The Future of Gene Editing Beyond CRISPR

Exploration into gene therapy techniques dates back to 1987 when researchers discovered an intriguing repetitive DNA sequence while studying genes involved in phosphate metabolism in the Escherichia coli genome. This sequence was later recognised as CRISPR, which stands for ‘clustered regularly interspaced short palindromic repeats’. The scientific community has since been invested in gene therapies because they can potentially be utilised to treat a broad spectrum of diseases, such as cancer, infectious diseases, and genetic disorders that were previously considered untreatable, positioning them as a powerful class of therapeutics. 

In 2023, CRISPR took the world by storm following the FDA approval of Casgevy, the first gene therapy approved for sickle cell disease. This sparked significant interest in CRISPR from the media and the public. While CRISPR is undeniably captivating, there are a variety of other gene editing techniques that could potentially pave the way for new therapeutic solutions, which we’ll explore in this article.

Gene editing, also known as genome editing, can be used to amend a faulty gene or replace it with a healthy one or to add, delete, or introduce a specific base or sequence in the genome. Other types of gene editing techniques include base editing, prime editing, Zinc Finger Nuclease (ZFNs), and Transcriptor Activator-like Effector Nuclease (TALENs).

Base editing – one nucleotide at a time 

This technique goes down to the nucleotide level. Unlike CRISPR, which involves cutting the DNA to insert or delete sequences, base editing allows scientists to precisely replace one DNA base with another without making double-strand breaks. Since only a single nucleotide is replaced, this makes it a favourable technique due to the lower risk of introducing errors in the DNA strand. It has the potential to correct harmful mutations responsible for conditions like sickle cell disease and Tay-Sachs disease. 

Several promising therapies using base editing are in development. This includes Verve-101 by Verve Therapeutics, which targets the PCSK9 gene to treat familial hypercholesterolemia, and Beam Therapeutics' BEAM-101 and BEAM-102, designed to treat sickle cell disease and beta-thalassemia.

Prime editing – a new technique on the horizon 

Prime editing is one of the newest genome editing techniques, allowing for more precise DNA modifications than CRISPR or base editing. Compared to other techniques, prime editing does not cut both strands of DNA; it instead uses a "prime editor” protein to make targeted changes, such as inserting, deleting, or swapping DNA bases. This unique approach offers more versatility, allowing for a wider range of edits with reduced risks of unintended, off-target effects. However, more research is needed to measure the long-term effects of therapies designed using this technique. Prime editing has a significant potential to correct genetic mutations that cause diseases like cystic fibrosis or Huntington's disease.

This technique is relatively new and still in the early stages of development. However, a couple of promising therapies are being developed, mainly by Beam Therapeutics, who are using prime editing to develop treatments for sickle cell anaemia and beta-thalassemia. As this technology advances, we expect to see more applications in rare genetic conditions and other therapeutic areas.

Zinc Finger Nucleases (ZFNs) – binding to a specific site

ZFNs are DNA-binding proteins that can create targeted double-strand breaks in DNA, enabling the precise insertion, deletion, or modification of specific genes. They consist of a zinc finger “DNA-binding domain” and a “DNA-cleavage domain” that cuts DNA at a desired location. While ZFNs target specific sites, it cannot be ruled out that ZFNs cut DNA at off-target sites, and the proteins can induce an immune response, leading to side effects in patients receiving the therapy. Furthermore, this technique is more complex to design in comparison to CRISPR, therefore becoming more costly and time-consuming. 

Despite these challenges, ZFNs are being studied for numerous applications, such as the treatment of HIV, where this method has been used to modify immune cells to resist the virus. Sangamo Therapeutics is developing several therapies using ZFNs, including a treatment for haemophilia and sickle cell disease.

Transcription Activator-Like Effector Nucleases (TALENs) – more precision and flexibility

TALENs are used for more targeted and efficient gene editing in live cells, enabling precise edits to be made to the genome. TALENs can be built from a simple “protein-DNA-code” that can be customised to “specifically recognise a unique DNA sequence” to make specific modifications to the genome, including insertion, deletion, repair, and replacement. This method is less prone to off-target effects. Cellectis has used this method to develop several CAR-T therapies for treating blood cancers by editing immune cells to target tumours. 

Looking forward, what is next?

More than 4,000 gene, cell, and RNA therapies are currently in development. The biotech industry is constantly looking for innovative solutions to treat diseases that have been difficult to target with traditional therapies. The field is exponentially growing, with constant developments in gene-editing technologies such as CRISPR, TALENs, base editing, prime editing and ZFNs, as well as breakthroughs in delivery methods such as lipid nanoparticles and viral vectors. These scientific and technological advancements offer hope for curing genetic disorders, some cancers, and rare diseases that previously had no prior treatment options.

As we anticipate the growth and future success of genome editing therapies, it is also important to note the ethical considerations of this field. For example, concerns over germline editing, equitable access to treatments, and ensuring patient safety must be responsibly managed to ensure that gene-editing technologies are used for the benefit of society as a whole.