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A new era of gene editing for the treatment of human diseases.
The treatment of human diseases using gene-editing technology has been envisioned for several decades with the realisation that so many were associated with mutations in DNA. The Human Genome Project opened new doors for identifying the genetic bases for human suffering. Research on gene editing has been active since the 1970s, but the technology has seen substantial growth and application just within the past decade. Simply stated, CRISPR technology has become a phenomenon in both biomedical and therapeutics research. Concurrently, cell therapies and pluripotent stem cell research have also been refined and now interfaced with CRISPR technology to enhance and maximise their potential in modelling as well as treatment of human diseases. In this review, we discuss the novel and revolutionary modality of gene editing, as this marks a new era in research and medicine. We also discuss gene-modifying technologies leading to CRISPR, as they are still being used for a wide variety of genomic applications. The modes and challenges for delivery of gene editing components are also discussed. Lastly, we review examples of human diseases that are not only amenable to gene editing techniques, but also show true promise of cure in the early 21st century of genetic correction and gene repair.
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CRISPR-Cas Systems: A Functional Perspective and Innovations.
Adaptation is a fundamental tenet of evolutionary biology and is essential for the survival of all organisms, including prokaryotes. The evolution of clustered regularity exemplifies this principle of interspaced short palindromic repeats (CRISPR) and associated proteins (Cas), an adaptive immune system that confers resistance to viral infections. By integrating short segments of viral genomes into their own, bacteria and archaea develop a molecular memory that enables them to mount a rapid and targeted response upon subsequent viral challenges. The fortuitous discovery of this immune mechanism prompted many studies and introduced researchers to novel tools that could potentially be developed from CRISPR-Cas and become clinically relevant as biotechnology rapidly advances in this area. Thus, a deeper understanding of the underpinnings of CRISPR-Cas and its possible therapeutic applications is required. This review analyses the mechanism of action of the CRISPR-Cas systems in detail and summarises the advances in developing biotechnological tools based on CRISPR, opening the field for further research.
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Universal crRNA Acylation Strategy for Robust Photo-Initiated One-Pot CRISPR-Cas12a Nucleic Acid Diagnostics.
Spatiotemporal regulation of clustered regularly interspaced short palindromic repeats (CRISPR) system is attractive for precise gene editing and accurate molecular diagnosis. Although many efforts have been made, versatile and efficient strategies to control CRISPR system are still desirable. Here, we proposed a universal and accessible acylation strategy to regulate the CRISPR-Cas12a system by efficient acylation of 2'-hydroxyls (2'-OH) on crRNA strand with photolabile agents (PLGs). The introduction of PLGs confers efficient suppression of crRNA function and rapid restoration of CRISPR-Cas12a reaction upon short light exposure regardless of crRNA sequences. Based on this strategy, we constructed a universal PhotO-Initiated CRISPR-Cas12a system for Robust One-pot Testing (POIROT) platform integrated with recombinase polymerase amplification (RPA), which showed two orders of magnitude more sensitive than the conventional one-step assay and comparable to the two-step assay. For clinical sample testing, POIROT achieved high-efficiency detection performance comparable to the gold-standard quantitative PCR (qPCR) in sensitivity and specificity, but faster than the qPCR method. Overall, we believe the proposed strategy will promote the development of many other universal photo-controlled CRISPR technologies for one-pot assay, and even expand applications in the fields of controllable CRISPR-based genomic editing, disease therapy, and cell imaging.
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A One-Pot CRISPR/Cas9-Typing PCR for DNA Detection and Genotyping.
Clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated endonuclease Cas9 (Cas9) has high specificity to its target DNA as a gene editing tool. This characteristic makes it useful for DNA detection. Combining the advantages of CRISPR/Cas9 and PCR, this study establishes a novel CRISPR/Cas9-based DNA detection method, named CRISPR/Cas9-typing PCR version 4.0 (ctPCR4.0). This method can detect target DNA in one pot with high specificity and sensitivity. In a homogenous reaction, the target DNA is first cleaved by a pair of Cas9- single-guide RNA complexes and thus releases two single strands with free 3' ends, allowing a pair of oligonucleotides to anneal with the strands. The annealed oligonucleotides provide templates for DNA polymerization from the free 3' ends. A universal primer annealing site is thus produced at the end of two single strands. The target DNA is then amplified by PCR using a universal primer. This method was first verified by accurately detecting the cloned L1 fragments of 10 genotypes of high-risk human papilloma viruses (HPVs). This method was then validated by detecting the L1 fragments of two highest-risk HPVs, HPV 16 and HPV 18, in the genomic DNA of two HPV-positive cervical carcinoma cells, HeLa and SiHa. Finally, this method was further validated by accurately detecting 10 high-risk HPVs in 30 clinical samples.
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Gene Editing Expands the Donor Pool for CCR5-Negative Stem Cell Transplants.
Cell therapy efforts for treating HIV+ patients are challenged by limited availability of donors with naturally occurring CCR5 mutations conferring resistance. Xu et al. (2019) report a CRISPR-based method for disrupting CCR5 in hematopoietic stem cells prior to transplant, providing a proof of concept for expanding the pool of potential donors.
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[Preface for genome editing special issue].
Genome editing technology, as an innovative biotechnology, has been widely used for editing the genome from model organisms, animals, plants and microbes. CRISPR/Cas9-based genome editing technology shows its great value and potential in the dissection of functional genomics, improved breeding and genetic disease treatment. In the present special issue, the principle and application of genome editing techniques has been summarized. The advantages and disadvantages of the current genome editing technology and future prospects would also be highlighted.
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Somatic Genome Editing Goes Viral.
Generating new mouse models of cancer is a challenging and laborious task that can require years of investment to interrogate a single gene. Now, Jonkers and colleagues describe the first application of CRISPR-based genome editing in the mammary gland, providing a new approach to dissect complex genetic interactions in vivo.
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Crossing the line.
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Optimized CRISPR guide RNA design for two high-fidelity Cas9 variants by deep learning.
Highly specific Cas9 nucleases derived from SpCas9 are valuable tools for genome editing, but their wide applications are hampered by a lack of knowledge governing guide RNA (gRNA) activity. Here, we perform a genome-scale screen to measure gRNA activity for two highly specific SpCas9 variants (eSpCas9(1.1) and SpCas9-HF1) and wild-type SpCas9 (WT-SpCas9) in human cells, and obtain indel rates of over 50,000 gRNAs for each nuclease, covering ~20,000 genes. We evaluate the contribution of 1,031 features to gRNA activity and develope models for activity prediction. Our data reveals that a combination of RNN with important biological features outperforms other models for activity prediction. We further demonstrate that our model outperforms other popular gRNA design tools. Finally, we develop an online design tool DeepHF for the three Cas9 nucleases. The database, as well as the designer tool, is freely accessible via a web server, http://www.DeepHF.com/ .
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Commentary: Divine decree or a novel panacea in Clustered Regularly Interspaced Short Palindromic Repeats Associated 9-steered cellular reprogramming in the fate of failing heart.
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