Base editing is bringing the next breakthrough in cell and gene therapy, explains Michelle Fraser.
Cell and gene therapies (CGTs) hold the promise to transform medicine for patients globally. These therapies work by correcting DNA to treat a genetic disease, or by modifying cells from the immune system to specifically target diseased tissue, for example. Recent advancements in CGT have led to promising treatment options with the potential to cure patients living with inherited genetic diseases (such as rare diseases), and chronic conditions (such as cancers), rather than treating their symptoms. This type of therapy, however, comes with some new challenges, both technical and clinical, which the industry is working hard to overcome.
The field of CGT comprises multiple technical approaches to perform the cell and gene modification. Correction of the genetic sequence via editing at the genome level, knocking out, repressing or increasing a gene at the DNA or RNA level or insertion of a replacement gene or control sequence allows scientists to address the root cause of the disorder. These various approaches can be used to create therapies that stimulate an immune response towards targeted cells, such as CAR-T cells, or replace the function of diseased cells, providing a longer lasting treatment or cure in patients living with chronic disorders. For example, education of the body’s own immune cells to recognise and fight cancer cells, known as CAR-T (chimeric antigen receptor T cell) therapy, has revolutionised cancer treatment for blood-borne cancers such as lymphomas. This ‘education’ starts with the isolation of T cells (from the patient or a donor); then the information for recognising and fighting tumour cells is transferred by means of a gene transfer vehicle or ‘vector’, which enables the cells to express chimeric antigen receptors specific to the cancer on their surface. These genetically modified cells are reinfused to the blood stream eliciting an immune response to the CAR-specific antigen on the cancer cell, leading to durable complete remission for many patients.
CRISPR: the foundation for a new era in therapeutics
In recent years, a new type of gene editing technology known as CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) has begun unlocking new potential in CGT. The CRISPR-Cas9 gene editing tool is the most significant recent breakthrough within CRISPR, claiming the Nobel Prize in Chemistry in 2020. To date, more than 30 cell and gene therapies developed using CRISPR technology have been approved by the FDA to treat conditions ranging from rare diseases to different cancer types. However, there are ongoing concerns over the risk of CRISPR technologies activating a cytotoxic and potentially oncogenic p53 response or the harmful occurrence of unintended genetic insertions and deletions or off-target editing, posing a threat to genomic integrity and cell function. These risks call for CGT editing solutions with a higher accuracy, efficacy and manageable safety profile.
Base editing: cutting-edge CRISPR technology
Base editing, is one the newest CGT technologies, built on the foundation laid by CRISPR-based technologies. It stands out from its predecessors by facilitating multiple, simultaneous edits in a wide variety of therapeutically relevant cell types with a significantly improved safety profile and without compromising the cell’s viability and functionality.
Base editors function by recruiting a nickase and a deaminase enzyme to the target nucleotide using a guide RNA, where the deaminase generates a target point mutation in the DNA via chemical modification, rather than physical replacement, that facilitates a C–G > T–A (cytidine base editors, CBEs) or A–G > T–C transition (adenine base editors, ABEs). The nickase nicks the opposing strand, which is then repaired using the cell’s own repair system completing the base edit on both strands. Whilst traditional CRISPR technologies use the fully functional Cas9 enzyme to create a double-stranded cut in the DNA at the site where the CRISPR guide RNA sequence binds, base editors nick only one of the strands of DNA to enable the recruited enzyme to make a very specific base change to the DNA.
Specific base changes with reduced risks
Because base editors facilitate a specific base change to the target DNA, they allow scientists to have additional control over the edit and hence look at the impact that a very specific change to the DNA makes to the function of the cell. Using these insights, scientists can create disease mimicking cell lines and models to better understand the genetic causes of a disease, create novel cell and gene therapies, and screen drug candidates to gain greater insight on their mechanism of action and risk of adverse response. In practice, the capacity to introduce a single-base conversion can enable correction of a pathogenic point mutation, silencing of a disease-causing gene, skipping of a disease-causing exon, activation of a specific gene, or fine-tuning of engineered immune cell therapies.
Base editors are also expected to reduce the time required to create therapies, because editing can be performed concurrently rather than needing to be performed sequentially. This is especially important in sensitive cell types that are not able to tolerate multiple editing reactions.
The safety features of base editors make the technology an extremely attractive prospect for cell and gene therapy applications. Unlike traditional CRISPR -Cas systems, base editors do not introduce double-stranded breaks, reducing the risks of unwanted effects or alterations in the genome. Multiplex base editing has also been shown to have no impact on cell viability, so the yields will be unaffected.
From concept to clinical application
The Pin-point base editing system is an example of one of the latest generation CRISPR-Cas-derived genome editing technologies. It has been demonstrated that Pin-point is able to knock-out immunogenic proteins and knock-in a targeted CAR within the same editing reaction, creating an effective functional CAR-T cell line with tumour-killing activity in a single editing reaction. The technology is being further investigated for use in cancer immunotherapy for the generation of universal, off-the-shelf allogeneic CAR-T cells, with the promise of making CAR-T treatments safer, faster to manufacture, and less costly.
Further studies are currently evaluating the potential for base editing technologies to correct single nucleotide variants (SNVs) involved in the pathogenesis of genetic conditions including Duchenne Muscular Dystrophy and Hutchinson-Gilford progeria.
With the progress and promising outcomes seen in base editing to date, researchers continue to work on applying these technologies in the clinic, with the potential to transform cell and gene therapies for patients awaiting life-changing cures for their conditions.
Michelle Fraser is head of Cell and Gene Therapy at Revvity.
References
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