Harnessing CRISPR/Cas systems for programmable transcriptional and post-transcriptional regulation

An RPA-Assisted CRISPR/Cas12a Assay Combining Fluorescence and Lateral Flow Strips for the Rapid Detection of Enterotoxigenic Bacillus cereus

Bacillus cereus (B. cereus) is a foodborne pathogen that can produce tripartite enterotoxins, which can cause a variety of diseases after infection. It is critical to rapidly and accurately detect strains with enteropathogenic potential to safeguard human health. In this study, a dual-signal visualized detection platform with fluorescence assay and paper-based lateral flow assay (LFA) based on recombinase polymerase amplification (RPA), CRISPR/Cas12a system, and self-developed CRISPR nucleic acid test strips was constructed for enterotoxigenic B. cereus. The genes that encode two tripartite enterotoxins─nheA, nheB, and nheC for nonhemolytic enterotoxin and hblA, hblC, and hblD for hemolysin BL─were utilized as detection targets. The platform was capable of detecting six enterotoxin genes at the same genomic DNA level. The limits of detection for each gene were 10-3 ng/μL in fluorescence assay and 10-4 ng/μL in LFA. Furthermore, 101-102 CFU/mL of B. cereus in pure culture was detected. Additionally, a smartphone miniprogram could assist in evaluating the results in LFA. The platform demonstrated good utility by detecting B. cereus in food samples, including milk and rice. The results indicate that our RPA-CRISPR/Cas12a dual-signal visualized detection platform can quickly and easily detect B. cereus with three-component enterotoxin-producing potentials. The whole analytic process took less than 60 min without complex operation or expensive equipment.

Utilization of CRISPR-Cas genome editing technology in filamentous fungi: function and advancement potentiality

Filamentous fungi play a crucial role in environmental pollution control, protein secretion, and the production of active secondary metabolites. The evolution of gene editing technology has significantly improved the study of filamentous fungi, which in the past was laborious and time-consuming. But recently, CRISPR-Cas systems, which utilize small guide RNA (sgRNA) to mediate clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated proteins (Cas), have demonstrated considerable promise in research and application for filamentous fungi. The principle, function, and classification of CRISPR-Cas, along with its application strategies and research progress in filamentous fungi, will all be covered in the review. Additionally, we will go over general matters to take into account when editing a genome with the CRISPR-Cas system, including the creation of vectors, different transformation methodologies, multiple editing approaches, CRISPR-mediated transcriptional activation (CRISPRa) or interference (CRISPRi), base editors (BEs), and Prime editors (PEs).

Enhancement of specialized metabolites using CRISPR/Cas gene editing technology in medicinal plants

Plants are the richest source of specialized metabolites. The specialized metabolites offer a variety of physiological benefits and many adaptive evolutionary advantages and frequently linked to plant defense mechanisms. Medicinal plants are a vital source of nutrition and active pharmaceutical agents. The production of valuable specialized metabolites and bioactive compounds has increased with the improvement of transgenic techniques like gene silencing and gene overexpression. These techniques are beneficial for decreasing production costs and increasing nutritional value. Utilizing biotechnological applications to enhance specialized metabolites in medicinal plants needs characterization and identification of genes within an elucidated pathway. The breakthrough and advancement of CRISPR/Cas-based gene editing in improving the production of specific metabolites in medicinal plants have gained significant importance in contemporary times. This article imparts a comprehensive recapitulation of the latest advancements made in the implementation of CRISPR-gene editing techniques for the purpose of augmenting specific metabolites in medicinal plants. We also provide further insights and perspectives for improving metabolic engineering scenarios in medicinal plants.

Advances in application of CRISPR-Cas13a system

Clustered Regularly Interspaced Short Palindromic Repeats (CRISPRs) and CRISPR-associated (Cas) proteins serve as an adaptive immune system that safeguards prokaryotes and some of the viruses that infect prokaryotes from foreign nucleic acids (such as viruses and plasmids). The genomes of the majority of archaea and about half of all bacteria contain various CRISPR-Cas systems. CRISPR-Cas systems depend on CRISPR RNAs (crRNAs). They act as a navigation system to specifically cut and destroy foreign nucleic acids by recognizing invading foreign nucleic acids and binding Cas proteins. In this review, we provide a brief overview of the evolution and classification of the CRISPR-Cas system, focusing on the functions and applications of the CRISPR-Cas13a system. We describe the CRISPR-Cas13a system and discuss its RNA-directed ribonuclease function. Meanwhile, we briefly introduce the mechanism of action of the CRISPR-Cas13a system and summarize the applications of the CRISPR-Cas13a system in pathogen detection, eukaryotes, agriculture, biosensors, and human gene therapy. We are right understanding of CRISPR-Cas13a has been broadened, and the CRISPR-Cas13a system will be useful for developing new RNA targeting tools. Therefore, understanding the basic details of the structure, function, and biological characterization of CRISPR-Cas13a effector proteins is critical for optimizing RNA targeting tools.

Recent advances in the application of induced pluripotent stem cell technology to the study of myeloid malignancies

Acquired myeloid malignancies are a spectrum of clonal disorders known to be caused by sequential acquisition of genetic lesions in hematopoietic stem and progenitor cells, leading to their aberrant self-renewal and differentiation. The increasing use of induced pluripotent stem cell (iPSC) technology to study myeloid malignancies has helped usher a paradigm shift in approaches to disease modeling and drug discovery, especially when combined with gene-editing technology. The process of reprogramming allows for the capture of the diversity of genetic lesions and mutational burden found in primary patient samples into individual stable iPSC lines. Patient-derived iPSC lines, owing to their self-renewal and differentiation capacity, can thus be a homogenous source of disease relevant material that allow for the study of disease pathogenesis using various functional read-outs. Furthermore, genome editing technologies like CRISPR/Cas9 enable the study of the stepwise progression from normal to malignant hematopoiesis through the introduction of specific driver mutations, individually or in combination, to create isogenic lines for comparison. In this review, we survey the current use of iPSCs to model acquired myeloid malignancies including myelodysplastic syndromes (MDS), myeloproliferative neoplasms (MPN), acute myeloid leukemia and MDS/MPN overlap syndromes. The use of iPSCs has enabled the interrogation of the underlying mechanism of initiation and progression driving these diseases. It has also made drug testing, repurposing, and the discovery of novel therapies for these diseases possible in a high throughput setting.

Molecular Marvels: Small Molecules Paving the Way for Enhanced Gene Therapy

In the rapidly evolving landscape of genetic engineering, the advent of CRISPR-Cas technologies has catalyzed a paradigm shift, empowering scientists to manipulate the genetic code with unprecedented accuracy and efficiency. Despite the remarkable capabilities inherent to CRISPR-Cas systems, recent advancements have witnessed the integration of small molecules to augment their functionality, introducing new dimensions to the precision and versatility of gene editing applications. This review delves into the synergy between CRISPR-Cas technologies based specifically on Cas9 and small-molecule drugs, elucidating the pivotal role of chemicals in optimizing target specificity and editing efficiency. By examining a diverse array of applications, ranging from therapeutic interventions to agricultural advancements, we explore how the judicious use of chemicals enhances the precision of CRISPR-Cas9-mediated genetic modifications. In this review, we emphasize the significance of small-molecule drugs in fine-tuning the CRISPR-Cas9 machinery, which allows researchers to exert meticulous control over the editing process. We delve into the mechanisms through which these chemicals bolster target specificity, mitigate off-target effects, and contribute to the overall refinement of gene editing outcomes. Additionally, we discuss the potential of chemical integration in expanding the scope of CRISPR-Cas9 technologies, enabling tailored solutions for diverse genetic manipulation challenges. As CRISPR-Cas9 technologies continue to evolve, the integration of small-molecule drugs emerges as a crucial avenue for advancing the precision and applicability of gene editing techniques. This review not only synthesizes current knowledge but also highlights future prospects, paving the way for a deeper understanding of the synergistic interplay between CRISPR-Cas9 systems and chemical modulators in the pursuit of more controlled and efficient genetic modifications.

