Prime Editing — A Saving Tool
I remember sitting in the movie theatre bawling my eyes out watching Five Feet Apart. Who knew that people around the world weren’t able to properly interact with someone who had gone through or is going through the same thing as them, who could understand their pain, thoughts and feelings the most. They say a picture is worth a thousand words: Will Newman’s drawings were worth a thousand lives.
The 2019 film Five Feet Apart gave lots of exposure to a genetic disorder called cystic fibrosis. According to the CF Foundation, “genetic diseases like cystic fibrosis, are caused by mutations in a single gene. A gene contains DNA ‘letters’ that spell out the instructions to make a specific protein. When the protein isn’t made correctly, it can lead to a cascade of problems.” Cystic fibrosis is not the only kind of genetic disorder; there are over 6000 genetic disorders that affect millions of people each day. There are no cures for genetic disorders, instead there are treatments in place to manage the signs and symptoms. For cystic fibrosis, the main courses of treatment include antibiotics to prevent and treat chest infections and medicines to make the mucus in the lungs thinner; easier to cough up and open up airways. Even with a lung transplant patients are not guaranteed to live long. As seen, these treatments only ease the symptoms and don’t treat the root of the cause, the error in the DNA. This is where gene editing comes in.
Before we start, here’s a few things to know:
- Genome editing (also called gene editing) is a type of technology that allows scientists to artificially induce and specify a mutation.
- DNA has two strands and is shaped like a twisted ladder or a double helix.
- Each strand has a nitrogen base identified by letters (A, T, C, and G). These letters form complementary base-pairs: A can only bond with T and C can only bond with G.
- RNA (Ribonucleic Acid) is able to copy a DNA’s code and bond with an “unzipped” strand of DNA. It creates a sequence of complementary base pairs using the knowledge from the copied DNA.
Intro to Gene Editing and CRISPR
About seven years ago, the CRISPR gene editing tool changed the way scientists approached gene editing. CRISPR-Cas9 is a gene editing tool that allows you to edit a specific segment of DNA. CRISPR-Cas9 is made up of two main components: the guide RNA and the Cas9 protein.
The Guide RNA (gRNA) is a special type of RNA that can locate any part of the DNA. It can be programmed to find a particular DNA sequence segment (also known as the target DNA) in any cell.
The Cas9 protein is an endonuclease (think of it as genetic scissors) that cuts the targeted DNA with the help of the gRNA. CRISPR was able to target a section of DNA and cut it out, leaving the body to repair itself by trying to bond random base-pairs together, like skin repairing itself after you’ve scraped a knee. To minimize errors, scientists capitalized on making DNA primers that acted as a starting point for DNA synthesis.
As much as CRISPR was able to provide solutions to a wide range of health problems, it was not foolproof and had certain limitations. One of its biggest downfalls was off-target editing. Imagine landing a plane. Planes don’t land on the exact same spot on the runway every time. Same goes for CRISPR. There are cases in which CRISPR accidentally cuts a perfectly normal segment of DNA which could result in errors in the repairing process. Luckily prime editing solves the problem.
What is it Prime Editing?
Through a joint collaboration between Harvard and MIT scientists, we are now introduced to an all-in-one genome-editing system that can correct specific nucleotides with greater precision and efficiency. Prime editing is a variant of CRISPR, a true search and replace tool. Remember writing an essay on Word where you misspelled a word that you have already written over 50 times? Luckily you just hit Ctrl+H, searched for the word and replaced all of them. Prime editors are like that. Its technology is utilized by scientists to re-edit genetic codes to change mutations and eliminate sequence errors (such as mutations causing sickle cell anemia).
How Does it Work?
As a variant of CRISPR, prime editing uses the CRISPR-Cas9 method with a few tweaks. Prime editing uses a modified version of Cas9. In the original version, Cas9 was used as scissors to cut two strands of DNA. The modified version is now able to cut one strand of DNA. Instead of fully cutting it off, a flap is created on the strand of DNA keeping the others intact.
In addition, a new component is added; the reverse transcription enzyme. The reverse transcription enzyme reads the RNA and finds a complementary base pair. It is like a base editor which was capable of directly writing a DNA letter. The reverse transcription enzyme writes a new stream of DNA code and replaces the initial flapped area. The work is only half done. For the cells to be stable the strands of DNA need to be complementary base pairs (so C with G and T with A).
In a TED TALK, David R Lui — one of the scientists who created prime editors — goes over an excellent walkthrough explaining how CRISPR works, which is similar to what prime editors do. I highly recommend it.
Can we cure genetic diseases by rewriting DNA?
So, DNA can only bond with its complementary base pairs. Though the correct edits have been made on one side of the DNA strand it still doesn’t match the other side. To solve this issue another gRNA and Cas9 protein is sent out to find the mismatched section and cut it off. As a result we are left with the edited strand of DNA. The cell then repairs itself using the edited strand as a guide and creating its complementary base pair, leaving no room for unprecedented edits or mutations.
