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CRISPR-Based Assessment of Gene Specialization in the Gibberellin Metabolic Pathway in Rice.
Gibberellin (GA) functions as an essential natural regulator of growth and development in plants. For each step of the GA metabolic pathway, different copy numbers can be found in different species, as is the case with the 13 genes across four enzymatic steps in rice (Oryza sativa). A common view is that such gene duplication creates homologs that buffer organisms against loss-of-function (LOF) mutations. Therefore, knockouts of any single homolog might be expected to have little effect. To test this question, we generated clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR associated protein 9 (Cas9) knockouts for these homologs and measured effects on growth and reproduction. Surprisingly, we report here that there is consistently one or more essential gene at each enzymatic step, for which LOF mutation induces death or sterility-suggesting that the GA pathway does not have a redundancy route and that each gene family is essential for GA metabolism. In most of these genes from the same gene family, we observed defects in plant height and infertility, suggesting that the duplicated members retain functions related to GA synthesis or degradation. We identified both subfunctionalization of the three recently diversified homologs OsKO1, OsKO2, and OsKO5 and neofunctionalization in OsKO3 and OsKO4 Thus, although the function of each step is conserved, the evolution of duplicates in that step is diversified. Interestingly, the CRISPR/Cas9 lines at the SD1 locus were typically sterile, whereas the natural sd1 mutants, related to the "Green Revolution" in rice, show normal setting rates. Collectively, our results identify candidates for control of GA production and provide insight into the evolution of four critical gene families in plants.
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Use of genome-editing tools to treat sickle cell disease.
Recent advances in genome-editing techniques have made it possible to modify any desired DNA sequence by employing programmable nucleases. These next-generation genome-modifying tools are the ideal candidates for therapeutic applications, especially for the treatment of genetic disorders like sickle cell disease (SCD). SCD is an inheritable monogenic disorder which is caused by a point mutation in the β-globin gene. Substantial success has been achieved in the development of supportive therapeutic strategies for SCD, but unfortunately there is still a lack of long-term universal cure. The only existing curative treatment is based on allogeneic stem cell transplantation from healthy donors; however, this treatment is applicable to a limited number of patients only. Hence, a universally applicable therapy is highly desirable. In this review, we will discuss the three programmable nucleases that are commonly used for genome-editing purposes: zinc finger nucleases (ZFNs), transcription activator-like effector nucleases (TALENs) and clustered regularly interspaced short palindromic repeats/CRISPR-associated protein 9 (CRISPR/Cas9). We will continue by exemplifying uses of these methods to correct the sickle cell mutation. Additionally, we will present induction of fetal globin expression as an alternative approach to cure sickle cell disease. We will conclude by comparing the three methods and explaining the concerns about their use in therapy.
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Gene editing in clinical isolates of Candida parapsilosis using CRISPR/Cas9.
Candida parapsilosis is one of the most common causes of candidiasis, particularly in the very young and the very old. Studies of gene function are limited by the lack of a sexual cycle, the diploid genome, and a paucity of molecular tools. We describe here the development of a plasmid-based CRISPR-Cas9 system for gene editing in C. parapsilosis. A major advantage of the system is that it can be used in any genetic background, which we showed by editing genes in 20 different isolates. Gene editing is carried out in a single transformation step. The CAS9 gene is expressed only when the plasmid is present, and it can be removed easily from transformed strains. There is theoretically no limit to the number of genes that can be edited in any strain. Gene editing is increased by homology-directed repair in the presence of a repair template. Editing by non-homologous end joining (NHEJ) also occurs in some genetic backgrounds. Finally, we used the system to introduce unique tags at edited sites.
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Focusing on Human Rights: a framework for CRISPR germline genome editing ethics and regulation.
The late 2018 announcement of the claimed births of CRISPR-edited babies has stimulated widespread condemnation and calls by some leading scientists for a moratorium on any further germline genome editing (GGE) for reproductive purposes. Concurrently, national and international bodies are calling for the development of robust guidelines and regulations that will identify permissible conditions under which such GGE efforts might eventually proceed. Crucially, these conditions go beyond rigorous safety standards to address some of the social and ethical concerns that arise with germline interventions. As these bodies convene to navigate this unique terrain, we suggest an important standard for generating ethically robust guidelines. Our approach builds from concerns about social exclusion and social justice with a focus on fundamental human rights. We believe that a deontological or rights-based approach, rather than a utilitarian approach, is needed to ensure that this socially disruptive technology minimizes further marginalization of people with disabilities and does not create a new form of social injustice. In pursuit of a deontological framework, we propose the implementation of an objective assessment tool: the Human Rights Impact Assessment (HRIA). Use of the HRIA establishes necessary constraints on applications of GGE in order to safeguard the most vulnerable members of society.
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Time to start intervening in the human germline? A utilitarian perspective.