Overview on century progress in research on mosaic disease of apple (Malus domestica Borkh) incited by apple mosaic virus/apple necrotic mosaic virus

Apple mosaic is widely distributed disease throughout the apple growing regions leading to the major adverse effects both qualitatively and quantitatively. Earlier the apple mosaic virus-ApMV was regarded as the only causal agent of the disease, but recently a novel virus apple necrotic mosaic virus-ApNMV have been reported as the causal pathogen from various apple growing countries. Accurate diagnosis of disease and detection of ApMV and ApNMV are of utmost importance, because without this ability we can neither understand nor control this disease. Both the viruses are mostly controlled through quarantine, isolation, sanitation and certification programs depending on sensitive and specific detection methods available. Here we review the 100-year progress in research on apple mosaic disease, which includes history, yield losses, causal agents, their genome organization, replication, traditional to recent detection methods, transmission, distribution and host range of associated viruses and management of the disease.

CRISPR-cas9 screening identified lethal genes enriched in Hippo kinase pathway and of predictive significance in primary low-grade glioma

BACKGROUND

Low-grade gliomas (LGG) are a type of brain tumor that can be lethal, and it is essential to identify genes that are correlated with patient prognosis. In this study, we aimed to use CRISPR-cas9 screening data to identify key signaling pathways and develop a genetic signature associated with high-risk, low-grade glioma patients.

METHODS

The study used CRISPR-cas9 screening data to identify essential genes correlated with cell survival in LGG. We used RNA-seq data to identify differentially expressed genes (DEGs) related to cell viability. Moreover, we used the least absolute shrinkage and selection operator (LASSO) method to construct a genetic signature for predicting overall survival in patients. We performed enrichment analysis to identify pathways mediated by DEGs, overlapping genes, and genes shared in the Weighted correlation network analysis (WGCNA). Finally, the study used western blot, qRT-PCR, and IHC to detect the expression of hub genes from signature in clinical samples.

RESULTS

The study identified 145 overexpressed oncogenes in low-grade gliomas using the TCGA database. These genes were intersected with lethal genes identified in the CRISPR-cas9 screening data from Depmap database, which are enriched in Hippo pathways. A total of 19 genes were used to construct a genetic signature, and the Hippo signaling pathway was found to be the predominantly enriched pathway. The signature effectively distinguished between low- and high-risk patients, with high-risk patients showing a shorter overall survival duration. Differences in hub gene expression were found in different clinical samples, with the protein and mRNA expression of REP65 being significantly up-regulated in tumor cells. The study suggests that the Hippo signaling pathway may be a critical regulator of viability and tumor proliferation and therefore is an innovative new target for treating cancerous brain tumors, including low-grade gliomas.

CONCLUSION

Our study identified a novel genetic signature associated with high-risk, LGG patients. We found that the Hippo signaling pathway was significantly enriched in this signature, indicating that it may be a critical regulator of tumor viability and proliferation in LGG. Targeting the Hippo pathway could be an innovative new strategy for treating LGG.

Bio-SCAN V2: A CRISPR/dCas9-based lateral flow assay for rapid detection of theophylline

Rapid, specific, and robust diagnostic strategies are needed to develop sensitive biosensors for small molecule detection, which could aid in controlling contamination and disease transmission. Recently, the target-induced collateral activity of Cas nucleases [clustered regularly interspaced short palindromic repeats (CRISPR)-associated nucleases] was exploited to develop high-throughput diagnostic modules for detecting nucleic acids and small molecules. Here, we have expanded the diagnostic ability of the CRISPR-Cas system by developing Bio-SCAN V2, a ligand-responsive CRISPR-Cas platform for detecting non-nucleic acid small molecule targets. The Bio-SCAN V2 consists of an engineered ligand-responsive sgRNA (ligRNA), biotinylated dead Cas9 (dCas9-biotin), 6-carboxyfluorescein (FAM)-labeled amplicons, and lateral flow assay (LFA) strips. LigRNA interacts with dCas9-biotin only in the presence of sgRNA-specific ligand molecules to make a ribonucleoprotein (RNP). Next, the ligand-induced ribonucleoprotein is exposed to FAM-labeled amplicons for binding, and the presence of the ligand (small molecule) is detected as a visual signal [(dCas9-biotin)-ligRNA-FAM labeled DNA-AuNP complex] at the test line of the lateral flow assay strip. With the Bio-SCAN V2 platform, we are able to detect the model molecule theophylline with a limit of detection (LOD) up to 2 μM in a short time, requiring only 15 min from sample application to visual readout. Taken together, Bio-SCAN V2 assay provides a rapid, specific, and ultrasensitive detection platform for theophylline.

A Review on the Mechanism and Applications of CRISPR/Cas9/Cas12/Cas13/Cas14 Proteins Utilized for Genome Engineering

The clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated protein (CRISPR/Cas) system has altered life science research offering enormous options in manipulating, detecting, imaging, and annotating specific DNA or RNA sequences of diverse organisms. This system incorporates fragments of foreign DNA (spacers) into CRISPR cassettes, which are further transcribed into the CRISPR arrays and then processed to make guide RNA (gRNA). The CRISPR arrays are genes that encode Cas proteins. Cas proteins provide the enzymatic machinery required for acquiring new spacers targeting invading elements. Due to programmable sequence specificity, numerous Cas proteins such as Cas9, Cas12, Cas13, and Cas14 have been exploited to develop new tools for genome engineering. Cas variants stimulated genetic research and propelled the CRISPR/Cas tool for manipulating and editing nucleic acid sequences of living cells of diverse organisms. This review aims to provide detail on two classes (class 1 and 2) of the CRISPR/Cas system, and the mechanisms of all Cas proteins, including Cas12, Cas13, and Cas14 discovered so far. In addition, we also discuss the pros and cons and recent applications of various Cas proteins in diverse fields, including those used to detect viruses like severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2). This review enables the researcher to gain knowledge on various Cas proteins and their applications, which have the potential to be used in next-generation precise genome engineering.

CRISPR-Cas-mediated diagnostics

An ideal molecular diagnostic method should be sensitive, specific, low cost, rapid, portable, and easy to operate. Traditional nucleic acid detection methods based mainly on PCR technology have not only high sensitivity and specificity, but also some limitations, such as the need for expensive equipment and skilled technicians, being both time and labor intensive, and difficult to implement in some regions. However, with the continuous development of CRISPR-Cas technology and its application in molecular diagnosis, new approaches have been used for the construction of molecular diagnostic systems. In this review, we discuss recent advances in CRISPR-based molecular diagnostic technologies and highlight the revolution they bring to the field of molecular diagnostics.

CRISPR-Cas13: A new technology for the rapid detection of pathogenic microorganisms

Pathogenic microorganisms have major impacts on human lives. Rapid and sensitive diagnostic tools are urgently needed to facilitate the early treatment of microbial infections and the effective control of microbial transmission. CRISPR-Cas13 employs programmable RNA to produce a sensitive and specific method with high base resolution and thus to provide a novel tool for the rapid detection of microorganisms. The review aims to provide insights to spur further development by summarizing the characteristics of effectors of the CRISPR-Cas13 system and by describing the latest research into its application in the rapid detection of pathogenic microorganisms in combination with nucleic acid extraction, isothermal amplification, and product detection.

