A simple and efficient CRISPR/Cas9 system permits ultra-multiplex genome editing in plants

The development and maturation of the CRISPR/Cas genome editing system provides a valuable tool for plant functional genomics and genetic improvement.Currently available genome-editing tools have a limited number of targets,restricting their application in genetic research.In this study,we developed a novel CRISPR/Cas9 plant ultra-multiplex genome editing system consisting of two template vectors,eight donor vectors,four destination vectors,and one primer-design software package.By combining the advantages of Golden Gate cloning to assemble multiple repetitive fragments and Gateway recombination to assemble large fragments and by changing the structure of the amplicons used to assemble sg RNA expression cassettes,the plant ultra-multiplex genome editing system can assemble a single binary vector targeting more than 40 genomic loci.A rice knockout vector containing 49 sg RNA expression cassettes was assembled and a high co-editing efficiency was observed.This plant ultra-multiplex genome editing system advances synthetic biology and plant genetic engineering.

Development of delivery strategies for CRISPR-Cas9 genome editing

The clustered regularly interspaced short palindromic repeats(CRISPR)and CRISPR-related protein 9(Cas9)genome editing system has attracted much attention due to its powerful genome editing capacity.However,CRISPR-Cas9 components are easily degraded by acids,enzymes,and other substances in the body fluids after entering the organism,thus efficiently delivering the CRISPRCas9 system into targeted organs or cells has been a central theme for promoting the application of CRISPR-Cas9 technology.Although several physical methods and viral vectors have been developed for CRISPR-Cas9 delivery,their clinical application still suffers from disadvantages,such as the risks of mutagenesis,cell damage,and poor specificity.As an alternative,non-viral nanocarriers hold great promise for circumventing these challenges.Furthermore,with aim to realize more efficient and precise genome editing and reduce the undesirable side effects,stimuli-responsive nanocarriers are designed for the spatiotemporal CRISPR-Cas9 delivery in responsive to various stimuli.In this review,we will summarize the recent progress in delivery strategies for CRISPR-Cas9 genome editing.The mechanisms and advantages of these strategies were reviewed,providing a comprehensive review of the rational design of materials and techniques for efficient and precise genome editing.At last,the potential challenges of current CRISPR-Cas9 delivery are discussed.

Cdk5 knocking out mediated by CRISPR-Cas9 genome editing for PD-L1 attenuation and enhanced antitumor immunity

Blocking the programmed death-ligand 1(PD-L1)on tumor cells with monoclonal antibody therapy has emerged as powerful weapon in cancer immunotherapy.However,only a minority of patients presented immune responses in clinical trials.To develop an alternative treatment method based on immune checkpoint blockade,we designed a novel and efficient CRISPR-Cas9 genome editing system delivered by cationic copolymer aPBAE to downregulate PD-L1 expression on tumor cells via specifically knocking out Cyclin-dependent kinase 5(Cdk5)gene in vivo.The expression of PD-L1 on tumor cells was significantly attenuated by knocking out Cdk5,leading to effective tumor growth inhibition in murine melanoma and lung metastasis suppression in triple-negative breast cancer.Importantly,we demonstrated that aPBAE/Cas9-Cdk5 treatment elicited strong T cell-mediated immune responses in tumor microenvironment that the population of CD8^+T cells was significantly increased while regulatory T cells(Tregs)was decreased.It may be the first case to exhibit direct in vivo PD-L1 downregulation via CRISPR-Cas9 genome editing technology for cancer therapy.It will provide promising strategy for preclinical antitumor treatment through the combination of nanotechnology and genome engineering.

A double-edged sword: CRISPR-Cas9 is emerging as a revolutionary technique for genome editing

In May 2015, professor Xiao Yang authored a review on the development of CRISPR-Cas9 techniques in the journal of Military Medical Research. This review provided a valuable overview of this major scientific advance. It has been four years since the first publication of the CRISPR-Cas9 breakthrough. The use of this technique has expanded into various scientific areas and is being developed into a systematic technical platform that may contribute to many bioengineering fields involving DNA sequence editing.

