Putting Simple Science to Work on Complex Problems 

Clustered Regularly Interspaced Short Palindromic Repeats or CRISPR for short. Within DNA clusters there are sequences that are exactly that—regularly interspaced, palindromic in that they can be read the same way frontward and backward, and repeating. And between them are what scientists call spacers, which are identical to viruses that infect bacteria called bacteriophages. 

CRISPR serves as a defense mechanism for bacteria, shielding it from bacteriophages that want to attack it. Upon attack, the CRISPR system scans the genetic material of the virus, and when it finds it to be a foe, it targets the invader to render it harmless. Over time, bacteria update their viral defense to remember past threats and swiftly neutralize them. Scientists can take advantage of this by directing CRISPR to be used as “genetic scissors,” precisely editing DNA by either disabling a faulty gene or inserting new genetic material. 

How Was CRISPR Discovered?
CRISPR was first discovered in 2011, when Emmanuelle Charpentier discovered the tracrRNA while studying the bacteria Streptococcus pyogenes. Through her work, she demonstrated that tracrRNA is part of bacteria’s ancient immune system, CRISPR/Cas, that can disarm viruses by cleaving their DNA. She then initiated a collaboration with Jennifer Doudna, who had a lot of experience working with RNA. Their collaborative work pioneered the development of CRISPR, a simplified system for gene editing that is both precise and efficient. This has revolutionized the way we approach genetic research and therapy, and it offers new horizons in biomedical research and beyond. 

Upon recognizing in the 1970s that mutations in DNA contributed to disease, scientists have been working toward the development of gene editing. The discovery of restriction enzymes enabled scientists to “cut and paste” DNA for the first time, creating recombinant DNA, which are hybrid sequences that had never existed before. This laid the groundwork for gene therapy. And while gene therapy added new genes, it was random, with new sequences landing near silencing regulatory DNA or disrupting healthy genes. Scientists needed to find better tools to control the gene-editing process.  

By the early 2000s, scientists had synthesized artificial proteins, which included zinc finger nucleases, allowing for the precise targeting mutation in genomes. This was a much better approach than what the restriction enzymes were able to do, paving the way for CRISPR. 

How Are Scientists Putting CRISPR to Work? 
With an understanding of how CRISPR works, sequences can be designed relatively simply and put to work in laboratories. Because of its versatility and preciseness, scientists have found the technology useful in many different ways, including treating genetic diseases, creating genetically modified organisms, detecting pathogens, and even exploring gene therapies. The possibilities for use across human health, animal health, and agriculture are nearly endless.  

  • Agriculture – One of the earliest applications was in agriculture through the development of genetically modified crops. As climate change drives warmer temperatures, gene editing technology was used to help develop drought-resistant wheat and tomatoes that are blight resistant, both surviving conditions that previously would have killed them. They have also developed tomatoes and tobacco that are resistant to insect pests. This focus on modern agriculture can help reduce crop loss, improve yield and sustainability, and feed a hungry planet.  

  • Diagnostics – The first papers describing diagnostic applications with CRISPR were published in 2017, so many years after the gene therapy applications were first announced. Diagnostic applications utilize different Cas enzymes than for gene editing, mainly Cas12 and Cas13. And these have simpler requirements for assay design, which makes them more suitable for molecular approaches. Because these enzymes can detect both RNA and DNA, they can detect pathogens with both types of genomes. Because of its simple application, the technology was particularly useful during the COVID-19 pandemic, as it helped accelerate the development of accurate and rapid diagnostic tests, including point-of-need diagnostics that received the first emergency use authorization (EUA) approvals from the FDA. CRISPR helped put these diagnostics in the hands of consumers when they needed them most, while keeping people safe and taking pressure off the healthcare system. Read more about the consumer expectations, benefits, and the chemistry of “Point-of-Need Diagnostics.”
  • Disease Therapeutics – There are thousands of diseases caused by our genetics. Some of them are caused by just a single mutation such as sickle cell disease or cystic fibrosis. Others involve a genetic predisposition that may or may not prompt the disease. In other cases, environmental factors and other complexities can be involved. Cancer immunotherapy and other treatments for certain kinds of leukemia and lymphoma have also now been approved. Read more about their application in “Bacteriophages as a Diagnostic and Therapeutic.” 
  • Emerging Pathogens – SARS-CoV-2, mpox, and even HIV are all diseases that at one point had newly appeared in a population or rapidly increased in incidence or range. Emerging pathogens can also be driven by a disease vector, such as mosquitoes, which may increase their range due to climate change or by hitching a ride with a traveler. When they do, the range of the diseases they spread also increases, infecting new populations of people. This has contributed to the emergence of diseases such as dengue, Zika virus, and West Nile virus in additional parts of the world, including the U.S. 

Current methods such as quantitative or qualitative PCR called qPCR or reverse transcriptase, QCR RTPCR, or even isothermal methods such as RPA or LAMP, have limitations due to costs, the sample-to-answer time, and personnel and equipment requirements, which limit widespread deployment. Other methods can be more cost effective, but have trade-offs, like only being able to multiplex a few samples at a time, or there’s an upper limit to that readout, accessibility, sensitivity, specificity, and testing throughput. Because CRISPR-based diagnostic tools are very precise and sensitive, but do not need expensive laboratory equipment to operate, they can enhance conventional procedures in field-forward environments where emerging pathogens are often found. Read more about detection and diagnostics capabilities for use in remote environments in “Field-Forward Devices Democratize Diagnostics.”

In response to an emerging pathogen, the rapid design and deployment of accurate tests to those environments enable scientists to better understand the disease, assess the disease spread, determine who is at risk, and ultimately control the disease. Using CRISPR, technology developed by the MRIGlobal team as part of the Detect It with Gene Editing Technologies project enables a quick response from assay design through deployment and detection by directly detecting the pathogen genomic material through signal amplification to achieve the appropriate sensitivity. The project aims to deliver low-cost, mobile tech that uses CRISPR technology to identify thousands of different emerging pathogens — including infectious ones like SARS-C0V-2 — using DNA and RNA samples. 

Because the use of CRISPR is still in its infancy, there is still a great deal of potential for its use in the future. Today, researchers are investigating the modification of pig organs for transplant into humans, eradicating infectious diseases like HIV, and treating thousands of other diseases that are genetically acquired.


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