Expanding the CRISPR armamentarium to fight human disease
Rolf Turk, Ph.D., senior staff scientist at Integrated DNA Technologies guides readers through the future biomedical applications of CRISPR.
With clustered regularly interspaced short palindromic repeats (CRISPR) gene editing therapies entering Phase I clinical trials - some employing the high-fidelity Cas9 nuclease we devised at Integrated DNA Technologies (IDT) - it makes sense for us to look ahead and anticipate the needs of researchers developing new biomedical applications for CRISPR. Beyond the treatment of genetic diseases and genetic-related diseases, such as cancer, there are many other key applications of CRISPR being investigated. We will focus on three.
CRISPR-based kit enables simple and fast diagnosis at home
As we embark on the Fourth Industrial Revolution, computing is transforming virtually every facet of our lives, from the way we live and work, to how we communicate and relate to each other. A key characteristic of this revolution is the fusion of technologies that is blurring the lines between the physical, digital, and biological spheres.
For example, Mammoth Biosciences is developing a direct-to-consumer molecular diagnostics kit, based on a CRISPR platform. A credit card-sized panel is made up of CRISPR proteins that have been designed to detect a variety of DNA- or RNA-based targets. When a biological sample – like blood, saliva, or urine – is added to the panel, any targets in the sample will be detected. These targets serve as biomarkers of disease (such as cancer) and pathogens (such as bacteria or viruses). When a target is present, the CRISPR protein recognises it and activates to cleave a reporter gene and trigger a colour change in the panel. These changes are then captured by taking a photograph with a smartphone and sending it to Mammoth Biosciences using their companion application (app). A diagnostic result is returned by the app within 30 minutes. This point-of-care diagnostic tool is able to detect multiple diseases on a single panel.
Gene edited viruses to combat antibiotic-resistant pathogens
Bacteriophages (phages) are viruses that attack bacteria, invading their cells, and multiplying to such numbers that they burst and kill the cell. Last year, a 15-year-old teenager was successfully treated with a cocktail of genetically engineered phages designed, using Bacteriophage Recombineering of Electroporated DNA (BRED), to destroy the specific strain of multidrug-resistant Mycobacterium abscessus the patient was infected with. This precision medicine was so specific though that it would only work for this particular infection and not for infections with other strains, as there is substantial variation in M. abscessus phage susceptibilities1.
However, a new breed of phage therapies is being developed, using CRISPR technology to weaponise the phages, and machine learning to design precision CRISPR-engineered phage constructs to create optimal phage cocktails against any pathogen on demand. Locus Biosciences have developed a CRISPR-phage platform to engineer phages that contain CRISPR nucleases, which precisely targets bacterial DNA and shreds through them, causing cell death. These precision antibacterial products are aimed at treating drug-resistant bacterial diseases, and microbiome-related conditions, by selectively removing harmful bacteria while leaving healthy bacteria intact. Clinical development programs are underway and clinical trials are expected to begin soon to evaluate CRISPR-phage therapies to treat urinary tract, gastrointestinal and respiratory infections, inflammatory bowel disease, cancer, microbiome dysbiosis, and central nervous system disorders.
Eradicating disease vectors using gene drives
Another radically different application of CRISPR to tackle disease is in the development of a designer molecular approach called a gene drive. Researchers from Imperial College London, UK, have demonstrated that this innovative form of heritable CRISPR-driven genetic engineering is able to drive the spread or propagation of a specific gene throughout a population of malaria-vector mosquitoes in captivity. Their proof-of-principle experiments involved using CRISPR/Cas9 technology to disrupt the Anopheles gambaiae mosquito gene, doublesex, that encodes two alternatively spliced transcripts to control the differentiation of the two sexes. The disruption targeted a section of the doublesex gene, at the intron 4–exon 5 boundary, which blocked the formation of the splice variant conferring female sex, resulting in an intersex phenotype that was completely sterile. This disruption did not affect the transcript conferring male sex, and thus male development and fertility were unaffected.
By implementing this CRISPR-based gene editing, the researchers were able to ensure that all offspring were male. As this CRISPR-engineered mutation spread throughout the population, generation after generation, fewer and fewer females were hatched. This resulted in the progressive reduction of egg production. With the CRISPR construct rising to 100% prevalence in the caged mosquito populations, the point of total population collapse was reached. This was achieved within 7–11 generations. The mosquito species used in the experiments, Anopheles gambiae, is one that transmits malaria. The application of gene drives could prove a solution to eradicate disease vectors. However, the decision to intentionally make a species extinct is not one that should be taken without forethought. As with all applications of powerful technologies, such as CRISPR, these decisions should be made with due consideration of potential outcomes, broader long-term effects, and ethical and social implications.
Improving the CRISPR toolkit for battling disease
Since the discovery of CRISPR technologies and their application in gene editing, many researchers and manufacturers have moved to improve the CRISPR toolkit. Although Cas9 is the most commonly used CRISPR nuclease, other nucleases are being discovered and applications developed for them. These other enzymes can work in complement with Cas9 or can be used to serve radically different functions. For example, Mammoth Biosciences are looking to possibly include Cas12a, Cas13a, and Cas14 in their CRISPR diagnostic platform. The use of multiple Cas nucleases means that a larger range of sequences can be recognized, thus allowing the panel to provide diagnostic information on a broader range of diseases, conditions, and pathogens. A different example is that of Locus Biosciences, who use a CRISPR/Cas3 system for their CRISPR-phage platform. Cas3 is the most abundant Cas nuclease in the natural world, unlike Cas9, which is relatively rare.2,3 Also, unlike the precise scissoring function of Cas9 for gene editing, Cas3 works to precisely recognise specific genetic sequences and subsequently degrades the DNA, leading to deletions of up to 100 kilobases.
Here at IDT, we have rationally engineered two new Cas nucleases, which are proving extremely useful as part of the CRISPR armamentarium in life sciences. By devising an unbiased bacterial screen, we were able to isolate a high-fidelity Cas9 that has greater targeting specificity than the wild-type Cas9, while retaining comparable nuclease efficiency. In fact, our HiFi-Cas9 is the most active and specific high-fidelity Cas9 enzyme available, delivered either in a plasmid, or especially as an RNP complex that provides additional targeting specificity.4 We used a similar screen to also isolate a Cas12a mutant, which is not only highly specific in its targeting but also has nuclease activity that is comparable with that of wild-type Cas9. Our Cas12a Ultra is also active at a broader range of temperatures, enabling it to function well in endothermic and ectothermic species, as well as plants.
While CRISPR gene editing is intended to make permanent modifications to DNA at a single, specific location, sometimes DNA cleavage and editing occur at additional sites in the genome that have similar DNA sequence from the intended site. Such events are called “off-target effects” (OTEs). OTEs mostly occur in areas of the genome with no known function, however there is always a risk that some OTEs might have unwanted adverse consequences. To best ensure that researchers have the information required to decide and act responsibly, we also provide tools that allow them to monitor and better understand OTEs. One such tool we have recently developed is our rhAmpSeq platform, which is designed to enable monitoring of all specified OTEs in one multiplex reaction. The multiplex reaction cuts down on the unnecessary repetition of singleplex reactions, which can be more error prone, as well as more time- and resource-consuming.
Moreover, to equip researchers with cutting-edge tools for CRISPR, IDT has invested in bioinformatics solutions, such the CRISPR-Cas9 guide RNA design selector, generator and checker, and an upcoming tool to support homology-directed repair (HDR) experiments. At IDT, we continue to deliver leading edge technology, for researchers and clinicians to responsibly navigate their own journeys in biomedical innovation.