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Multiplexed CRISPR technologies for gene editing and transcriptional regulation.
Multiplexed CRISPR technologies, in which numerous gRNAs or Cas enzymes are expressed at once, have facilitated powerful biological engineering applications, vastly enhancing the scope and efficiencies of genetic editing and transcriptional regulation. In this review, we discuss multiplexed CRISPR technologies and describe methods for the assembly, expression and processing of synthetic guide RNA arrays in vivo. Applications that benefit from multiplexed CRISPR technologies, including cellular recorders, genetic circuits, biosensors, combinatorial genetic perturbations, large-scale genome engineering and the rewiring of metabolic pathways, are highlighted. We also offer a glimpse of emerging challenges and emphasize experimental considerations for future studies.
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Nanoparticles-mediated intratumoral gene editing targeting PD-L1 and Galectin-9 for improved cancer immunotherapy.
PD-L1, a typical immune checkpoint expressed on tumor cells, reduces the effectiveness of T cell-mediated killing, which is further aggravated by Galectin-9 (Gal-9) co-expression through the TIM3/Gal-9 pathway. Although immune checkpoint inhibitors have shown promise in cancer therapy, limitations remain including low response rate, systemic toxicities, and the need of frequent treatments. Here, we described a dual knockout approach targeting PD-L1 and Gal-9 in tumor cells, achieved by nanoparticle-assisted CRISPR-Cas9 delivery, aimed at improved cancer immunotherapy. A calcium phosphate nanoparticle (CaP NP) was engineered for co-delivery of CRISPR-Cas9/sgRNA ribonucleoprotein (RNP) and initiation of anti-tumor immunity. Intratumoral administration of RNP-loaded CaP NPs effectively knocked out PD-L1 and Gal-9 in tumor cells, evoking robust anti-tumor immunity. Additionally, Ca2+ overload due to the degradation of CaP NPs led to release of damage-associated molecular patterns (DAMPs) signals, further enhancing T-cell-mediated antitumor immune responses. Our results demonstrated that this treatment effectively evoked both local and systemic anti-tumor immune responses, significantly inhibiting the growth of primary and distant tumors in mouse models. Importantly, local treatment also altered the phenotypes of circulating tumor cells, as a substantial of circulating tumor cells originated from RNP-CaP-treated primary tumors and exhibited dual knockouts, which led to reduced lung metastasis.
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Profiling Genome-Wide Specificity of CRISPR-Cas9 Using Digenome-Seq.
Digenome-seq is a highly sensitive method for analyzing the genome-wide specificity of CRISPR-Cas9 nuclease activity. In this procedure, genomic DNA is first subjected to digestion by CRISPR-Cas9 in vitro and then to whole genome sequencing, which results in unusual patterns of straight alignments at on-target and potential off-target sites. Analysis of these data with the Digenome-seq computer program allows for identification of the in vitro cleavage sites associated with the straight alignments. Here, we present a detailed Digenome-seq protocol for genome-wide profiling of in vitro CRISPR-Cas9 nuclease cleavage sites.
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Engineering Delivery Vehicles for Genome Editing.
The field of genome engineering has created new possibilities for gene therapy, including improved animal models of disease, engineered cell therapies, and in vivo gene repair. The most significant challenge for the clinical translation of genome engineering is the development of safe and effective delivery vehicles. A large body of work has applied genome engineering to genetic modification in vitro, and clinical trials have begun using cells modified by genome editing. Now, promising preclinical work is beginning to apply these tools in vivo. This article summarizes the development of genome engineering platforms, including meganucleases, zinc finger nucleases, TALENs, and CRISPR/Cas9, and their flexibility for precise genetic modifications. The prospects for the development of safe and effective viral and nonviral delivery vehicles for genome editing are reviewed, and promising advances in particular therapeutic applications are discussed.
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CRISPR/Cas9 Genome Engineering in Human Pluripotent Stem Cells for Modeling of Neurological Disorders.
Recent advances in genome editing have brought new hopes for personalized and precision medicine but have also dramatically facilitated disease modeling studies. Combined with reprogramming approaches, stem cells and differentiation toward neural lineages, genome engineering holds great potential for regenerative approaches and to model neurological disorders. The use of patient-specific induced pluripotent stem cells combined with neural differentiation allows studying the effect of specific mutations in different brain cells. New genome editing tools such as CRISPR/Cas9 represent a step further by facilitating the introduction or correction of specific mutations within the same cell line, thus eliminating variability due to differences in the genetic background. Here, we present a step-by-step protocol from design to generation of human pluripotent stem cell lines with specific mutations introduced or corrected with CRISPR/Cas9 gene editing that can be used in combination with transcription factor-based protocols to dissect underlying mechanisms of neurological disorders.
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CRISPR-Cas9 Methods and Key Considerations in the Production of Aedes aegypti Mutant Strains.
Since the characterization of the CRISPR-Cas9 system in prokaryotes, it has become the prime choice in gene editing because of its exceptional flexibility, ease of use, high efficiency, and superior specificity. As a result, CRISPR-Cas9-mediated gene-editing technologies have enabled researchers not only to engineer transgenic animal strains with site-directed insertions more efficiently but also to generate desired mutants for previously intractable species. One such species is the invasive yellow fever mosquito, Aedes aegypti, which is notorious for its ability to transmit many blood-borne human pathogens. Methods for developing new transgenic strains of the yellow fever mosquito may aid in the effort to control its populations and provide significant benefits for the public. Here, we provide an overview of injection and noninjection methods for generating transgenic mosquitoes and also highlight important experimental design features.