Overview of guide RNA design tools for CRISPR-Cas9 genome editing technology

CRISPR-Cas （Clustered, Regularly Interspaced, Short Palindromic Repeats - CRISPR-associated （Cas）） RNA guided endonuclease has emerged as the most effective and widely used genome editing technology, which has become the most exciting and rapidly advancing research field. Efficient genome editing by the CRISPR-Cas9 system has been demonstrated in many species, and several laboratories have established CRISPR-Cas9 as a screening tool for systematic genetic analysis, similar to sbRNA screening. At least three companies have been founded to leverage this technology for therapeutic uses. To facilitate the implementation of this technology, many software tools have been developed to identify guide RNAs that effectively target a desired genomic region. Here, I provide an overview of the technology, focusing on guide RNA design principles, available software tools and their strengths and weaknesses.

The Application of CRISPR-Cas9 Genome Editing in Caenorhabditis elegans

Genome editing using the Cas9 endonuclease of Streptococcus pyogenes has demonstrated unparalleled efficacy and facility for modifying genomes in a wide variety of organisms. Caenorhabditis elegans is one of the most convenient multicellular organisms for genetic analysis, and the application of this novel genome editing technique to this organism promises to revolutionize analysis of gene function in the future. CRISPR-Cas9 has been successfully used to generate imprecise insertions and deletions via non-homologous end-joining mechanisms and to create precise mutations by homology-directed repair from donor templates. Key variables are the methods used to deliver the Cas9 endonuclease and the efficiency of the single guide RNAs. CRISPR-Cas9-mediated editing appears to be highly specific in C. elegans, with no reported off-target effects. In this review, 1 briefly summarize recent progress in CRISPR-Cas9-based genome editing in C. elegans, highlighting technical improvements in mutagenesis and mutation detection, and discuss potential future appli- cations of this technique.

Genome-edited rabbits:Unleashing the potential of a promising experimental animal model across diverse diseases

Animal models are extensively used in all aspects of biomedical research,with substantial contributions to our understanding of diseases,the development of pharmaceuticals,and the exploration of gene functions.The field of genome modification in rabbits has progressed slowly.However,recent advancements,particularly in CRISPR/Cas9-related technologies,have catalyzed the successful development of various genome-edited rabbit models to mimic diverse diseases,including cardiovascular disorders,immunodeficiencies,agingrelated ailments,neurological diseases,and ophthalmic pathologies.These models hold great promise in advancing biomedical research due to their closer physiological and biochemical resemblance to humans compared to mice.This review aims to summarize the novel gene-editing approaches currently available for rabbits and present the applications and prospects of such models in biomedicine,underscoring their impact and future potential in translational medicine.

Recent advances in CRISPR-based genome editing technology and its applications in cardiovascular research

The rapid development of genome editing technology has brought major breakthroughs in the fields of life science and medicine. In recent years, the clustered regularly interspaced short palindromic repeats(CRISPR)-based genome editing toolbox has been greatly expanded, not only with emerging CRISPR-associated protein(Cas) nucleases, but also novel applications through combination with diverse effectors. Recently, transposon-associated programmable RNA-guided genome editing systems have been uncovered, adding myriads of potential new tools to the genome editing toolbox. CRISPR-based genome editing technology has also revolutionized cardiovascular research. Here we first summarize the advances involving newly identified Cas orthologs, engineered variants and novel genome editing systems, and then discuss the applications of the CRISPR-Cas systems in precise genome editing, such as base editing and prime editing. We also highlight recent progress in cardiovascular research using CRISPR-based genome editing technologies, including the generation of genetically modified in vitro and animal models of cardiovascular diseases(CVD) as well as the applications in treating different types of CVD. Finally, the current limitations and future prospects of genome editing technologies are discussed.

