Base Editing vs. CRISPR: Navigating Precision Gene Therapy

Gene therapy is marking new frontiers with the recent FDA approvals of innovative treatments for sickle cell disease (SCD). Casgevy is one of the first two cell-based gene therapies approved for the treatment of sickle cell disease, representing a significant breakthrough in treating disorders at the genetic level and highlighting the essential role of high-quality biomaterials, such as enzymes used in efficient gene editing workflows.

Sickle cell disease is also being targeted through the promising technology of base editing. For example, Beam Therapeutics’ clinical-phase sickle cell disease pipeline BEAM-101, uses targeted base edits to target activation of fetal hemoglobin production in human cells. 

Amid these landmark approvals, the relevance of advanced gene editing enzymes in medical science has never been greater. Traditional CRISPR-Cas9 methods have demonstrated immense potential for precise genome editing particularly when targeting specific DNA sequences within target cells. However, base editing, which modifies DNA without double-stranded DNA cleavage—is now being evaluated as a more controlled strategy for precision genome editing when avoiding a double-strand break is necessary. Advancement in both of these technologies now prompts us to ask: When should we utilize CRISPR, and when might base editing offer a superior approach? 

What Is CRISPR?

CRISPR, short for Clustered Regularly Interspaced Short Palindromic Repeats, has revolutionized gene editing since its discovery. By using the CRISPR Cas9 protein, researchers can precisely target specific DNA sequences and introduce cuts. Once the DNA sequence is cut, the cell's natural repair mechanisms are activated, either through cellular DNA repair pathways like non-homologous end joining (NHEJ), which can introduce mutations, or through homology-directed repair (HDR), which allows precise edits if a repair template is provided. HDR can support precise genomic alterations if a repair template is present.

The mechanism enables broad versatility—from basic research applications to therapeutic pipeline development. However, the formation of off-target sites remains a known challenge, and cutting the genome can create unpredictable off-target editing. This becomes especially relevant in sensitive systems such as primary T cells, human pluripotent stem cells, living cells, or in vivo genome editing applications.

Figure 1. CRISPR Cas9 DNA repair mechansims non-homologus end joining (NHEJ) and homology-directed repair (HDR) [1]. 

CRISPR Cas9 has become the go-to tool for many gene editing applications because of its high accuracy, versatility, and efficiency. Its ability to make double-stranded breaks in DNA enables the removal, insertion, or modification of genes.

However, while CRISPR Cas9 is powerful, it is not without challenges. One of the primary limitations is the possibility of off-target effects, where unintended sites in the genome are cut, leading to unpredictable consequences. Additionally, the double-strand break mechanism can trigger unwanted mutations, making the need for more precise tools even more critical.

Enter Base Editing

Base editing emerged as a next-generation gene editing tool designed to address some of the limitations of CRISPR. Instead of making double-strand breaks, base editors make precise changes to individual DNA bases—the building blocks of our genetic code. The two main types of base editors are cytosine base editors (CBEs) and adenine base editors (ABEs). These systems convert cytosine (C) to thymine (T) or adenine (A) to guanine (G), respectively, without cutting the DNA strand at predefined target sites [2].

This is particularly useful when correcting pathogenic mutations found in the human genome, and when the target base lies within the available editing window. Base editing also benefits from directed evolution and protein engineering improvements, which continue to expand the cytosine base editing scope and improve editing efficiency in mammalian cells.

This technique allows for more controlled and predictable gene edits, reducing the risk of unintended consequences. Base editing is particularly valuable for correcting point mutations, which are responsible for hundreds of genetic diseases. 

Key Differences Between Base Editing and CRISPR

While both CRISPR and base editing are groundbreaking tools for gene editing, they operate differently, offering distinct advantages and disadvantages:

Precision

CRISPR Cas9 introduces cuts in the DNA, which can result in a variety of outcomes, including insertions or deletions (indels) during repair. While precise edits can be made, there is always the potential for off-target site effects to emerge.

Base editors make single-base changes without cutting the DNA. This reduces the risk of unwanted mutations and makes base editing more predictable. Our AccuBase™ Base Editor has been engineered to have near-zero off-target effects. 

Figure 1. Measurement of off-target effects by GOTI. By leveraging the GOTI (genome-wide off-target analysis by teo-cell embryo injection) to measure the off-target effects throughout the whole genome, it was shown that compared to the control base editor (with 700 SNVs detected), the number of SNV obtained after editing by AccuBase™ is similar to the GFP (negative control) group, suggesting a near-to-zero off-target effects of AccuBase™.

Applications

CRISPR is more versatile modifying target genes more extensively. It can delete, insert, or replace entire sequences of DNA, making it a powerful tool for many types of gene modifications. Our GMP Cas9 protein shows high editing activity in various cell types and target genes.