Onsite detection of plant viruses using isothermal amplification assays

Plant diseases caused by viruses limit crop production and quality, resulting in significant losses. However, options for managing viruses are limited; for example, as systemic obligate parasites, they cannot be killed by chemicals. Sensitive, robust, affordable diagnostic assays are needed to detect the presence of viruses in plant materials such as seeds, vegetative parts, insect vectors, or alternative hosts and then prevent or limit their introduction into the field by destroying infected plant materials or controlling insect hosts. Diagnostics based on biological and physical properties are not very sensitive and are time-consuming, but assays based on viral proteins and nucleic acids are more specific, sensitive, and rapid. However, most such assays require laboratories with sophisticated equipment and technical skills. By contrast, isothermal-based assays such as loop-mediated isothermal amplification (LAMP) and recombinase polymerase amplification (RPA) are simple, easy to perform, reliable, specific, and rapid and do not require specialized equipment or skills. Isothermal amplification assays can be performed using lateral flow devices, making them suitable for onsite detection or testing in the field. To overcome non-specific amplification and cross-contamination issues, isothermal amplification assays can be coupled with CRISPR/Cas technology. Indeed, the collateral activity associated with some CRISPR/Cas systems has been successfully harnessed for visual detection of plant viruses. Here, we briefly describe traditional methods for detecting viruses and then examine the various isothermal assays that are being harnessed to detect viruses.

Characterization of a thermostable Cas13 enzyme for one-pot detection of SARS-CoV-2

Type VI CRISPR-Cas systems have been repurposed for various applications such as gene knockdown, viral interference, and diagnostics. However, the identification and characterization of thermophilic orthologs will expand and unlock the potential of diverse biotechnological applications. Herein, we identified and characterized a thermostable ortholog of the Cas13a family from the thermophilic organism Thermoclostridium caenicola (TccCas13a). We show that TccCas13a has a close phylogenetic relation to the HheCas13a ortholog from the thermophilic bacterium Herbinix hemicellulosilytica and shares several properties such as thermostability and inability to process its own pre-CRISPR RNA. We demonstrate that TccCas13a possesses robust cis and trans activities at a broad temperature range of 37 to 70 °C, compared with HheCas13a, which has a more limited range and lower activity. We harnessed TccCas13a thermostability to develop a sensitive, robust, rapid, and one-pot assay, named OPTIMA-dx, for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) detection. OPTIMA-dx exhibits no cross-reactivity with other viruses and a limit of detection of 10 copies/μL when using a synthetic SARS-CoV-2 genome. We used OPTIMA-dx for SARS-CoV-2 detection in clinical samples, and our assay showed 95% sensitivity and 100% specificity compared with qRT-PCR. Furthermore, we demonstrated that OPTIMA-dx is suitable for multiplexed detection and is compatible with the quick extraction protocol. OPTIMA-dx exhibits critical features that enable its use at point of care (POC). Therefore, we developed a mobile phone application to facilitate OPTIMA-dx data collection and sharing of patient sample results. This work demonstrates the power of CRISPR-Cas13 thermostable enzymes in enabling key applications in one-pot POC diagnostics and potentially in transcriptome engineering, editing, and therapies.

CRISPR-Cas system and its use in the diagnosis of infectious diseases

Rapid and accurate diagnostic methods for detecting pathogens are needed for effective management and treatment of infectious diseases. The conventional pathogen detection approach based on culture is considered the gold standard method, but needs several days to corroborate its results. Using nucleic acids from pathogens as detection targets has a considerable advantage in overcoming these time-consuming issues. The development of several molecular techniques has started to change the landscape of infectious disease diagnosis. However, these require expensive reagents, equipment, and sophisticated infrastructure, as well as highly trained workers. In this context, it is necessary to identify new diagnostic strategies to overcome these issues. Recently, CRISPR/Cas based diagnosis has revolutionized the area of molecular diagnostics of pathogenic diseases. In this review, we have discussed the different classes of CRISPR-Cas systems and their functions, and then focused on recent advances in CRISPR-based diagnosis technologies and the perspective of using this as a potential biosensing platform to detect infectious disease.

Engineering Toehold-Mediated Switches for Native RNA Detection and Regulation in Bacteria

RNA switches are versatile tools in synthetic biology for sensing and regulation applications. The discoveries of RNA-mediated translational and transcriptional control have facilitated the development of complexde novodesigns of RNA switches. Specifically, RNA toehold-mediated switches, in which binding to the toehold sensing domain controls the transition between switch states via strand displacement, have been extensively adapted for coupling systems responses to specifictrans-RNA inputs. This review highlights some of the challenges associated with applying these switches for native RNA detectionin vivo, including transferability between organisms. The applicability and design considerations of toehold-mediated switches are discussed by highlighting twelve recently developed switch designs. This review finishes with future perspectives to address current gaps in the field, particularly regarding the power of structural prediction algorithms for improved in vivo functionality of RNA switches.

Resistance Management through Brassica Crop–TuMV–Aphid Interactions: Retrospect and Prospects

Turnip mosaic virus (TuMV) is an important threat to the yield and quality of brassica crops in China, and has brought serious losses to brassica crops in the Far East, including China and the north. Aphids (Hemiptera, Aphidoidea) are the main mediators of TuMV transmission in field production, and not only have strong virus transmission ability (small individuals, strong concealment, and strong fecundity), but are also influenced by the environment, making them difficult to control. Till now, there have been few studies on the resistance to aphids in brassica crops, which depended mainly on pesticide control in agriculture production. However, the control effect was temporarily effective, which also brought environmental pollution, pesticide residues in food products, and destroyed the ecological balance. This study reviews the relationship among brassica crop–TuMV, TuMV–aphid, and brassica crop–aphid interactions, and reveals the influence factors (light, temperature, and CO2 concentration) on brassica crop–TuMV–aphid interactions, summarizing the current research status and main scientific problems about brassica crop–TuMV–aphid interactions. It may provide theoretical guidance for opening up new ways of aphid and TuMV management in brassica crops.

Human Induced Pluripotent Stem Cell as a Disease Modeling and Drug Development Platform-A Cardiac Perspective

A comprehensive understanding of the pathophysiology and cellular responses to drugs in human heart disease is limited by species differences between humans and experimental animals. In addition, isolation of human cardiomyocytes (CMs) is complicated because cells obtained by biopsy do not proliferate to provide sufficient numbers of cells for preclinical studies in vitro. Interestingly, the discovery of human-induced pluripotent stem cell (hiPSC) has opened up the possibility of generating and studying heart disease in a culture dish. The combination of reprogramming and genome editing technologies to generate a broad spectrum of human heart diseases in vitro offers a great opportunity to elucidate gene function and mechanisms. However, to exploit the potential applications of hiPSC-derived-CMs for drug testing and studying adult-onset cardiac disease, a full functional characterization of maturation and metabolic traits is required. In this review, we focus on methods to reprogram somatic cells into hiPSC and the solutions for overcome immaturity of the hiPSC-derived-CMs to mimic the structure and physiological properties of the adult human CMs to accurately model disease and test drug safety. Finally, we discuss how to improve the culture, differentiation, and purification of CMs to obtain sufficient numbers of desired types of hiPSC-derived-CMs for disease modeling and drug development platform.