CRISPR-Cas9-based genome-editing technologies in engineering bacteria for the production of plant-derived terpenoids

Terpenoids are widely used as medicines,flavors,and biofuels.However,the use of these natural products is largely restricted by their low abundance in native plants.Fortunately,heterologous biosynthesis of terpenoids in microorganisms offers an alternative and sustainable approach for efficient production.Various genome-editing technologies have been developed for microbial strain construction.Clustered regularly interspaced short palin-dromic repeats(CRISPR)-CRISPR associated protein 9(Cas9)is the most commonly used system owing to its outstanding efficiency and convenience in genome editing.In this review,the basic principles of CRISPR-Cas9 systems are briefly introduced and their applications in engineering bacteria for the production of plant-derived terpenoids are summarized.The aim of this review is to provide an overview of the current developments of CRISPR-Cas9-based genome-editing technologies in bacterial engineering,concluding with perspectives on the challenges and opportunities of these technologies.

Genome editing of PAR2 through targeted delivery of CRISPR-Cas9 system for alleviating acute lung inflammation via ERK/NLRP3/IL-1β and NO/iNOS signalling

Excessive and uncontrollable inflammatory responses in alveoli can dramatically exacerbate pulmonary disease progressions through vigorous cytokine releases,immune cell infiltration and protease-driven tissue damages.It is an urgent need to explore potential drug strategies for mitigating lung inflammation.Protease-activated receptor 2(PAR2)as a vital molecular target principally participates in various inflammatory diseases via intracellular signal transduction.However,it has been rarely reported about the role of PAR2 in lung inflammation.This study applied CRISPR-Cas9 system encoding Cas9 and sg RNA(p Cas9-PAR2)for PAR2 knockout and fabricated an anionic human serum albuminbased nanoparticles to deliver p Cas9-PAR2 with superior inflammation-targeting efficiency and stability(TAP/p Cas9-PAR2).TAP/p Cas9-PAR2 robustly facilitated p Cas9-PAR2 to enter and transfect inflammatory cells,eliciting precise gene editing of PAR2 in vitro and in vivo.Importantly,PAR2 deficiency by TAP/p Cas9-PAR2 effectively and safely promoted macrophage polarization,suppressed proinflammatory cytokine releases and alleviated acute lung inflammation,uncovering a novel value of PAR2.It also revealed that PAR2-mediated pulmonary inflammation prevented by TAP/p Cas9-PAR2was mainly dependent on ERK-mediated NLRP3/IL-1β and NO/i NOS signalling.Therefore,this work indicated PAR2 as a novel target for lung inflammation and provided a potential nanodrug strategy for PAR2 deficiency in treating inflammatory diseases.

Applications of CRISPR-Cas9 mediated genome engineering

Targeted mutagenesis based on homologous recombination has been a powerful tool for understanding the mechanisms underlying development, normal physiology, and disease. A recent breakthrough in genome engineering technology based on the class of RNA-guided endonucleases, such as clustered regularly interspaced short palindromic repeats(CRISPR)-associated Cas9, is further revolutionizing biology and medical studies. The simplicity of the CRISPR-Cas9 system has enabled its widespread applications in generating germline animal models, somatic genome engineering, and functional genomic screening and in treating genetic and infectious diseases. This technology will likely be used in all fields of biomedicine, ranging from basic research to human gene therapy.

CRISPR/Cas9:A powerful tool for crop genome editing

The CRISPR/Cas9 technology is evolved from a type II bacterial immune system and represents a new generation of targeted genome editing technology that can be applied to nearly all organisms. Site-specific modification is achieved by a single guide RNA(usually about 20nucleotides) that is complementary to a target gene or locus and is anchored by a protospaceradjacent motif. Cas9 nuclease then cleaves the targeted DNA to generate double-strand breaks(DSBs), which are subsequently repaired by non-homologous end joining(NHEJ) or homology-directed repair(HDR) mechanisms. NHEJ may introduce indels that cause frame shift mutations and hence the disruption of gene functions. When combined with double or multiplex guide RNA design, NHEJ may also introduce targeted chromosome deletions,whereas HDR can be engineered for target gene correction, gene replacement, and gene knock-in. In this review, we briefly survey the history of the CRISPR/Cas9 system invention and its genome-editing mechanism. We also describe the most recent innovation of the CRISPR/Cas9 technology, particularly the broad applications of modified Cas9 variants, and discuss the potential of this system for targeted genome editing and modification for crop improvement.

