Last updated on June 4, 2020
CRISPR-Cas9 has made genetic engineering easier, faster, and cheaper than ever before. A scientist interested in manipulating a particular gene only needs to search the gene’s sequence for a suitable PAM. Once a PAM is found, the corresponding Cas9 can be ordered or harvested from its bacterial strain (and as I mentioned last week, even if a PAM isn’t found, it is possible to engineer a Cas9 to recognize a new PAM sequence). An appropriate sgRNA (the crRNA:tracrRNA fusion molecule) can be designed by identifying the target sequence 20 nucleotides upstream of the chosen PAM. These sgRNA’s can be engineered by the scientist directly or ordered via synthetic production.
Together, the sgRNA and the Cas9 protein can produce a highly specific double-strand break that can deactivate a gene. Or, if a template strand of DNA is also provided, the gene can be precisely modified or replaced. The simplicity of this technology is outmatched only by its scope. CRISPR-Cas9 could be used to control animal populations, modify and improve crops, prevent disease, or even cure cancer. And, in the not so distant future, it may even be possible to alter human genetics.
In 2017, researchers at Harvard used CRISPR-Cas9 to encode a GIF of a galloping horse into the DNA of a bacterial cell. After growing the bacterial culture for multiple generations, the researchers were able to retrieve the gif data by sequencing the bacteria’s genome. The retrieved GIF was a 90% accurate recreation of the original. While this may seem like a useless feat, it’s an interesting proof of concept for how CRISPR-Cas9 could be used to store data within DNA.
DNA is a remarkably stable and efficient data storage solution. A single gram of DNA can store roughly 215 petabytes of data (or 215 million gigabytes—equivalent to about 430,000 laptops). The DNA inside one of your cells, if stretched out, would measure about 2 meters (about 6’7”—probably much taller than you, unless you’re my cousin), but through a complex system of coiling and folding, it fits into a space only 6 microns across the inside of the nucleus of the cell. In the future, if researchers can perfect precise methods to write data to DNA and cost effective ways to retrieve that data through sequencing, then vast amounts of data could be stored long-term, packed inside DNA.
The DNA-encoded horse GIF is a good demonstration of the power and precision of CRISPR-Cas9 to make specific changes in the genetic code. In 2018, researchers at Imperial College London used CRISPR-Cas9 to eradicate malaria-carrying mosquitos through a gene drive. In the study, they modified 150 male mosquitos to carry a modified version of the sex-determining gene. The sex-determining gene in mosquitos contains the code for both male and female gene expression, but it is normally selectively cut up into either the male or female form. Only female mosquitos transmit malaria, so disrupting the formation of the female gene form could limit the spread of the disease.
In the experiment, the researchers used CRISPR-Cas9 to prevent proper formation of the female gene form. Mosquitos carrying this modified gene were by default either male or infertile. By releasing the modified mosquitos into a larger population of normal mosquitos, the researchers were able to observe how the modified gene spreads through the population. Eventually, after 7-11 generations, the modified gene reached 100% prevalence, leading to complete population collapse. In addition to this kind of gene driven extermination, it may be possible to modify mosquitos’ susceptibility to the malaria parasite through CRISPR-Cas9.
In addition to eliminating disease vectors, CRISPR-Cas9 may prove effective at creating targeted cancer treatments. Recently, researchers have been investigating a CRISPR-Cas9 cancer treatment that modifies a patient’s own immune cells to specifically target cancerous cells. In Chimeric Antigen Receptor T-cell therapy (CAR-T cell therapy), researchers harvest T-cells (the immune cells responsible for destroying infected cells in the body) from the patient and modify those T-cells with a gene that helps it recognize cancerous cells. With CRISPR, the researchers have also been able to knock out certain genes in the T-cells that prevent efficient targeting and destruction of cancer cells. CRISPR-Cas9 cancer treatments are still in the experimental phase of development, but the preliminary results are very promising.
As scientists shift their focus to Covid-19, some researchers have been looking for ways to utilize CRISPR-Cas to test for, treat, or prevent Covid-19 infection. In early May, a CRISPR-based Covid-19 assay by Sherlock Biosciences was given emergency approval by the FDA. The test utilizes a different CRISPR enzyme, Cas13, to enable detection. Cas13 targets and cuts up SARS-CoV-2 RNA, just like Cas9 would, but once Cas13 has been activated, it continues cutting other genetic material in the solution. The test utilizes special modified genetic material that turns fluorescent when cut. The presence of fluorescence in the sample is visible confirmation of the presence of SARS-CoV-2 RNA in the sample, which is required for Cas13 activation. These tests are especially useful because they are comparatively fast and don’t require specialized machinery.
A potential CRISPR-Cas based treatment for Covid-19 has also been identified, called PAC-MAN (which stands for Prophylactic Antiviral Crispr in huMAN cells—not the circular chomping video game character). PAC-MAN also uses a different CRISPR enzyme, Cas13d, which targets particular regions of the SARS-CoV-2 genome and cuts it up. While this method has shown success on inactivated SARS-CoV-2 and live H1N1, it is yet to be tested on live coronavirus. Scientists are also unsure how to get the PAC-MAN system into actual infected human cells, so a viable treatment using this method could be a years off at best.
Another possibility for this technology, which poses interesting scientific and ethical dilemmas, is whether we could edit ourselves to resist infection by coronaviruses. Human embryo CRISPR editing could allow us to modify the ACE2 receptors, which coronaviruses use to enter our cells. If approved, such a method could prevent future coronavirus outbreaks (important to note that, since this is genetic engineering at the embryo stage, no one alive today would be able to gain immunity in this way). Genetic engineering of human embryos is still a hotly contested ethical debate. It has the potential to improve quality and length of life by eliminating genetic disorders and preventing diseases. But it also has the potential to go horribly wrong, either through flaws in the technology itself or through its misuse by a society riddled with its own biases.
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