Attomolar analyte sensing techniques (AttoSens): a review on a decade of progress on chemical and biosensing nanoplatforms

Detecting the ultra-low abundance of analytes in real-life samples, such as biological fluids, water, soil, and food, requires the design and development of high-performance biosensing modalities. The breakthrough efforts from the scientific community have led to the realization of sensing technologies that measure the analyte's ultra-trace level, with relevant sensitivity, selectivity, response time, and sampling efficiency, referred to as Attomolar Analyte Sensing Techniques (AttoSens) in this review. In an AttoSens platform, 1 aM detection corresponds to the quantification of 60 target analyte molecules in 100 μL of sample volume. Herein, we review the approaches listed for various sensor probe design, and their sensing strategies that paved the way for the detection of attomolar (aM: 10^-18 M) concentration of analytes. A summary of the technological advances made by the diverse AttoSens trends from the past decade is presented.

Advances in gene therapy for neurogenetic diseases: a brief review

Neurogenetic diseases are neurological conditions with a genetic cause (s). There are thousands of neurogenetic diseases, and most of them are incurable. The development of bioinformatics and elucidation of the mechanism of pathogenesis have allowed the development of gene therapy approaches, which show great potential in treating neurogenetic diseases. Viral vectors delivery, antisense oligonucleotides, gene editing, RNA interference, and burgeoning viroid delivery technique are promising gene therapy strategies, and commendable therapeutic effects in the treatment of neurogenetic diseases have been achieved (Fig. 1). This review highlights a sampling of advances in gene therapies for neurogenetic disorders. Fig. 1 Examples of gene therapy strategies used in the treatment of neurogenetic diseases. The schematic diagram shows different gene therapy approaches used for treating a sampling of neurogenetic disorders, such as ASO therapy, gene editing, gene augmentation, and RNA interference.

Advancing sensing technology with CRISPR: From the detection of nucleic acids to a broad range of analytes - A review

The CRISPR/Cas technology, derived from an adaptive immune system in bacteria, has been awarded the Nobel Prize in Chemistry in 2020 for its success in gene editing. Increasing reports reveal that CRISPR/Cas technology has a wide scope of applications and it could be incorporated into biosensors for detecting critical analytes. CRISPR-powered biosensors have attracted significant research interest due to their advantages including high accuracy, good specificity, rapid response, and superior integrity. Now the CRISPR technology is not only admirable in nucleic acid monitoring, but also promising for other kinds of biomarkers' detection, including metal ions, small molecules, peptides, and proteins. Therefore, it is of great worth to explore the prospect, and summarize the strategies in applying CRISPR technology for the recognition of a broad range of targets. In this review, we summarized the strategies of CRISPR biosensing for non-nucleic-acid analytes, the latest development of nucleic acid detection, and proposed the challenges and outlook of CRISPR-powered biosensors.

Application of the CRISPR/Cas9-based gene editing technique in basic research, diagnosis, and therapy of cancer

The 2020 Nobel Prize in Chemistry was awarded to Emmanuelle Charpentier and Jennifer Doudna for the development of the Clustered regularly interspaced short palindromic repeats/CRISPR-associated nuclease9 (CRISPR/Cas9) gene editing technology that provided new tools for precise gene editing. It is possible to target any genomic locus virtually using only a complex nuclease protein with short RNA as a site-specific endonuclease. Since cancer is caused by genomic changes in tumor cells, CRISPR/Cas9 can be used in the field of cancer research to edit genomes for exploration of the mechanisms of tumorigenesis and development. In recent years, the CRISPR/Cas9 system has been increasingly used in cancer research and treatment and remarkable results have been achieved. In this review, we introduced the mechanism and development of the CRISPR/Cas9-based gene editing system. Furthermore, we summarized current applications of this technique for basic research, diagnosis and therapy of cancer. Moreover, the potential applications of CRISPR/Cas9 in new emerging hotspots of oncology research were discussed, and the challenges and future directions were highlighted.

Novel CRISPR/Cas applications in plants: from prime editing to chromosome engineering

In the last years, tremendous progress has been made in the development of CRISPR/Cas-mediated genome editing tools. A number of natural CRISPR/Cas nuclease variants have been characterized. Engineered Cas proteins have been developed to minimize PAM restrictions, off-side effects and temperature sensitivity. Both kinds of enzymes have, by now, been applied widely and efficiently in many plant species to generate either single or multiple mutations at the desired loci by multiplexing. In addition to DSB-induced mutagenesis, specifically designed CRISPR/Cas systems allow more precise gene editing, resulting not only in random mutations but also in predefined changes. Applications in plants include gene targeting by homologous recombination, base editing and, more recently, prime editing. We will evaluate these different technologies for their prospects and practical applicability in plants. In addition, we will discuss a novel application of the Cas9 nuclease in plants, enabling the induction of heritable chromosomal rearrangements, such as inversions and translocations. This technique will make it possible to change genetic linkages in a programmed way and add another level of genome engineering to the toolbox of plant breeding. Also, strategies for tissue culture free genome editing were developed, which might be helpful to overcome the transformation bottlenecks in many crops. All in all, the recent advances of CRISPR/Cas technology will help agriculture to address the challenges of the twenty-first century related to global warming, pollution and the resulting food shortage.

Functional Features and Current Applications of the RNA-Targeting Type VI CRISPR-Cas Systems

CRISPR-Cas systems are a form of prokaryotic adaptive immunity that employs RNA-guided endonucleases (Cas effectors) to cleave foreign genetic elements. Due to their simplicity, targeting programmability, and efficiency, single-effector CRISPR-Cas systems have great potential for application in research, biotechnology, and therapeutics. While DNA-targeting Cas effectors such as Cas9 and Cas12a have become indispensable tools for genome editing in the past decade, the more recent discovery of RNA-targeting CRISPR-Cas systems has opened the door for implementation of CRISPR-Cas technology in RNA manipulation. With an increasing number of studies reporting their application in transcriptome engineering, viral interference, nucleic acid detection, and RNA imaging, type VI CRISPR-Cas systems and the associated Cas13 effectors particularly hold promise as RNA-targeting or RNA-binding tools. However, even though previous structural and biochemical characterization provided a firm basis for leveraging type VI CRISPR-Cas systems into such tools, the lack of comprehension of certain mechanisms underlying their functions hinders more sophisticated and conventional use. This review will summarize current knowledge on structural and mechanistic properties of type VI CRISPR-Cas systems, give an overview on the reported applications, and discuss functional features that need further investigation in order to improve performance of Cas13-based tools.

Small nucleic acids and the path to the clinic for anti-CRISPR

CRISPR-based therapeutics have entered clinical trials but no methods to inhibit Cas enzymes have been demonstrated in a clinical setting. The ability to inhibit CRISPR-based gene editing or gene targeting drugs should be considered a critical step in establishing safety standards for many CRISPR-Cas therapeutics. Inhibitors can act as a failsafe or as an adjuvant to reduce off-target effects in patients. In this review we discuss the need for clinical inhibition of CRISPR-Cas systems and three existing inhibitor technologies: anti-CRISPR (Acr) proteins, small molecule Cas inhibitors, and small nucleic acid-based CRISPR inhibitors, CRISPR SNuBs. Due to their unique properties and the recent successes of other nucleic acid-based therapeutics, CRISPR SNuBs appear poised for clinical application in the near-term.

Human iPSCs and Genome Editing Technologies for Precision Cardiovascular Tissue Engineering

Induced pluripotent stem cells (iPSCs) originate from the reprogramming of adult somatic cells using four Yamanaka transcription factors. Since their discovery, the stem cell (SC) field achieved significant milestones and opened several gateways in the area of disease modeling, drug discovery, and regenerative medicine. In parallel, the emergence of clustered regularly interspaced short palindromic repeats (CRISPR)-associated protein 9 (CRISPR-Cas9) revolutionized the field of genome engineering, allowing the generation of genetically modified cell lines and achieving a precise genome recombination or random insertions/deletions, usefully translated for wider applications. Cardiovascular diseases represent a constantly increasing societal concern, with limited understanding of the underlying cellular and molecular mechanisms. The ability of iPSCs to differentiate into multiple cell types combined with CRISPR-Cas9 technology could enable the systematic investigation of pathophysiological mechanisms or drug screening for potential therapeutics. Furthermore, these technologies can provide a cellular platform for cardiovascular tissue engineering (TE) approaches by modulating the expression or inhibition of targeted proteins, thereby creating the possibility to engineer new cell lines and/or fine-tune biomimetic scaffolds. This review will focus on the application of iPSCs, CRISPR-Cas9, and a combination thereof to the field of cardiovascular TE. In particular, the clinical translatability of such technologies will be discussed ranging from disease modeling to drug screening and TE applications.