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CRISPR-mediated Genome Editing of the Human Fungal Pathogen Candida albicans.
This method describes the efficient CRISPR mediated genome editing of the diploid human fungal pathogen Candida albicans. CRISPR-mediated genome editing in C. albicans requires Cas9, guide RNA, and repair template. A plasmid expressing a yeast codon optimized Cas9 (CaCas9) has been generated. Guide sequences directly upstream from a PAM site (NGG) are cloned into the Cas9 expression vector. A repair template is then made by primer extension in vitro. Cotransformation of the repair template and vector into C. albicans leads to genome editing. Depending on the repair template used, the investigator can introduce nucleotide changes, insertions, or deletions. As C. albicans is a diploid, mutations are made in both alleles of a gene, provided that the A and B alleles do not harbor SNPs that interfere with guide targeting or repair template incorporation. Multimember gene families can be edited in parallel if suitable conserved sequences exist in all family members. The C. albicans CRISPR system described is flanked by FRT sites and encodes flippase. Upon induction of flippase, the antibiotic marker (CaCas9) and guide RNA are removed from the genome. This allows the investigator to perform subsequent edits to the genome. C. albicans CRISPR is a powerful fungal genetic engineering tool, and minor alterations to the described protocols permit the modification of other fungal species including C. glabrata, N. castellii, and S. cerevisiae.
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CRISPR/Cas9-based application for cancer therapy: Challenges and solutions for non-viral delivery.
CRISPR/Cas9 genome editing is a promising therapeutic technique, which makes precise and rapid gene editing technology possible on account of its high sensitivity and efficiency. CRISPR/Cas9 system has been proved to able to effectively disrupt and modify genes, which shows great potential for cancer treatment. Current researches proves that virus vectors are capable of effectively delivering the CRISPR/Cas9 system, but immunogenicity and carcinogenicity caused by virus transmission still trigger serious consequences. Therefore, the greatest challenge of CRISPR/Cas9 for cancer therapy lies on how to deliver it to the target tumor site safely and effectively. Non-viral delivery systems with specific targeting, high loading capacity, and low immune toxicity are more suitable than viral vectors, which limited by uncontrollable side effects. Their medical advances and applications have been widely concerned. Herein, we present the molecule mechanism and different construction strategies of CRISPR/Cas9 system for editing genes at the beginning of this research. Subsequently, several common CRISPR/Cas9 non-viral deliveries for cancer treatment are introduced. Lastly, based on the main factors limiting the delivery efficiency of non-viral vectors proposed in the existing researches and literature, we summarize and discuss the main methods to solve these limitations in the existing tumor treatment system, aiming to introduce further optimization and innovation of the CRISPR/Cas9 non-viral delivery system suitable for cancer treatment.
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Genome Editing and Cardiac Regeneration.
Although the field of cardiac regeneration is relatively young, it is progressing rapidly with technological advancements. Genome editing tools are allowing researchers to creatively influence signaling pathways to be able to shed light on them and are important for addressing certain issues and limitations associated with in vitro and in vivo aspects of cardiac regeneration, such as imaging and immune rejection. In this chapter, the pathways involved in cardiac regeneration will be highlighted, and the role of gene-editing tools in endogenous and exogenous approaches to regenerate injured myocardium is discussed.
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Pursuit of chlorovirus genetic transformation and CRISPR/Cas9-mediated gene editing.
Genetic and molecular modifications of the large dsDNA chloroviruses, with genomes of 290 to 370 kb, would expedite studies to elucidate the functions of both identified and unidentified virus-encoded proteins. These plaque-forming viruses replicate in certain unicellular, eukaryotic chlorella-like green algae. However, to date, only a few of these algal species and virtually none of their viruses have been genetically manipulated due to lack of practical methods for genetic transformation and genome editing. Attempts at using Agrobacterium-mediated transfection of chlorovirus host Chlorella variabilis NC64A with a specially-designed binary vector resulted in successful transgenic cell selection based on expression of a hygromycin-resistance gene, initial expression of a green fluorescence gene and demonstration of integration of Agrobacterium T-DNA. However, expression of the integrated genes was soon lost. To develop gene editing tools for modifying specific chlorovirus CA-4B genes using preassembled Cas9 protein-sgRNA ribonucleoproteins (RNPs), we tested multiple methods for delivery of Cas9/sgRNA RNP complexes into infected cells including cell wall-degrading enzymes, electroporation, silicon carbide (SiC) whiskers, and cell-penetrating peptides (CPPs). In one experiment two independent virus mutants were isolated from macerozyme-treated NC64A cells incubated with Cas9/sgRNA RNPs targeting virus CA-4B-encoded gene 034r, which encodes a glycosyltransferase. Analysis of DNA sequences from the two mutant viruses showed highly targeted nucleotide sequence modifications in the 034r gene of each virus that were fully consistent with Cas9/RNP-directed gene editing. However, in ten subsequent experiments, we were unable to duplicate these results and therefore unable to achieve a reliable system to genetically edit chloroviruses. Nonetheless, these observations provide strong initial suggestions that Cas9/RNPs may function to promote editing of the chlorovirus genome, and that further experimentation is warranted and worthwhile.
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