The gene editing tool changing the world

CRISPR-Cas9 is one of the biggest discoveries of the 21st century. Since it was developed in 2012, this gene-editing tool has revolutionized biology research, making it easier to study disease and faster to discover drugs. The technology is also significantly impacting the development of crops, foods, and industrial fermentation processes.

The one application that has made it famous is the modification of the human genome, which brings the promise of using CRISPR to cure diseases. Since 2012, a lot has happened and drug candidates have progressed so far that one has even reached approval. So while scientists keep venturing into tweaking our DNA, it is worth taking the time to fully understand what CRISPR is, and what the actual benefits and possibilities are.

First of all, what is CRISPR-Cas9?

CRISPR is short for ‘clustered regularly interspaced short palindromic repeats.’ The term refers to a series of repetitive patterns in the DNA of bacteria and archaea that were extensively researched by Spanish scientist Francis Mojica in the ‘90s. 

These patterns are the basis of a primitive immune system that bacteria use to ‘remember’ the DNA of viral invaders by incorporating the DNA sequence of the virus within the CRISPR patterns. The Cas9 protein is then able to recognize the DNA sequence stored within CRISPR patterns and cut any DNA molecules with a matching sequence.

But it wasn’t until 2012 that Jennifer Doudna and Emmanuelle Charpentier took the discovery a step further and proposed that CRISPR-Cas9 could be used to cut any desired DNA sequence by just providing it with the right template. Two other papers published just a few months later by Feng Zhang and George Church from the Broad Institute also reported some early uses of CRISPR as a gene-editing tool.

It is important to note that CRISPR is not the first system that allows us to edit DNA in all sorts of organisms. However, CRISPR brings an important advantage over these other techniques: it is much easier and faster to use. Most previous technologies required creating a gene-editing protein from scratch for each specific DNA modification. With CRISPR, the same Cas9 molecule can be directed to any sequence just by providing it with a guide RNA molecule, which is much easier to synthesize. 

Since the initial development of CRISPR-Cas9, researchers have introduced more precise gene-editing techniques, notably base editing and prime editing.

Base editing enables the direct conversion of one DNA base into another without causing double-stranded DNA breaks. For example, cytosine base editors (CBEs) can change a cytosine (C) to a thymine (T), and adenine base editors (ABEs) can convert an adenine (A) to a guanine (G). This precision reduces the risk of unintended mutations and is particularly useful for correcting point mutations associated with genetic diseases.

Prime editing, often referred to as “search-and-replace” editing, allows for the insertion, deletion, or substitution of DNA sequences without introducing double-stranded breaks. It utilizes a fusion of a catalytically impaired Cas9 and a reverse transcriptase enzyme, guided by a prime editing guide RNA (pegRNA) that specifies the target site and the desired edit. This versatility enables the correction of a wide range of genetic mutations with high precision.

What can CRISPR do?

In theory, CRISPR gene editing could be used to make any modification to the DNA of virtually any living being. While we think first of editing the human genome to cure diseases, CRISPR could play an important part in fighting global warming too. Indeed, an example given by Doudna herself in an interview about the potential of artificial intelligence and CRISPR combination is creating a methane-free cow. While we are not there yet, Doudna is confident this is scientifically feasible.

In agriculture, CRISPR could be used to produce crops with better yields or that can resist drought, much faster than is possible with traditional breeding techniques. It can also be used to add new features to crops or to remove others — for example making gluten-free wheat or decaf coffee beans. Indeed, CRISPR allowed the creation of a sweeter tomato, increasing its fructose and glucose concentration by 30%. While it seems more consumer-oriented rather than the world-changing application of CRISPR we are waiting for, it does indicate the potential of the tool.

However, regulations can limit the use of these technologies. While the U.S. has already seen the launch of CRISPR-modified crops, things have been a bit slower in Europe. In the European Union, a proposal to deregulate gene-edited crops by banning patents has sparked debate. Critics argue that the inability to protect intellectual property through patents could discourage investment in research and development, potentially stifling innovation. Despite objections, these proposed regulations might become law by early 2025. While relaxing the regulations around gene-edited crops is a step in the right direction, Europe is still lagging behind the U.S.

Beyond agricultural and environmental applications, CRISPR’s most promising use lies In health. The most obvious application is treating genetic diseases such as sickle cell disease, caused by a mutation in the HBB gene. That is exactly the focus of Casgevy, the first-ever CRISPR-based therapy approved by the U.S. Food and Drug Administration (FDA). CRISPR can also be used to edit T-cells to develop CAR-T therapies for cancer.

However, the medical applications of CRISPR also highlight ethical challenges. In 2018, the controversial birth of genetically edited twins in China, often referred to as the “CRISPR babies,” shocked the global scientific community. Chinese scientist He Jiankui used CRISPR-Cas9 to edit the CCR5 gene in embryos, allegedly to make the twins resistant to HIV. The experiment was widely condemned for its lack of transparency, ethical oversight, and potential long-term risks. It became a cautionary tale and reinforced international calls for stringent regulations on human germline editing.