Wheat omics: Classical breeding to new breeding technologies

Wheat is an important cereal crop, and its significance is more due to compete for dietary products in the world. Many constraints facing by the wheat crop due to environmental hazardous, biotic, abiotic stress and heavy matters factors, as a result, decrease the yield. Understanding the molecular mechanism related to these factors is significant to figure out genes regulate under specific conditions. Classical breeding using hybridization has been used to increase the yield but not prospered at the desired level. With the development of newly emerging technologies in biological sciences i.e., marker assisted breeding (MAB), QTLs mapping, mutation breeding, proteomics, metabolomics, next-generation sequencing (NGS), RNA_sequencing, transcriptomics, differential expression genes (DEGs), computational resources and genome editing techniques i.e. (CRISPR cas9; Cas13) advances in the field of omics. Application of new breeding technologies develops huge data; considerable development is needed in bioinformatics science to interpret the data. However, combined omics application to address physiological questions linked with genetics is still a challenge. Moreover, viroid discovery opens the new direction for research, economics, and target specification. Comparative genomics important to figure gene of interest processes are further discussed about considering the identification of genes, genomic loci, and biochemical pathways linked with stress resilience in wheat. Furthermore, this review extensively discussed the omics approaches and their effective use. Integrated plant omics technologies have been used viroid genomes associated with CRISPR and CRISPR-associated Cas13a proteins system used for engineering of viroid interference along with high-performance multidimensional phenotyping as a significant limiting factor for increasing stress resistance in wheat.

HIF1α epigenetically repressed macrophages via CRISPR/Cas9-EZH2 system for enhanced cancer immunotherapy

Immune suppressive microenvironment in tumor emerges as the main obstacle for cancer immunotherapy. In this study, we identified that HIF1α was activated in the tumor associated macrophages and acted as an important factor for the immune suppressive microenvironment. Epigenetically silencing of Hif1α via histone H3 methylation in the promoter region was achieved by CRISPR/dCas9-EZH2 system, in which histone H3 methylase EZH2 was recruited to the promoter region specifically. The Hif1α silenced macrophage, namely HERM (Hif1α Epigenetically Repressed Macrophage) manifested as inheritable tumor suppressing phenotype. In the subcutaneous B16-F10 melanoma syngeneic model, intratumoral injection of HERMs reprogrammed the immune suppressive microenvironment to the active one, reducing tumor burden and prolonging overall survival. Additionally, HERMs therapy remarkably inhibited tumor angiogenesis. Together, our study has not only identified a promising cellular and molecular target for reverting immune suppressive microenvironment, but also provided a potent strategy for reprogramming tumor microenvironment via epigenetically reprogrammed macrophages.

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Macrophage are trained to promote cancer progression under hypoxic tumor microenvironment.

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HIF1α epigenetically repressed macrophage (HERM) is characterized as anti-tumoral function and suppress tumor progression.

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HERMs unleash immune suppression and promote cancer immunity.

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HERMs inhibit tumor angiogenesis and reduce tumor burden.

Sophisticated CRISPR/Cas tools for fine-tuning plant performance

Over the last years, the discovery of various natural and the development of a row of engineered CRISPR/Cas nucleases have made almost every site of plant genomes accessible for the induction of specific changes. Newly developed tools open up a wide range of possibilities for the induction of genetic variability, from changing a single bp to Mbps, and thus to fine-tune plant performance. Whereas early approaches focused on targeted mutagenesis, recently developed tools enable the induction of precise and predefined genomic modifications. The use of base editors allows the substitution of single nucleotides, whereas the use of prime editors and gene targeting methods enables the induction of larger sequence modifications from a few bases to several kbp. Recently, through CRISPR/Cas-mediated chromosome engineering, it became possible to induce heritable inversions and translocations in the Mbp range. Thus, a novel way of breaking and fixing genetic linkages has come into reach for breeders. In addition, sequence-specific recruitment of various factors involved in transcriptional and post-transcriptional regulation has been shown to provide an additional class of methods for the fine tuning of plant performance. In this review, we provide an overview of the most recent progress in the field of CRISPR/Cas-based tool development for plant genome engineering and try to evaluate the importance of these developments for breeding and biotechnological applications.

CRISPR-Mediated Engineering across the Central Dogma in Plant Biology for Basic Research and Crop Improvement

The central dogma (CD) of molecular biology is the transfer of genetic information from DNA to RNA to protein. Major CD processes governing genetic flow include the cell cycle, DNA replication, chromosome packaging, epigenetic changes, transcription, posttranscriptional alterations, translation, and posttranslational modifications. The CD processes are tightly regulated in plants to maintain genetic integrity throughout the life cycle and to pass genetic materials to next generation. Engineering of various CD processes involved in gene regulation will accelerate crop improvement to feed the growing world population. CRISPR technology enables programmable editing of CD processes to alter DNA, RNA, or protein, which would have been impossible in the past. Here, an overview of recent advancements in CRISPR tool development and CRISPR-based CD modulations that expedite basic and applied plant research is provided. Furthermore, CRISPR applications in major thriving areas of research, such as gene discovery (allele mining and cryptic gene activation), introgression (de novo domestication and haploid induction), and application of desired traits beneficial to farmers or consumers (biotic/abiotic stress-resilient crops, plant cell factories, and delayed senescence), are described. Finally, the global regulatory policies, challenges, and prospects for CRISPR-mediated crop improvement are discussed.

Peptides and pseudopeptide ligands: a powerful toolbox for the affinity purification of current and next-generation biotherapeutics

Following the consolidation of therapeutic proteins in the fight against cancer, autoimmune, and neurodegenerative diseases, recent advancements in biochemistry and biotechnology have introduced a host of next-generation biotherapeutics, such as CRISPR-Cas nucleases, stem and car-T cells, and viral vectors for gene therapy. With these drugs entering the clinical pipeline, a new challenge lies ahead: how to manufacture large quantities of high-purity biotherapeutics that meet the growing demand by clinics and biotech companies worldwide. The protein ligands employed by the industry are inadequate to confront this challenge: while featuring high binding affinity and selectivity, these ligands require laborious engineering and expensive manufacturing, are prone to biochemical degradation, and pose safety concerns related to their bacterial origin. Peptides and pseudopeptides make excellent candidates to form a new cohort of ligands for the purification of next-generation biotherapeutics. Peptide-based ligands feature excellent target biorecognition, low or no toxicity and immunogenicity, and can be manufactured affordably at large scale. This work presents a comprehensive and systematic review of the literature on peptide-based ligands and their use in the affinity purification of established and upcoming biological drugs. A comparative analysis is first presented on peptide engineering principles, the development of ligands targeting different biomolecular targets, and the promises and challenges connected to the industrial implementation of peptide ligands. The reviewed literature is organized in (i) conventional (α-)peptides targeting antibodies and other therapeutic proteins, gene therapy products, and therapeutic cells; (ii) cyclic peptides and pseudo-peptides for protein purification and capture of viral and bacterial pathogens; and (iii) the forefront of peptide mimetics, such as β-/γ-peptides, peptoids, foldamers, and stimuli-responsive peptides for advanced processing of biologics.