Wheat genome editing expedited by efficient transformation techniques:Progress and perspectives

Genome editing is one of the most promising biotechnologies to improve crop performance.Common wheat is a staple food for mankind. In the past few decades both basic and applied research on common wheat has lagged behind other crop species due to its complex,polyploid genome and difficulties in genetic transformation. Recent breakthroughs in wheat transformation permit a revolution in wheat biotechnology. In this review, we summarize recent progress in wheat genetic transformation and its potential for wheat improvement. We then review recent progress in plant genome editing, which is now readily available in wheat. We also discuss measures to further increase transformation efficiency and potential applications of genome editing in wheat. We propose that, together with a high quality reference genome, the time for efficient genetic engineering and functionality studies in common wheat has arrived.

Genome Editing as A Versatile Tool to Improve Horticultural Crop Qualities

The quality traits of horticultural crops,including the accumulation of nutrients and flavor substances,morphology,and texture,affect the palatability and nutritional value.For many years,efforts have been made to improve the quality of horticultural crops.The recent establishment of gene editing technology,with its potential applications in horticultural crops,provides a strategy for achieving this goal in a rapid and efficient manner.Here,we summarize research efforts aimed at improving horticultural crop quality through genome editing.We describe specific genome editing systems that have been used and traits that have been targeted in these efforts.Additionally,we discuss limiting factors and future perspectives of genome editing technology in improving horticultural crop qualities in both research and plant breeding.In summary,genome editing technology is emerging as a powerful tool for efficiently and rapidly improving horticultural crop quality,and we believe that the cautious application of genome editing in horticultural crops will generate new germplasms with improved quality in the near future.

In vivo genome editing thrives with diversified CRISPR technologies

Prokaryotic type II adaptive immune systems have been developed into the versatile CRISPR technology, which has been widely applied in site- specific genome editing and has revolutionized biomedical research due to its superior efficiency and flexibility. Recent studies have greatly diversified CRISPR technologies by coupling it with various DNA repair mechanisms and targeting strategies. These new advances have significantly expanded the generation of genetically modified animal models, either by including species in which targeted genetic modification could not be achieved previously, or through introducing complex genetic modifications that take multiple steps and cost years to achieve using traditional methods. Herein, we review the recent developments and applications of CRISPR-based technology in generating various animal models, and discuss the everlasting impact of this new progress on biomedical research.

Genome editing technology and application in soybean improvement

Soybean(Glycine max)is a legume crop with great economic value that provides rich protein and oil for human food and animal feed.In order to cope with the ever-increasing need for soybean products and the changing environment,soybean genetic improvement needs to be accelerated.In recent years,the rapid developed genome editing technologies,such as zinc finger nuclease(ZFNs),transcription activator-like effector nucleases(TALENs),and clustered regularly interspaced short palindromic repeats/CRISPR associated protein(CRISPR/Cas),have shown broad application prospects in gene function research and improvement of important agronomic traits in many crops,and has also brought opportunities for soybean breeding.Here we systematically reviewed recent advances in genome editing technology.We also summarized the significances,current applications,challenges and future perspectives in soybean genome editing,which could provide references for exerting the feature and advantage of this technology to better soybean improvement.

Progress and challenges in CRISPR-mediated therapeutic genome editing for monogenic diseases

There are an estimated 10000 monogenic diseases affecting tens of millions of individuals worldwide.The application of CRISPR/Cas genome editing tools to treat monogenic diseases is an emerging strategy with the potential to generate personalized treatment approaches for these patients.CRISPR/Cas-based systems are programmable and sequence-specific genome editing tools with the capacity to generate base pair resolution manipulations to DNA or RNA.The complexity of genomic insults resulting in heritable disease requires patientspecific genome editing strategies with consideration of DNA repair pathways,and CRISPR/Cas systems of different types,species,and those with additional enzymatic capacity and/or delivery methods.In this review we aim to discuss broad and multifaceted therapeutic applications of CRISPR/Cas gene editing systems including in harnessing of homology directed repair,non-homologous end joining,microhomology-mediated end joining,and base editing to permanently correct diverse monogenic diseases.