Recent developments in the CRISPR field

The most significant recent event related to CRISPR has to be the 2023 FDA approval of the first CRISPR-based therapy, Casgevy. Developed collaboratively by Vertex Pharmaceuticals and CRISPR Therapeutics, Casgevy is designed to treat sickle cell disease and transfusion-dependent beta-thalassemia. The therapy involves editing patients’ hematopoietic stem cells to induce the production of fetal hemoglobin, thereby alleviating disease symptoms. 

While this first approval is undoubtedly a milestone for the field, there are some concerns about the accessibility of the therapy. Indeed with a price tag of $2 million per patient, one can wonder if the scientific prowess of CRISPR will one day be broadly employed to treat patients, especially in low-to-middle-income regions.

Administering Casgevy involves a complex and time-intensive process. Patients undergo harvesting of their hematopoietic stem cells, which are then genetically edited to produce healthy hemoglobin before being reinfused. This procedure can span several months and requires substantial medical infrastructure, potentially limiting its availability to patients in resource-constrained settings.

Another development is the FDA clearance to initiate the first clinical trial utilizing prime editing technology. In May 2024, Prime Medicine received approval to proceed with a trial focused on treating chronic granulomatous disease (CGD), a rare inherited immune deficiency. The advantage of prime editing is that it doesn’t induce DNA breaks to correct genetic mutations, potentially enhancing safety profiles compared to traditional CRISPR methods. 

Other CRISPR-based therapies are progressing through the clinic. For example, Intellia Therapeutics’ NTLA-2001, an in vivo CRISPR therapy for transthyretin amyloidosis (ATTR), has shown remarkable promise. ATTR is a life-threatening condition caused by misfolded proteins, and NTLA-2001 uses lipid nanoparticles to deliver the CRISPR components directly to the liver, where they disable the TTR gene responsible for the disease. Early results from ongoing phase 1 trials indicate sustained reductions in disease-causing protein levels.

Meanwhile, Editas Medicine is advancing EDIT-301, a therapy for sickle cell disease and beta-thalassemia that takes a novel approach using CRISPR-Cas12a (Cpf1). This method edits the HBG1 and HBG2 promoter regions, reactivating fetal hemoglobin production to replace defective hemoglobin. Phase 1/2 clinical trials are underway, and early data suggests that the therapy effectively increases hemoglobin levels in treated patients.

In the field of cardiovascular health, Verve Therapeutics is developing VERVE-101, a base-editing therapy for familial hypercholesterolemia (FH). This genetic disorder leads to dangerously high cholesterol levels, increasing the risk of heart disease. VERVE-101 works by permanently inactivating the PCSK9 gene, which plays a key role in regulating cholesterol levels. The therapy is currently in phase 1.

What’s next for CRISPR?

More and more companies are developing CRISPR-based therapy and advancing candidates through the clinic. While Casgevy has certainly demonstrated CRISPR can be safe and effective as a treatment, it will definitely take some time and additional approvals to prove for good the broader safety of the technology. 

The variety of potential applications for CRISPR seems limitless. In healthcare alone, we are already seeing CRISPR-based programs focusing on a wide diversity of diseases. CRISPR Therapeutics, for instance, in addition to Casgevy, is developing programs for cardiovascular diseases, type 1 diabetes, as well as CAR-T therapies for cancer. 

Eligo Bioscience, a French company, is applying CRISPR to edit the microbiome to address various diseases associated with microbiome dysbiosis, including antibiotic-resistant infections and chronic diseases. The company’s flagship candidate, EB005, targets acne vulgaris.

Several companies are also stepping away from the cas9 protein to develop their CRISPR-based therapies. Locus Biosciences is an example, with its CRISPR Cas3 anti-bacterial therapy technology. The company’s lead candidate LBP-EC01 targets Escherichia coli (E. coli) infections.

Mammoth Biosciences, a company co-founded by Doudna, uses ultra-small Cas14 and CasΦ (phi) enzymes. The smaller size of these enzymes enables easier delivery into cells, especially for diseases that affect the central nervous system. 

Since Casgevy’s approval, companies are getting even more creative with CRISPR to develop tailored approaches. This diversification will accelerate in the years to come with the integration of AI with CRISPR as it will allow for faster discovery of more efficient cas variants. 

The market is growing too – valued at $3.12 billion in 2022, it reached an estimated $4.69 billion in 2024. According to Grand View Research, there has been a notable rise in investments in CRISPR technology. The growing demand for gene therapeutics, advancements in genome editing technologies, and expanded applications in diagnostics and agriculture have been key drivers attracting investments in the CRISPR sector.

The Grand View Research report also notes that the shift toward more flexibility in European regulations regarding gene editing in agriculture has been a driver for investment in this specific area. 

Gene editing and CRISPR are definitely some of the hottest markets in biotech and as new candidates come closer to approval and AI gets further integrated into the technology, the field is bound to accelerate.