A New Tool for CRISPR-Cas13a-Based Cancer Gene Therapy

Cas13a has already been successfully applied to virus detection. However, as a new gene interference tool, its potential in cancer treatment was not fully explored until now. This study constructed a new Cas13a expression vector, decoy minimal promoter-Cas13a-U6-guide RNA (DMP-Cas13a-U6-gRNA [DCUg]), by controlling the Cas13a and gRNA expression with a nuclear factor κB (NF-κB)-specific promoter and U6 promoter, respectively. DCUg could specifically and effectively knock down the expression of reporter genes in the 293T and HepG2 cells. DCUg could also similarly knock down the expression of endogenous oncogenes (TERT, EZH2, and RelA) at both mRNA and protein levels in a human hepatoma cell HepG2, which led to significant apoptosis and growth inhibition. In contrast, the same transfection did not affect the target gene expression, cell apoptosis, and growth of a human normal liver cell HL7702. Finally, DCUg targeting these oncogenes was packaged into adeno-associated virus (AAV) and treated four cells (HepG2, HL7702, WEHI-3, and Hepa1-6) and tumor-bearing mice. As results, the recombinant AAV significantly inhibited the growth of three cancer cells (HepG2, Hepa1-6, and WEHI-3) in vitro and the xenografted Hepa1-6 and WEHI-3 tumors in mice. This study therefore developed a new tool for the CRISPR-Cas13a-based cancer gene therapy.

CRISPR-Cas systems: Overview, innovations and applications in human disease research and gene therapy

Genome editing is the modification of genomic DNA at a specific target site in a wide variety of cell types and organisms, including insertion, deletion and replacement of DNA, resulting in inactivation of target genes, acquisition of novel genetic traits and correction of pathogenic gene mutations. Due to the advantages of simple design, low cost, high efficiency, good repeatability and short-cycle, CRISPR-Cas systems have become the most widely used genome editing technology in molecular biology laboratories all around the world. In this review, an overview of the CRISPR-Cas systems will be introduced, including the innovations, the applications in human disease research and gene therapy, as well as the challenges and opportunities that will be faced in the practical application of CRISPR-Cas systems.

iSCAN: An RT-LAMP-coupled CRISPR-Cas12 module for rapid, sensitive detection of SARS-CoV-2

The COVID-19 pandemic caused by SARS-CoV-2 affects all aspects of human life. Detection platforms that are efficient, rapid, accurate, specific, sensitive, and user friendly are urgently needed to manage and control the spread of SARS-CoV-2. RT-qPCR based methods are the gold standard for SARS-CoV-2 detection. However, these methods require trained personnel, sophisticated infrastructure, and a long turnaround time, thereby limiting their usefulness. Reverse transcription-loop-mediated isothermal amplification (RT-LAMP), a one-step nucleic acid amplification method conducted at a single temperature, has been used for colorimetric virus detection. CRISPR-Cas12 and CRISPR-Cas13 systems, which possess collateral activity against ssDNA and RNA, respectively, have also been harnessed for virus detection. Here, we built an efficient, rapid, specific, sensitive, user-friendly SARS-CoV-2 detection module that combines the robust virus amplification of RT-LAMP with the specific detection ability of SARS-CoV-2 by CRISPR-Cas12. Furthermore, we combined the RT-LAMP-CRISPR-Cas12 module with lateral flow cells to enable highly efficient point-of-care SARS-CoV-2 detection. Our iSCAN SARS-CoV-2 detection module, which exhibits the critical features of a robust molecular diagnostic device, should facilitate the effective management and control of COVID-19.

Nucleic Acid Detection Using CRISPR/Cas Biosensing Technologies

For infectious diseases, rapid and accurate identification of the pathogen is critical for effective management and treatment, but diagnosis remains challenging, particularly in resource-limited areas. Methods that accurately detect pathogen nucleic acids can provide robust, accurate, rapid, and ultrasensitive technologies for point-of-care diagnosis of pathogens, and thus yield information that is invaluable for disease management and treatment. Several technologies, mostly PCR-based, have been employed for pathogen detection; however, these require expensive reagents and equipment, and skilled personnel. CRISPR/Cas systems have been used for genome editing, based on their ability to accurately recognize and cleave specific DNA and RNA sequences. Moreover, following recognition of the target sequence, certain CRISPR/Cas systems including orthologues of Cas13, Cas12a, and Cas14 exhibit collateral nonspecific catalytic activities that can be employed for nucleic acid detection, for example by degradation of a labeled nucleic acid to produce a fluorescent signal. CRISPR/Cas systems are amenable to multiplexing, thereby enabling a single diagnostic test to identify multiple targets down to attomolar (10-18 mol/L) concentrations of target molecules. Developing devices that couple CRISPR/Cas with lateral flow systems may allow inexpensive, accurate, highly sensitive, in-field deployable diagnostics. These sensors have myriad applications, from human health to agriculture. In this review, we discuss the recent advances in the field of CRISPR-based biosensing technologies and highlight insights of their potential use in a myriad of applications.

CRISPR interference-mediated noggin knockdown promotes BMP2-induced osteogenesis and calvarial bone healing

Healing of large calvarial bone defects remains a challenging task in the clinical setting. Although BMP2 (bone morphogenetic protein 2) is a potent growth factor that can induce bone repair, BMP2 provokes the expression of antagonist Noggin that self-restricts its bioactivity. CRISPR interference (CRISPRi) is a technology for programmable gene suppression but its application in regenerative medicine is still in its infancy. We reasoned that Nog inhibition, concurrent with BMP2 overexpression, can promote the osteogenesis of adipose-derived stem cells (ASC) and improve calvarial bone healing. We designed and exploited a hybrid baculovirus (BV) system for the delivery of BMP2 gene and CRISPRi system targeting Nog. After BV-mediated co-delivery into ASC, the system conferred prolonged BMP2 expression and stimulated Nog expression while the CRISPRi system effectively repressed Nog upregulation for at least 14 days. The CRISPRi-mediated Nog knockdown, along with BMP2 overexpression, additively stimulated the osteogenic differentiation of ASC. Implantation of the CRISPRi-engineered ASC into the critical size defects at the calvaria significantly enhanced the calvarial bone healing and matrix mineralization. These data altogether implicate the potentials of CRISPRi-mediated gene knockdown for cell fate regulation and tissue regeneration.

Tuning up Transcription Factors for Therapy

The recent developments in the delivery and design of transcription factors put their therapeutic applications within reach, exemplified by cell replacement, cancer differentiation and T-cell based cancer therapies. The success of such applications depends on the efficacy and precision in the action of transcription factors. The biophysical and genetic characterization of the paradigmatic prokaryotic repressors, LacI and TetR and the designer transcription factors, transcription activator-like effector (TALE) and CRISPR-dCas9 revealed common principles behind their efficacy, which can aid the optimization of transcriptional activators and repressors. Further studies will be required to analyze the linkage between dissociation constants and enzymatic activity, the role of phase separation and squelching in activation and repression and the long-range interaction of transcription factors with epigenetic regulators in the context of the chromosomes. Understanding these mechanisms will help to tailor natural and synthetic transcription factors to the needs of specific applications.