CRISPR-based genome editing technology and its applications in oil crops

Oil crops,mainly comprised of soybean,rapeseed,groundnut,sunflower and etc.,have provided substantial edible oil and other tremendous nutrients for human beings,as well as valuable biofuels for associated industries.The genetic improvement of significant oil crops and/or domesticating novel high-yielding oil crops are in urgent need to cope with the ever-increasing demand for various oil crop products.CRISPR(Clustered Regularly Interspaced Short Palindromic Repeats)-based genome editing technology,born a few years ago,edits stretches of DNA in a targeted and RNA-dependent fashion.The Characteristics of targeted mutagenesis and easy manipulation owned by the technology make it have been applied to many plants and exhibited great potential in the genetic improvement of many important oil crops.In the face of growing need for oil crop products and the rapid developments in CRISPR-based genome editing technology,a critical review regarding the technology and its application in oil crops is badly required to provide references for the better use of this technology to modify the oil crops for higher yield.In this review paper,we briefly described the CRISPR-based genome editing technology and summarized its applications and future prospects in oil crops.

Genome Editing Strategies Towards Enhancement of Rice Disease Resistance

The emerging pests and phytopathogens have reduced the crop yield and quality, which hasthreatened the global food security. Traditional breeding methods, molecular marker-based breedingapproaches and use of genetically modified crops have played a crucial role in strengthening the foodsecurity worldwide. However, their usages in crop improvement have been highly limited due to multiplecaveats. Genome editing tools like transcriptional activator-like effector nucleases and clustered regularlyinterspaced short palindromic repeats (CRISPR)-associated endonuclease Cas9 (CRISPR/Cas9) haveeffectively overcome limitations of the conventional breeding methods and are being widely accepted forimprovement of crops. Among the genome editing tools, the CRISPR/Cas9 system has emerged as themost powerful tool of genome editing because of its efficiency, amicability, flexibility, low cost andadaptability. Accumulated evidences indicate that genome editing has great potential in improving thedisease resistance in crop plants. In this review, we offered a brief introduction to the mechanisms of differentgenome editing systems and then discussed recent developments in CRISPR/Cas9 system-based genomeediting towards enhancement of rice disease resistance by different strategies. This review also discussed thepossible applications of recently developed genome editing approaches like CRISPR/Cas12a (formerlyknown as Cpf1) and base editors for enhancement of rice disease resistance.

Expanding the targeting scope of CRISPR/Cas9-mediated genome editing by Cas9 variants in Brassica

CRISPR/Cas9,presently the most widely used genome editing technology,has provided great potential for functional studies and plant breeding.However,the strict requirement for a protospacer adjacent motif(PAM)has hindered the application of the CRISPR/Cas9 system because the number of targetable genomic sites is limited.Recently,the engineered variants Cas9-NG,SpG,and SpRY,which recognize non-canonical PAMs,have been successfully tested in plants(mainly in rice,a monocot).In this study,we evaluated the targeted mutagenesis capabilities of these Cas9 variants in two important Brassica vegetables,Chinese cabbage(Brassica rapa spp.pekinensis)and cabbage(Brassica oleracea var.capitata).Both Cas9-NG and SpG induced efficient mutagenesis at NGN PAMs,while SpG outperformed Cas9-NG at NGC and NGT PAMs.SpRY achieved efficient editing at almost all PAMs(NRN>NYN),albeit with some self-targeting activity at transfer(T)-DNA sequences.And SpRY-induced mutants were detected in cabbage plants in a PAM-less fashion.Moreover,an adenine base editor was developed using SpRY and TadA8e deaminase that induced A-to-G conversions within target sites using non-canonical PAMs.Together,the toolboxes developed here induced successful genome editing in Chinese cabbage and cabbage.Our work further expands the targeting scope of genome editing and paves the way for future basic research and genetic improvement in Brassica.