soybean (<i>Glycine max</i>) in CRISPR/Cas9 studies, and the key researchers driving advancements in gene editing for food security.</p>","PeriodicalId":73086,"journal":{"name":"Frontiers in genome editing","volume":"7 ","pages":"1572292"},"PeriodicalIF":4.9,"publicationDate":"2025-05-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12140438/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144236104","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Efficient GBA1 editing via HDR with ssODNs by outcompeting pseudogene-mediated gene conversion upon CRISPR/Cas9 cleavage.","authors":"Joseph S Lagas, Monica F Sentmanat, Xiaoxia Cui","doi":"10.3389/fgeed.2025.1581743","DOIUrl":"https://doi.org/10.3389/fgeed.2025.1581743","url":null,"abstract":"<p><strong>Introduction: </strong>CRISPR/Cas9-edited induced pluripotent stem cells (iPSCs) are valuable research models for mechanistic studies. However, gene conversion between a gene-pseudogene pair that share high sequence identity and form direct repeats in proximity on the same chromosome can interfere with the precision of gene editing. Mutations in the human beta-glucocerebrosidase gene (GBA1) are associated with Gaucher disease, Parkinson's disease, and Lewy body dementia. During the creation of a GBA1 KO iPSC line, we detected about 70% gene conversion from its pseudogene GBAP1. These events maintained the reading frame and resulted from GBA1-specific cleavage by CRISPR/Cas9, without disrupting the GBA1 gene.</p><p><strong>Method: </strong>To increase the percentage of alleles with out-of-frame indels for triggering nonsense-mediated decay of the GBA1 mRNA, we supplied the cells with two single-stranded oligodeoxynucleotide (ssODN) donors as homology-directed repair (HDR) templates.</p><p><strong>Results: </strong>We demonstrate that HDR using the ssODN templates effectively competes with gene conversion and enabled biallelic KO clone isolation, whereas the nonallelic homologous recombination (NAHR)-based deletion rate remained the same.</p><p><strong>Discussion: </strong>Here, we report a generalizable method to direct cellular DNA repair of double strand breaks at a target gene towards the HDR pathway using exogenous ssODN templates, allowing specific editing of one gene in a gene-pseudogene pair without disturbing the other.</p>","PeriodicalId":73086,"journal":{"name":"Frontiers in genome editing","volume":"7 ","pages":"1581743"},"PeriodicalIF":4.9,"publicationDate":"2025-04-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12075325/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144082408","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Unraveling the future of genomics: CRISPR, single-cell omics, and the applications in cancer and immunology.","authors":"A Vipin Menon, Bicna Song, Lumen Chao, Diksha Sriram, Pamela Chansky, Ishnoor Bakshi, Jane Ulianova, Wei Li","doi":"10.3389/fgeed.2025.1565387","DOIUrl":"https://doi.org/10.3389/fgeed.2025.1565387","url":null,"abstract":"<p><p>The CRISPR system has transformed many research areas, including cancer and immunology, by providing a simple yet effective genome editing system. Its simplicity has facilitated large-scale experiments to assess gene functionality across diverse biological contexts, generating extensive datasets that boosted the development of computational methods and machine learning/artificial intelligence applications. Integrating CRISPR with single-cell technologies has further advanced our understanding of genome function and its role in many biological processes, providing unprecedented insights into human biology and disease mechanisms. This powerful combination has accelerated AI-driven analyses, enhancing disease diagnostics, risk prediction, and therapeutic innovations. This review provides a comprehensive overview of CRISPR-based genome editing systems, highlighting their advancements, current progress, challenges, and future opportunities, especially in cancer and immunology.</p>","PeriodicalId":73086,"journal":{"name":"Frontiers in genome editing","volume":"7 ","pages":"1565387"},"PeriodicalIF":4.9,"publicationDate":"2025-04-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12021818/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144001420","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}