Engineering Cancer with Next-Generation Genome Editing Tools

Unlike genetic modification, genome editing (GE) technologies can be used to yield transgene‐free outcomes, which is an important aspect in promoting consumer acceptance of GE foods. In addition, with the advent of the clustered regularly interspaced short palindromic repeats/Cas9 (CRISPR/Cas9) system, which is known to be exceptional among genome editing tools, GE has numerous potential applications in plant breeding technology to create diverse desirable traits, especially consumer‐targeted traits such as improved product quality and nutrition. It is expected that the GE foods market will overtake that of genetically modified (GM) foods. Although few GE products have been introduced to the market, some studies have already evaluated consumer acceptance and valuation of GE foods in comparison with GM and conventional foods. However, these studies mainly focused on traits relevant to cultivation efficiency and ignored consumer preferences for desirable traits. Further, it has been shown that consumers evaluate GE foods somewhat higher than GM foods; yet, as observed for GM foods, consumers expect a discounted price for GE foods. GE application for consumer‐targeted traits could, however, have a potentially positive effect on consumer acceptance. This study was conducted to evaluate consumer acceptance and valuation of quality‐improved consumer‐targeted GE products. We defined the determinants and estimated the willingness to pay a price premium for GE rice compared to GM and conventional rice by using the double‐bounded contingent valuation method under different information treatments. The survey was conducted in Vietnam, where consumers have not been exposed to information regarding GE via social media that could lead to a biased perspective. This context is ideal for investigating the effect of information provision during the introductory stage of GE products to the market. Our main findings suggest that consumers will widely accept quality‐improved GE foods targeted at consumer preferences, as well as the positive influence of in‐depth information provision on potential consumer acceptance. [EconLit Citations: Q10: Agriculture: General].

Three-dimensional (3D) stem cell differentiation cultures recently emerged as a novel model system for investigating human embryonic development and disease progression in vitro, complementing existing animal and two-dimensional (2D) cell culture models. Organoids, the 3D self-organizing structures derived from pluripotent or somatic stem cells, can recapitulate many aspects of structural organization and functionality of their in vivo organ counterparts, thus holding great promise for biomedical research and translational applications. Importantly, faithful recapitulation of disease and development processes relies on the ability to modify the genomic contents in organoid cells. The revolutionary genome engineering technologies, CRISPR/Cas9 in particular, enable investigators to generate various reporter cell lines for prompt validation of specific cell lineages as well as to introduce disease-associated mutations for disease modeling. In this review, we provide historical overviews, and discuss technical considerations, and potential future applications of genome engineering in 3D organoid models.

Potentials, prospects and applications of genome editing technologies in livestock production

Clustered regularly interspaced short palindromic repeat (CRISPR)-based genome editing (GED) technologies have unlocked exciting possibilities for understanding genes and improving medical treatments. On the other hand, Artificial intelligence (AI) helps genome editing achieve more precision, efficiency, and affordability in tackling various diseases, like Sickle cell anemia or Thalassemia. AI models have been in use for designing guide RNAs (gRNAs) for CRISPR-Cas systems. Tools like DeepCRISPR, CRISTA, and DeepHF have the capability to predict optimal guide RNAs (gRNAs) for a specified target sequence. These predictions take into account multiple factors, including genomic context, Cas protein type, desired mutation type, on-target/off-target scores, potential off-target sites, and the potential impacts of genome editing on gene function and cell phenotype. These models aid in optimizing different genome editing technologies, such as base, prime, and epigenome editing, which are advanced techniques to introduce precise and programmable changes to DNA sequences without relying on the homology-directed repair pathway or donor DNA templates. Furthermore, AI, in collaboration with genome editing and precision medicine, enables personalized treatments based on genetic profiles. AI analyzes patients' genomic data to identify mutations, variations, and biomarkers associated with different diseases like Cancer, Diabetes, Alzheimer's, etc. However, several challenges persist, including high costs, off-target editing, suitable delivery methods for CRISPR cargoes, improving editing efficiency, and ensuring safety in clinical applications. This review explores AI's contribution to improving CRISPR-based genome editing technologies and addresses existing challenges. It also discusses potential areas for future research in AI-driven CRISPR-based genome editing technologies. The integration of AI and genome editing opens up new possibilities for genetics, biomedicine, and healthcare, with significant implications for human health.

Promoting sustainable agriculture and improving nutrition are the main United Nation’s sustainable development goals by 2030. New technologies are required to achieve zero hunger, and genome editing technology is the most promising one. In the last decade, genome editing (GE) using the CRISPR/Cas system has attracted researchers as a safer and easy tool for genome editing in several living organisms. GE has revolutionized the field of agriculture by improving biotic and abiotic stresses and yield improvement. GE technologies were developed fast lately to avoid the obstacles that face GM crops. GE technology, depending on site directed nuclease (SDN), is divided into three categories according to the modification methods. Developing transgenic-free edited plants without introducing foreign DNA meet the acceptance and regulatory ratification of several countries. There are several ongoing efforts from different countries that are rapidly expanding to adopt the current technological innovations. This review summarizes the different GE technologies and their application as a way to help in ending hunger.

