CRISPR vs. Prime Editing: Which is the Superior Gene Editing Tool?🧬

The Rivalary 🤜💥🤛

Gene editing is the future of all medicine, allowing us to change our bodies to our will. For years, CRISPR has always been the number one choice for gene editing and the most well-known method. But CRISPR has a new competitor for the top spot in gene editing: Prime editing. Although fairly new, Prime editing has characteristics that rival CRISPR. this begs the question- which gene editing tool is the superior one?

How does CRISPR work?

To understand which gene editing method is superior, we need to look at how it works. For any gene editing tool to work, we need something to find the error, chop it off, and replace it with new code. Now knowing this, how does CRISPR find the specific location in the genetic code to cut off? Scientists use guide RNAs- CRISPR’s internal GPS. The guide RNAs are like a row of singular socks (bases) that are looking for their perfect pair called base pairs. When they’re placed in your body, they’re constantly searching for their match until they find the specific area in your DNA where all socks can have their match🧦.

Now that we have the internal GPS, we need something to cut the old gene to fit the new one in. CRISPR uses something called Cas9 to help cut the gene to make the desired change. Cas9 is part of a bacteria’s defense system against viruses, where its role is to remember the viruses that attack their nucleus and cut them out from the genome to prevent them from causing damage. So at its core, Cas9 is just a pair of micro-scissors ✂️.

The last component we need is the new genetic code to implement. Scientists program a new DNA code to replace the part that Cas9 cut out. The new code is then attached to the guide RNA, which allows the DNA to slide into place, completing the edit.

When you combine all these components, it makes CRISPR. A cut-and-paste tool to delete parts of your DNA and replace it with new changes.

But how is Prime editing any different? (In its components)

Prime editing components -https://www.synthego.com/guide/crispr-methods/prime-editing

Prime editing is not so different from CRISPR. The main difference is what enzyme each system uses to cut the DNA. CRISPR uses Cas9 to cut their DNA, but there are more variations to the Cas enzymes. The particular enzyme Prime editing uses is nCas9, the “n” stands for “nickase.” As the name suggests, instead of cutting both strands of DNA like Cas9 does, nCas9 takes a nick off, cutting only one strand of the DNA rather than both like Cas9 does. Prime editing’s guide RNA is also different, it uses pegRNA instead, which attaches to both strands of DNA making it more stable when nCas9 makes the cut. If both gene editing methods are so similar, how is one better than the other 🤔?

Will it be better than CRISPR?

A major risk that comes with the current CRISPR model is how Cas9 cuts through both strands of DNA. This puts the chromosomes at risk of accidental deletion, or other unwanted mutations that happen as a result of the edit 😬. We already went over how nCas9 only breaks one strand of DNA, meaning that the margin of error is significantly reduced, but there are more things that make Prime editing a better candidate for gene editing. Despite seemingly minimal variations of their components, there are many nuances in the way Prime editing works that make less of a risk of unwanted mutations. Prime editing uses pegRNA to bind with the strand of DNA that needs change and adds the new edit onto that strand. Because the original DNA strand that was once connected to it is still there, it competes with the edited strand to fill in the space, allowing the cell’s internal repair response to pick and choose which strand to fill it in, whereas CRISPR entirely cuts out parts of DNA to make room for the new code.

Prime editing diagram -https://www.youtube.com/watch?v=FzVV-AkS76I&t=37s

By allowing the cell’s internal systems to seamlessly bind with the edit, eliminates the occurrence of mutations that you would get through CRISPR editing. This simple change makes prime editing significantly safer and more effective than CRISPR.

Prime Editing’s Potential in Cystic Fibrosis

Cystic fibrosis is a common disease that often stems from genetic mutations. There are treatments out there for cystic fibrosis, but they have major side effects and can set you back $300,000(USD) per year 😭. Why constantly treat cystic fibrosis with inefficient medication, when you can get one single genetic therapy treatment to cure it for life? That is what researchers at MIT and Harvard thought. They utilized the incredibly precise properties of Prime editing to solve cystic fibrosis.

Cystic fibrosis is caused by mutations in the CFTR gene. The CFTR gene has around 700 mutations that cause diseases. The most common mutation (three base-pair CTT mutation), causes proteins to fold incorrectly and break down leading to cystic fibrosis. Attempts have been made to correct this genetic mutation with CRISPR, but CRISPR caused other mutations that overall proved ineffective or minimally beneficial.

With the advent of Prime editing, the precision of the tool allows it to surpass CRISPR’s limitations. During the testing of CRISPR’s efficiency in fixing the main mutation in cystic fibrosis, it only corrected ~1% of CTT mutations cultivated in a dish, whereas prime editing corrected ~25% of the mutations. Prime editing also has 3.5 times fewer unwanted mutations than CRISPR, proving its dominance over CRISPR. Prime editing has taken an incredible hurdle that CRISPR wasn’t able to achieve.

Downsides of Prime Editing 😓

With all this talk about the incredible success of Prime editing in cystic fibrosis, are there cons that we should be aware of? Prime editing is a fairly new development in the gene editing field. The idea only came to fruition in 2019, whereas CRISPR came about in 2012. Due to the delay in Prime editing’s development, there hasn’t been extensive research on it, meaning that there could be many problems with Prime editing that we haven’t seen yet.

Another major issue that plagues the gene editing industry as a whole is the steep price tag. Doing one gene therapy treatment can cost about $2 million(CAD). This creates a financial barrier for people trying to access this treatment. Prime editing will be no different in cost compared to its counterparts, meaning that the clinical benefits of Prime editing cannot be harnessed by the general public.

Conclusion 🎖️

Prime editing is far more efficient than CRISPR in editing and can reduce unwanted mutations that CRISPR may cause. This means that CRISPR’s time in the spotlight may be coming to an end, and we should make room for their new sibling to fill the role of the superior gene editing tool.

TLDR/ Main takeaways 💫

• CRISPR uses the Cas9 enzyme, while Prime editing uses nCas9 to cut DNA
• CRISPR can cause many mutations in the DNA after editing, so it is not very effective
• Prime editing creates fewer mutations than CRISPR because it uses the cell’s internal repair system to integrate the edit
• Prime editing is more efficient in treating cystic fibrosis than CRISPR
• Prime editing is relatively new and certain risks are still unknown
• Prime editing is the better gene editing tool 👑

Sources:

• https://www.nature.com/articles/s41551-024-01233-3
• https://www.fiosgenomics.com/prime-editing-crispr-cas9/
• https://www.nature.com/articles/s41434-021-00263-9
• https://www.cell.com/trends/biotechnology/fulltext/S0167-7799(23)00085-9#:~:text=A%20major%20limitation%20of%20prime,and%20optimizing%20the%20delivery%20strategy.
• https://www.synthego.com/guide/crispr-methods/prime-editing
• https://www.broadinstitute.org/news/prime-editing-efficiently-corrects-cystic-fibrosis-mutation-human-lung-cells
• https://www.youtube.com/watch?v=UKbrwPL3wXE
• https://www.youtube.com/watch?v=FzVV-AkS76I&t=37s