Why is it important?
Genetic disorders affect many more people than what is perceived. Just like at times we can’t tell when one is suffering from cancer or diabetes we can’t tell at times when one suffers from a genetic disorder. To put it into perspective, a study in 2017 published in the Annals of Internal Medicine says that about 20 percent of people in the world suffer from a genetic disorder. Many of those genetic disorders were inherited through parents who have a genetic abnormality. Due to this fact alone, we can see the percentage rising and rising if we don’t find cures for genetic disorders. Imagine the percentage today!
At the moment the only way to cure most genetic disorders is by reprogramming the mutated DNA. That is why prime editing is so important. It is not only saving lives but preventing the disorder to continue on down the line.
How are Prime Editors different from CRISPR? What is all the Hype About?
- Unlike CRISPR, prime editors don’t cut both DNA strands as a whole. By cutting both DNA strands the cell’s repair system is immediately triggered which is prone to errors. So prime editors give scientists more control over the type of edit they want.
- Prime editors are very multi-purpose. Previously, genome scientists believed that separate CRISPR tools would be required for each specific type of edit: delete a gene, insert new DNA code, or DNA letter substitutions. In contrast, prime editors can achieve all three functions without additional modification.
- Prime editing can swap any of the DNA letters into any other. Base editors were specific to swapping one letter to another. Now prime editors can target enormous amounts of inherited diseases. For example, sickle cell disease — which causes oxygen-carrying blood cells to deform into sharp sickle-like shapes — requires changing a T into an A at a precise spot.
- Prime editing can remove an exact number of letters from a given spot on the genome, at least up to 80. This allows scientists to precisely dictate the DNA sequences they want out, rather than relying on chance. Prime editing improves the chances that researchers will end up with only the edits they want, instead of a mix of changes that they can’t predict.
- Prime editing has already been optimized for commercial use on important crops like rice and wheat. In an article in Nature Biotechnology, David R Lui et al., adapted prime editors for use in plants. So far, it has resulted in point mutations, insertions and deletions in rice and wheat protoplasts. This demonstrates the versatility and potential that prime editing has in other fields, not just genomics.
What Might the Future Hold for Prime Editing?
Prime editing expands the scope and capabilities of genome editing, puting the cure for genetic diseases on the playing field. While its initial research has generated a lot of excitement, it is still too early to move it into clinics. Prime editing has only been tested in a small number of genetic diseases. It typically takes years to perform the necessary experiments on cells and animals before consideration of a potential trial of human therapy using prime editing, or any other genome editing technology.
For now, the development of prime editing highlights meaningful progress in the gene editing field. Future research will shed more light on the hope of bringing gene-based therapies into the clinic. There’s about 70,000 gene mutations that can cause diseases for people. David R. Liu and Andrew V. Anzalone estimated that 89 percent of known diseases linked to genetic mutations could theoretically be corrected using prime editing.
Although I have addressed lots of great things about prime editing, there are concerns about problems that may occur in the future. Ethics has and continues to play a role in new and experimental technologies.
Safety
According to Liu et al., “Since the era of human genome editing is in its fragile beginnings, it’s important that we do everything we can to minimize the risk of any adverse effects when we start to introduce these into people.” They add, “Minimizing this kind of elusive off-target editing is an important step toward achieving that goal.” As seen, safety is a top concern, and though with prime editing a fraction of off-target changes has decreased we are not able to determine or know if there will be any long term effects without human trials.
Equity and Rights
As with new emerging technology, there is always the stigma and concern that the only people who can afford it are those who are rich. How will people deal with those who are different because of the use and advancements of gene therapy? In addition, many people have moral and religious objections to the use of human embryos for research. Are we allowed to modify an embryo as it can affect future generations? How does consent come into play? These are a few complications that prime editing might face in the future.
Nevertheless, prime editing will be something that will revolutionize the world and impact many lives. And hopefully, as more research and trials are done, we can slowly transition to a world with no cystic fibrosis, sickle cell diseases or other genetic diseases.
Key Takeaways:
- Prime editing is an upgraded version of CRISPR. Known as the “search-and-replace” genome editing tool, it targets a certain spot in one strand of DNA, deletes and replaces it.
- Prime editing can be the potential tool to cure about 90 percent of genetic diseases that affect millions of people in the world.
- Though CRISPR-Cas9 and prime editing are similar in some ways, prime editing offers more opportunities and less harmful effects than CRISPR.
- The future for prime editing is bright. Though there are many issues surrounding ethics with this topic, these are problems to be tackled in the upcoming years.
When in doubt on the topic of gene editing, remember this explanation by David R. Lui: “If CRISPR is like scissors, base editors are like a pencil. Then you can think of prime editors like a word processor, capable of precise search and replace.”