The CRISPR/Cas9 (clustered regularly interspaced short palindromic repeats/CRISPR-associated protein-9 nuclease) genome editing technology has become more and more popular in gene editing because of its simple design and easy operation. Using the CRISPR/Cas9 system, researchers can perform site-directed genome modification at the base level. Moreover, it has been widely used in genome editing in multiple species and related cancer research. In this review, we summarize the application of the CRISPR/Cas9 system in cancer research based on the latest research progresses as well as our understanding of cancer research and genome editing techniques.

Genome editing technology can be used for gene engineering in many organisms. A target metabolite can be fortified by the knockout and modification of target genes encoding enzymes involved in catabolic and biosynthesis pathways, respectively, via genome editing technology. Genome editing is also applied to genes encoding proteins other than enzymes, such as chaperones and transporters. There are many reports of such metabolic engineering using genome editing technology in rice. Genome editing is used not only for site-directed mutagenesis such as the substitution of a single base in a target gene but also for random mutagenesis at a targeted region. The latter enables the creation of novel genetic alleles in a target gene. Recently, genome editing technology has been applied to random mutagenesis in a targeted gene and its promoter region in rice, enabling the screening of plants with a desirable trait from these mutants. Moreover, the expression level of a target gene can be artificially regulated by a combination of genome editing tools such as catalytically inactivated Cas protein with transcription activator or repressor. This approach could be useful for metabolic engineering, although expression cassettes for inactivated Cas fused to a transcriptional activator or repressor should be stably transformed into the rice genome. Thus, the rapid development of genome editing technology has been expanding the scope of molecular breeding including metabolic engineering. In this paper, we review the current status of genome editing technology and its application to metabolic engineering in rice.

Human pluripotent stem cells (hPSCs) offer unprecedented opportunities to study cellular differentiation and model human diseases. The ability to precisely modify any genomic sequence holds the key to realizing the full potential of hPSCs. Thanks to the rapid development of novel genome editing technologies driven by the enormous interest in the hPSC field, genome editing in hPSCs has evolved from being a daunting task a few years ago to a routine procedure in most laboratories. Here, we provide an overview of the mainstream genome editing tools, including zinc finger nucleases, transcription activator-like effector nucleases, clustered regularly interspaced short palindromic repeat/CAS9 RNA-guided nucleases, and helper-dependent adenoviral vectors. We discuss the features and limitations of these technologies, as well as how these factors influence the utility of these tools in basic research and therapies.

During the last few decades, the imergence of genome editing technology has helped Genetic Engineering and Biotechnology to revolutionize the sector of agriculture and decrease world hunger. Genome editing technology enables biotechnology researchers to modify living organisms and plants by the modification (insertion, deletion, or replacement) of the genetic material of its genome. Clustered regularly interspaced short palindromic repeats-associated protein 9 (CRISPR/Cas9) is a type of genome editing technology used worldwide to edit the genomes of several crop varieties. It is based on the mechanism of acquired immunity of bacteria against viral invasion. This third-generation genome editing tool is modern, error-free, more robust, well-programmable, and has considerably higher target site specificity when compared to other genome editing tools such as ZFNs (Zinc finger nucleases) or TALENS (transcription activator-like effector nucleases), gene expression suppression by siRNA. CRISPR/Cas9 genome editing technique has revolutionized plant science and agricultural research by developing germplasms with desired traits, thus resulting in more sustainable agriculture. This review expects to show the uses of the CRISPR/Cas9 genome editing technique for agricultural crop improvement and evaluate recent examples of crops whose genomes are successfully edited and improved by CRISPR/Cas9. In addition, we present the challenges and future expectancies of the CRISPR/Cas9 genome editing technique in agricultural crop improvement.

Genome editing technologies have emerged as powerful tools for making precise and targeted modifications in the DNA of living organisms, offering unprecedented opportunities to revolutionize agriculture amidst global challenges such as population growth, climate change, and diminishing resources. This review provides an overview of genome editing principles, its comparison with traditional breeding and genetic engineering methods, and the regulatory landscape governing its application. The CRISPR/Cas9 system, in particular, has revolutionized genome editing due to its efficiency, affordability, and versatility. By harnessing this system, researchers can induce specific modifications in plant genomes, enhancing traits such as yield, quality, and resilience to biotic and abiotic stresses. The review highlights recent advancements in CRISPR/Cas9 technology, including its adaptation for base editing and prime editing, which allow for precise nucleotide substitutions and broaden the scope of genetic modifications possible in crops. Addressing the regulatory environment surrounding genome-edited crops, the paper discusses existing regulations, international agreements, and ethical considerations. It emphasizes the need for science-informed regulations that balance innovation with transparency and public safety, crucial for fostering societal acceptance and facilitating global trade in genetically modified agricultural products. Furthermore, the review explores case studies and trends in genome editing applications across different crop species, illustrating how these technologies are being employed to address challenges in agriculture. From improving disease resistance to optimizing nutrient content and environmental adaptation, genome editing offers a pathway towards sustainable crop improvement. Looking forward, the review outlines future prospects and challenges in the field, including potential limitations such as off-target effects and the need for enhanced precision in editing techniques. It underscores the importance of integrating genome editing with conventional breeding methods to optimize agricultural productivity and resilience in the face of evolving environmental pressures. Genome editing holds immense promise for enhancing global food security and sustainability. By elucidating the current landscape of genome editing technologies and their applications in agriculture, this review aims to provide a comprehensive resource for policymakers, regulators, researchers, and the public, facilitating informed decision-making and supporting the responsible deployment of these transformative technologies in agriculture.