Programmable CRISPR interference for gene silencing using Cas13a in mosquitoes

In the CRISPR-Cas systems, Cas13a is an RNA-guided RNA nuclease specifically targeting single strand RNA. We developed a Cas13a mediated CRISPR interference tool to target mRNA for gene silencing in mosquitoes. A Cas13a expressing plasmid was delivered to mosquitoes by intrathoracic injection, and Cas13a transcripts were detectable at least 10 days post-delivery. The target specific crRNA was synthesized in vitro using T7 RNA polymerase. The Cas13a plasmid and target crRNA can be delivered by intrathoracic injection together, or the Cas13a construct can be provided first, and then target crRNA can be given later when appropriate. The machinery was tested in two mosquito species. In Anopheles gambiae, vitellogenin gene was silenced by Cas13a/Vg-crRNA, which was accompanied by a significant reduction in egg production. In Aedes aegypti, the α- and δ-subunits of COPI genes were silenced by Cas13a/crRNA, which resulted in mortality and fragile midguts, reproducing a phenotype reported previously. Co-silencing genes simultaneously is achievable when a cocktail of target crRNAs is given. No detectable collateral cleavages of non-target transcripts were observed in the study. In addition to dsRNA or siRNA mediated RNA interference, the programmable CRISPR interference method offers an alternative to knock down genes in mosquitoes.

Sharpening the Molecular Scissors: Advances in Gene-Editing Technology

The ability to precisely modify human genes has been made possible by the development of tools such as meganucleases, zinc finger nucleases, TALENs, and CRISPR/Cas. These now make it possible to generate targeted deletions, insertions, gene knock outs, and point variants; to modulate gene expression by targeting transcription factors or epigenetic machineries to DNA; or to target and modify RNA. Endogenous repair mechanisms are used to make the modifications required in DNA; they include non-homologous end joining, homology-directed repair, homology-independent targeted integration, microhomology-mediated end joining, base-excision repair, and mismatch repair. Off-target effects can be monitored using in silico prediction and sequencing and minimized using Cas proteins with higher accuracy, such as high-fidelity Cas9, enhanced-specificity Cas9, and hyperaccurate Cas9. Alternatives to Cas9 have been identified, including Cpf1, Cas12a, Cas12b, and smaller Cas9 orthologs such as CjCas9. Delivery of gene-editing components is performed ex vivo using standard techniques or in vivo using AAV, lipid nanoparticles, or cell-penetrating peptides. Clinical development of gene-editing technology is progressing in several fields, including immunotherapy in cancer treatment, antiviral therapy for HIV infection, and treatment of genetic disorders such as β-thalassemia, sickle cell disease, lysosomal storage disorders, and retinal dystrophy. Here we review these technological advances and the challenges to their clinical implementation.

Fusion of the Cas9 endonuclease and the VirD2 relaxase facilitates homology-directed repair for precise genome engineering in rice

Precise genome editing by systems such as clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 (Cas9) requires high-efficiency homology-directed repair (HDR). Different technologies have been developed to improve HDR but with limited success. Here, we generated a fusion between the Cas9 endonuclease and the Agrobacterium VirD2 relaxase (Cas9-VirD2). This chimeric protein combines the functions of Cas9, which produces targeted and specific DNA double-strand breaks (DSBs), and the VirD2 relaxase, which brings the repair template in close proximity to the DSBs, to facilitate HDR. We successfully employed our Cas9-VirD2 system for precise ACETOLACTATE SYNTHASE (OsALS) allele modification to generate herbicide-resistant rice (Oryza sativa) plants, CAROTENOID CLEAVAGE DIOXYGENASE-7 (OsCCD7) to engineer plant architecture, and generate in-frame fusions with the HA epitope at HISTONE DEACETYLASE (OsHDT) locus. The Cas9-VirD2 system expands our ability to improve agriculturally important traits in crops and opens new possibilities for precision genome engineering across diverse eukaryotic species.

Fusion of the Cas9 endonuclease and the VirD2 relaxase facilitates homology-directed repair for precise genome engineering in rice

Precise genome editing by systems such as clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 (Cas9) requires high-efficiency homology-directed repair (HDR). Different technologies have been developed to improve HDR but with limited success. Here, we generated a fusion between the Cas9 endonuclease and the Agrobacterium VirD2 relaxase (Cas9-VirD2). This chimeric protein combines the functions of Cas9, which produces targeted and specific DNA double-strand breaks (DSBs), and the VirD2 relaxase, which brings the repair template in close proximity to the DSBs, to facilitate HDR. We successfully employed our Cas9-VirD2 system for precise ACETOLACTATE SYNTHASE (OsALS) allele modification to generate herbicide-resistant rice (Oryza sativa) plants, CAROTENOID CLEAVAGE DIOXYGENASE-7 (OsCCD7) to engineer plant architecture, and generate in-frame fusions with the HA epitope at HISTONE DEACETYLASE (OsHDT) locus. The Cas9-VirD2 system expands our ability to improve agriculturally important traits in crops and opens new possibilities for precision genome engineering across diverse eukaryotic species.

Ali, Shami, Sedeek et al. generate a fusion between Cas9 and the VirD2 relaxase (Cas9-VirD2), which combines the functions of both proteins in producing targeted and specific double strand breaks and promoting homology-directed repair. They show the utility of their method by producing herbicide resistant rice.

CRISPR-Cas13d mediates robust RNA virus interference in plants

BACKGROUND

CRISPR-Cas systems endow bacterial and archaeal species with adaptive immunity mechanisms to fend off invading phages and foreign genetic elements. CRISPR-Cas9 has been harnessed to confer virus interference against DNA viruses in eukaryotes, including plants. In addition, CRISPR-Cas13 systems have been used to target RNA viruses and the transcriptome in mammalian and plant cells. Recently, CRISPR-Cas13a has been shown to confer modest interference against RNA viruses. Here, we characterized a set of different Cas13 variants to identify those with the most efficient, robust, and specific interference activities against RNA viruses in planta using Nicotiana benthamiana.

RESULTS

Our data show that LwaCas13a, PspCas13b, and CasRx variants mediate high interference activities against RNA viruses in transient assays. Moreover, CasRx mediated robust interference in both transient and stable overexpression assays when compared to the other variants tested. CasRx targets either one virus alone or two RNA viruses simultaneously, with robust interference efficiencies. In addition, CasRx exhibits strong specificity against the target virus and does not exhibit collateral activity in planta.

CONCLUSIONS

Our data establish CasRx as the most robust Cas13 variant for RNA virus interference applications in planta and demonstrate its suitability for studying key questions relating to virus biology.

Does co-transcriptional regulation of alternative splicing mediate plant stress responses?

Plants display exquisite control over gene expression to elicit appropriate responses under normal and stress conditions. Alternative splicing (AS) of pre-mRNAs, a process that generates two or more transcripts from multi-exon genes, adds another layer of regulation to fine-tune condition-specific gene expression in animals and plants. However, exactly how plants control splice isoform ratios and the timing of this regulation in response to environmental signals remains elusive. In mammals, recent evidence indicate that epigenetic and epitranscriptome changes, such as DNA methylation, chromatin modifications and RNA methylation, regulate RNA polymerase II processivity, co-transcriptional splicing, and stability and translation efficiency of splice isoforms. In plants, the role of epigenetic modifications in regulating transcription rate and mRNA abundance under stress is beginning to emerge. However, the mechanisms by which epigenetic and epitranscriptomic modifications regulate AS and translation efficiency require further research. Dynamic changes in the chromatin landscape in response to stress may provide a scaffold around which gene expression, AS and translation are orchestrated. Finally, we discuss CRISPR/Cas-based strategies for engineering chromatin architecture to manipulate AS patterns (or splice isoforms levels) to obtain insight into the epigenetic regulation of AS.