Focusing on present-day possibilities raised by existing technology, I consider the normative aspects of genetically modifying the human germline from a utilitarian standpoint. With reference to a hypothetical case, I examine the probable consequences of permitting a well-conceived attempt to correct a disease-associated gene in the human germline using current CRISPR gene-editing technology. I consider inter alia the likely effects on utility of creating healthy new lives, of discouraging adoption, and of kickstarting a revolution in human germline genetic modification (HGGM). I reject various objections to HGGM, including claims that the risks of genetic harm outweigh the likely benefits. From this utilitarian analysis, I conclude that strong grounds exist to support intervening in the human germline using current technology. Delay in commencing such work will impose a utility cost, because the longer we wait until commencing the HGGM revolution and moving towards a world of increased utility, the greater will be the quantity of suffering accrued meantime through genetically influenced disease. Nevertheless, considering residual safety concerns and the negative publicity engendered by an ethically problematic recent (2018) first attempt at HGGM, it seems prudent-and ultimately generative of the greatest amount of utility-to delay implementing HGGM for a modest period of time, in the order of 1-2 years.
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Genetically Encoded Double-Stranded DNA-Based Nanostructure Folded by a Covalently Bivalent CRISPR/dCas System.
DNA nanotechnology has been widely employed in the construction of various functional nanostructures. However, most DNA nanostructures rely on hybridization between multiple single-stranded DNAs. Herein, we report a general strategy for the construction of a double-stranded DNA-ribonucleoprotein (RNP) hybrid nanostructure by folding double-stranded DNA with a covalently bivalent clustered regularly interspaced short palindromic repeats (CRISPR)/nuclease-dead CRISPR-associated protein (dCas) system. In our design, dCas9 and dCas12a can be efficiently fused together through a flexible and stimuli-responsive peptide linker. After activation by guide RNAs, the covalently bivalent dCas9-12a RNPs (staples) can precisely recognize their target sequences in the double-stranded DNA scaffold and pull them together to construct a series of double-stranded DNA-RNP hybrid nanostructures. The genetically encoded hybrid nanostructure can protect genetic information in the folded state, similar to the natural DNA-protein hybrids present in chromosomes, and elicit efficient stimuli-responsive gene transcription in the unfolded form. This rationally developed double-stranded DNA folding and unfolding strategy presents a new avenue for the development of DNA nanotechnology.
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Exome sequencing in the knockin mice generated using the CRISPR/Cas system.
Knockin (KI) mouse carrying a point mutation has been an invaluable tool for disease modeling and analysis. Genome editing technologies using the CRISPR/Cas system has emerged as an alternative way to create KI mice. However, if the mice carry nucleotide insertions and/or deletions (InDels) in other genes, which could have unintentionally occurred during the establishment of the KI mouse line and potentially have larger impact than a point mutation, it would confound phenotyping of the KI mice. In this study, we performed whole exome sequencing of multiple lines of F1 heterozygous Ntrk1 KI mice generated using the CRISPR/Cas system in comparison to that of a wild-type mouse used as a control. We found three InDels in four KI mice but not in a control mouse. In vitro digestion assay suggested that each InDel occurred as a de novo mutation, was carried-over from the parental mice, or was incorporated through the Cas9 nuclease mediated off-target cleavage. These results suggest that frequency of InDels found in KI mice generated by the CRISPR/Cas technology is not high, but cannot be neglected and careful assessment of these mutations is warranted.
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Who Goes First? Deaf People and CRISPR Germline Editing.
The development of CRISPR technology has catapulted the issue of germline editing to the forefront of a debate between the goals of medical advancement and promotion of human diversity. The US National Academy of Sciences and the National Academy of Medicine recommended in a joint report that germline editing should be tightly regulated and pursued only for "serious diseases." A follow-up statement from an international summit on human genome editing emphasized a more general point that "the risks [are] too great to permit clinical trials of germline editing at this time." Here we review their recommendations in the context of genetic deafness, a condition that historically has been viewed by the medical community as a pathology. Deafness does not meet the standard of "serious disease" for experiments with human germline editing, but there is a real concern that scientists may soon begin to do germline editing with deaf individuals because, as we will discuss, they are in many ways ideal subjects for a clinical study of CRISPR, though their condition is neither fatal nor debilitating. In light of this, we worry about the potential for medical overreach and expediency. Drawing from examples of living deaf communities around the world, we propose an expansive view of human diversity that recognizes the value of genetic, linguistic, and cultural diversity to the future health of humankind.
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A CRISPR-dCas Toolbox for Genetic Engineering and Synthetic Biology.
Programmable control of gene expression is essential to understanding gene function, engineering cellular behaviors, and developing therapeutics. Beyond the gene editing applications enabled by the nuclease CRISPR-Cas9 and CRISPR-Cas12a, the invention of the nuclease-dead Cas molecules (dCas9 and dCas12a) offers a platform for the precise control of genome function without gene editing. Diverse dCas tools have been developed, which constitute a comprehensive toolbox that allows for interrogation of gene function and modulation of the cellular behaviors. This review summarizes current applications of the dCas tools for transcription regulation, epigenetic engineering, genome imaging, genetic screens, and chromatin immunoprecipitation. We also highlight the advantages and existing challenges of the current dCas tools in genetic engineering and synthetic biology, and provide perspectives on future directions and applications.
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Use of CRISPR/Cas9 for the Modification of the Mouse Genome.
The use of CRISPR/Cas9 to modify the mouse genome has gained immense interest in the past few years since it allows the direct modification of embryos, bypassing the need of labor-intensive procedures for the manipulation of embryonic stem cells. By shortening the overall timelines and reducing the costs for the generation of new genetically modified mouse lines (Li et al., Nat Biotechnol 31: 681-683, 2013), this technology has rapidly become a major tool for in vivo drug discovery applications.
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