Recently, there has been a remarkable increase in rice production owing to genetic improvement and increase in application of synthetic fertilizers. For sustainable agriculture, there is dire need to maintain a balance between profitability and input cost. To meet the steady growing demands of the farming community, researchers are utilizing all available resources to identify nutrient use efficient germplasm, but with very little success. Therefore, it is essential to understand the underlying genetic mechanism controlling nutrients efficiency, with the nitrogen use efficiency (NUE) being the most important trait. Information regarding genetic factors controlling nitrogen (N) transporters, assimilators, and remobilizers can help to identify candidate germplasms via high-throughput technologies. Large-scale field trials have provided morphological, physiological, and biochemical trait data for the detection of genomic regions controlling NUE. The functional aspects of these attributes are time-consuming, costly, labor-intensive, and less accurate. Therefore, the application of novel plant breeding techniques (NPBTs) with context to genome engineering has opened new avenues of research for crop improvement programs. Most recently, genome editing technologies (GETs) have undergone enormous development with various versions from Cas9, Cpf1, base, and prime editing. These GETs have been vigorously adapted in plant sciences for novel trait development to insure food quantity and quality. Base editing has been successfully applied to improve NUE in rice, demonstrating the potential of GETs to develop germplasms with improved resource use efficiency. NPBTs continue to face regulatory setbacks in some countries due to genome editing being categorized in the same category as genetically modified (GM) crops. Therefore, it is essential to involve all stakeholders in a detailed discussion on NPBTs and to formulate uniform policies tackling biosafety, social, ethical, and environmental concerns. In the current review, we have discussed the genetic mechanism of NUE and NPBTs for crop improvement programs with proof of concepts, transgenic and GET application for the development of NUE germplasms, and regulatory aspects of genome edited crops with future directions considering NUE.

The power and versatility of genome editing tools in crop improvement

Rice (Oryza sativa L.) is an important staple food crop worldwide. To meet the growing nutritional requirements of the increasing population in the face of climate change, qualitative and quantitative traits of rice need to be improved. During recent years, genome editing has played a great role in the development of superior varieties of grain crops. Genome editing and speed breeding have improved the accuracy and pace of rice breeding. New breeding technologies including genome editing have been established in rice, expanding the potential for crop improvement. Over a decade, site-directed mutagenesis tools like Zinc Finger Nucleases (ZFN), Transcriptional activator-like Effector Nucleases (TALENs), and Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)/CRISPR-associated protein 9 (Cas9) System were used and have played a great role in rice yield and quality enhancement. In addition, most recently other genome editing techniques like prime editing and base editors have also been used for efficient genome editing in rice. Since rice is an excellent model system for functional studies due to its small genome and close synthetic relationships with other cereal crops, new genome-editing technologies continue to be developed for use in rice. Genomic alteration employing genome editing technologies (GETs) like CRISPR/Cas9 for reverse genetics has opened new avenues in agricultural sciences such as rice yield and grain quality improvement. Currently, CRISPR/Cas9 technology is widely used by researchers for genome editing to achieve the desired biological objectives, because of its simple targeting, easy-to-design, cost-effective, and versatile tool for precise and efficient plant genome editing. Over the past few years many genes related to rice grain quality and yield enhancement have been successfully edited via CRISPR/Cas9 technology method to cater to the growing demand for food worldwide. The effectiveness of these methods is being verified by the researchers and crop scientists worldwide. In this review we focus on genome-editing tools for rice improvement to address the progress made and provide examples of genome editing in rice. We also discuss safety concerns and methods for obtaining transgene-free crops.

Chapter 15 - Genome editing: A potential tool for enhancing livestock production

Studies which seek fundamental, thorough knowledge of biological processes, and continuous advancement in natural sciences and biotechnology enable the establishment of molecular strategies and tools to treat disorders caused by genetic mutations. Over the years biological therapy evolved from using stem cells and viral vectors to RNA therapy and testing different genome editing tools as promising gene therapy agents. These genome editing technologies (Zinc finger nucleases, TAL effector nucleases), specifically CRISPR-Cas system, revolutionized the field of genetic engineering and is widely applied to create cell and animal models for various hereditary, infectious human diseases and cancer, to analyze and understand the molecular and cellular base of pathogenesis, to find potential drug/treatment targets, to eliminate pathogenic DNA changes in various medical conditions and to create future “precise medication”. Although different concerning factors, such as precise system delivery to the target cells, efficacy and accuracy of editing process, different approaches of making the DNA changes as well as worrying bioethical issues remain, the importance of genome editing technologies in medicine is undeniable. The future of innovative genome editing approach and strategies to treat diseases is complicated but interesting and exciting at once for all related parties – researchers, clinicians, and patients.