CRISPR technologies for stem cell engineering and regenerative medicine

CRISPR/Cas9 system exploits the concerted action of Cas9 nuclease and programmable single guide RNA (sgRNA), and has been widely used for genome editing. The Cas9 nuclease activity can be abolished by mutation to yield the catalytically deactivated Cas9 (dCas9). Coupling with the customizable sgRNA for targeting, dCas9 can be fused with transcription repressors to inhibit specific gene expression (CRISPR interference, CRISPRi) or fused with transcription activators to activate the expression of gene of interest (CRISPR activation, CRISPRa). Here we introduce the principles and recent advances of these CRISPR technologies, their delivery vectors and review their applications in stem cell engineering and regenerative medicine. In particular, we focus on in vitro stem cell fate manipulation and in vivo applications such as prevention of retinal and muscular degeneration, neural regeneration, bone regeneration, cartilage tissue engineering, as well as treatment of diseases in blood, skin and liver. Finally, the challenges to translate CRISPR to regenerative medicine and future perspectives are discussed and proposed.

Recent progress in single-molecule studies of mRNA localization in vivo

From biogenesis to degradation, mRNA goes through diverse types of regulation and interaction with other biomolecules. Uneven distribution of mRNA transcripts and the diverse isoforms and modifications of mRNA make us wonder how cells manage the complexity and keep the functional integrity for the normal development of cells and organisms. Single-molecule microscopy tools have expanded the scope of RNA research with unprecedented spatiotemporal resolution. In this review, we highlight the recent progress in the methods for labeling mRNA targets and analyzing the quantitative information from fluorescence images of single mRNA molecules. In particular, the MS2 system and its various applications are the main focus of this article. We also review how recent studies have addressed biological questions related to the significance of mRNA localization in vivo. Efforts to visualize the dynamics of single mRNA molecules in live cells will push forward our knowledge on the nature of heterogeneity in RNA sequence, structure, and distribution as well as their molecular function and coordinated interaction with RNA binding proteins.

Multiplex CRISPR Mutagenesis of the Serine/Arginine-Rich (SR) Gene Family in Rice

Plant growth responds to various environmental and developmental cues via signaling cascades that influence gene expression at the level of transcription and pre-mRNA splicing. Alternative splicing of pre-mRNA increases the coding potential of the genome from multiexon genes and regulates gene expression through multiple mechanisms. Serine/arginine-rich (SR) proteins, a conserved family of splicing factors, are the key players of alternative splicing and regulate pre-mRNA splicing under stress conditions. The rice (Oryza sativa) genome encodes 22 SR proteins categorized into six subfamilies. Three of the subfamilies are plant-specific with no mammalian orthologues, and the functions of these SR proteins are not well known. The clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 (Cas9) system is a genome engineering tool that cleaves the target DNA at specific locations directed by a guide RNA (gRNA). Recent advances in CRISPR/Cas9-mediated plant genome engineering make it possible to generate single and multiple functional knockout mutants in diverse plant species. In this study, we targeted each rice SR locus and produced single knockouts. To overcome the functional redundancy within each subfamily of SR genes, we utilized a polycistronic tRNA-gRNA multiplex targeting system and targeted all loci of each subfamily. Sanger sequencing results indicated that most of the targeted loci had knockout mutations. This study provides useful resource materials for understanding the molecular role of SR proteins in plant development and biotic and abiotic stress responses.

The emerging and uncultivated potential of CRISPR technology in plant science

The application of clustered regularly interspaced short palindromic repeats (CRISPR) for genetic manipulation has revolutionized life science over the past few years. CRISPR was first discovered as an adaptive immune system in bacteria and archaea, and then engineered to generate targeted DNA breaks in living cells and organisms. During the cellular DNA repair process, various DNA changes can be introduced. The diverse and expanding CRISPR toolbox allows programmable genome editing, epigenome editing and transcriptome regulation in plants. However, challenges in plant genome editing need to be fully appreciated and solutions explored. This Review intends to provide an informative summary of the latest developments and breakthroughs of CRISPR technology, with a focus on achievements and potential utility in plant biology. Ultimately, CRISPR will not only facilitate basic research, but also accelerate plant breeding and germplasm development. The application of CRISPR to improve germplasm is particularly important in the context of global climate change as well as in the face of current agricultural, environmental and ecological challenges.

Morphogenesis as Bayesian inference: A variational approach to pattern formation and control in complex biological systems

Recent advances in molecular biology such as gene editing [1], bioelectric recording and manipulation [2] and live cell microscopy using fluorescent reporters [3], [4] - especially with the advent of light-controlled protein activation through optogenetics [5] - have provided the tools to measure and manipulate molecular signaling pathways with unprecedented spatiotemporal precision. This has produced ever increasing detail about the molecular mechanisms underlying development and regeneration in biological organisms. However, an overarching concept - that can predict the emergence of form and the robust maintenance of complex anatomy - is largely missing in the field. Classic (i.e., dynamic systems and analytical mechanics) approaches such as least action principles are difficult to use when characterizing open, far-from equilibrium systems that predominate in Biology. Similar issues arise in neuroscience when trying to understand neuronal dynamics from first principles. In this (neurobiology) setting, a variational free energy principle has emerged based upon a formulation of self-organization in terms of (active) Bayesian inference. The free energy principle has recently been applied to biological self-organization beyond the neurosciences [6], [7]. For biological processes that underwrite development or regeneration, the Bayesian inference framework treats cells as information processing agents, where the driving force behind morphogenesis is the maximization of a cell's model evidence. This is realized by the appropriate expression of receptors and other signals that correspond to the cell's internal (i.e., generative) model of what type of receptors and other signals it should express. The emerging field of the free energy principle in pattern formation provides an essential quantitative formalism for understanding cellular decision-making in the context of embryogenesis, regeneration, and cancer suppression. In this paper, we derive the mathematics behind Bayesian inference - as understood in this framework - and use simulations to show that the formalism can reproduce experimental, top-down manipulations of complex morphogenesis. First, we illustrate this 'first principle' approach to morphogenesis through simulated alterations of anterior-posterior axial polarity (i.e., the induction of two heads or two tails) as in planarian regeneration. Then, we consider aberrant signaling and functional behavior of a single cell within a cellular ensemble - as a first step in carcinogenesis as false 'beliefs' about what a cell should 'sense' and 'do'. We further show that simple modifications of the inference process can cause - and rescue - mis-patterning of developmental and regenerative events without changing the implicit generative model of a cell as specified, for example, by its DNA. This formalism offers a new road map for understanding developmental change in evolution and for designing new interventions in regenerative medicine settings.

Serine/Arginine-rich protein family of splicing regulators: New approaches to study splice isoform functions

Serine/arginine-rich (SR) proteins are conserved RNA-binding proteins that play major roles in RNA metabolism. They function as molecular adaptors, facilitate spliceosome assembly and modulate constitutive and alternative splicing of pre-mRNAs. Pre-mRNAs encoding SR proteins and many other proteins involved in stress responses are extensively alternatively spliced in response to diverse stresses. Hence, it is proposed that stress-induced changes in splice isoforms contribute to the adaptation of plants to stress responses. However, functions of most SR genes and their splice isoforms in stress responses are not known. Lack of easy and robust tools hindered the progress in this area. Emerging technologies such as CRISPR/Cas9 will facilitate studies of SR function by enabling the generation of single and multiple knock-out mutants of SR subfamily members. Moreover, CRISPR/Cas13 allows targeted manipulation of splice isoforms from SR and other genes in a constitutive or tissue-specific manner to evaluate functions of individual splice variants. Identification of the in vivo targets of SR proteins and their splice variants using the recently developed TRIBE (Targets of RNA-binding proteins Identified By Editing) and other methods will help unravel their mode of action and splicing regulatory elements under various conditions. These new approaches are expected to provide significant new insights into the roles of SRs and splice isoforms in plants adaptation to diverse stresses.