CRISPR gene editing has been established as one of the most powerful tools to study disease biology and is also being broadly tested as a therapeutic platform to correct disease causing genetic defects. The CRISPR system was first described in 2012 and in the past decade, the platform has been extensively used for various drug discovery applications including disease biology research, preclinical model development and drug development1. Currently, there are several active clinical trials in various phases that use CRISPR to modify genes in cell therapies or directly edit genes in vivo across seven different disease areas: blood disorders, cancers, ocular diseases, diabetes, infectious diseases, inflammatory diseases, and protein-folding disorders2.
The CRISPR-Cas9 system edits DNA by introducing double stranded breaks to remove or replace genes. However, the creation of double stranded breaks has been shown to trigger the rearrangement of genomic DNA sequences, so using CRISPR as a therapeutic approach carries the risk of inducing significant systemic health issues or cause the development of another disease3. It has long been known that mammalian genomes have several mobile genetic elements called transposons and retrotransposons. These elements are nucleic sequences that have the ability to insert themselves into double stranded DNA breaks and have been associated with disease development including cancers3. Transposons are DNA elements that are inserted into genomic DNA that have double stranded breaks using a cut and paste approach, while retrotransposons are RNA elements that undergo reverse transcription to form DNA elements that are then pasted into genomic DNA. Due to the active transposition of the genetic elements in DNA sequences that have double stranded breaks, there are significant concerns about the short- and long-term safety of using CRISPR based gene therapies.
An alternative gene editing approach called base editing was described in 2016 by David Liu and his colleagues at the Broad Institute4. Base editing is a highly targeted approach that combines CRISPR-Cas9 and the enzyme, cytidine deaminase, to directly change single DNA bases without introducing double stranded DNA breaks. Cytidine deaminase converts cytidine to uridine that results in a C to T base changes. Similarly, a fusion of CRISPR-Cas9 with adenosine deaminase has been developed to change G to A5. There has been a significant amount of validation and testing of the base editors in the 5 years since they were first described. One of the more interesting in vivo studies were reported in 2021 where base editors were delivered in nonhuman primates to efficiently knockdown PCSK9 gene6, suggesting that base editors can be effectively delivered in vivo. Given the promising data from in vivo studies, it is not surprising that base editing technology has been fast tracked into the clinic as a therapy for specific genetic diseases.
In November 2021, Beam Therapeutics, a biotech company based in Cambridge MA, received FDA approval for the first IND filing for base editing technology to treat sickle cell disease7. The therapeutic candidate is an autologous hematopoietic cell therapy that has been modified using base editing to overexpress fetal hemoglobin to counteract the effect of low oxygenation in patients with sickle cell disease7. Another trial was launched in July 2022 where patients with heterozygous familial hypercholesterolemia (HeFH) will be dosed with lipid nanoparticles containing guide RNA and base editor sequences that induces an A to G base change in the PCSK9 gene that is defective in HeFH patients. The base change inactivates the defective PCSK9 gene and reduces LDL levels in patients that results in lower risk for cardiovascular diseases8. While it is too early to predict the success of base editing technology in humans, the chances of success are increased due to the precision and sophistication of targeting individual nucleotides with minimal impacts on local or genome wide sequences.