Breaking genetic shackles: The advance of base editing in genetic disorder treatment

Abstract

The rapid evolution of gene editing technology has markedly improved the outlook for treating genetic diseases. Base editing, recognized as an exceptionally precise genetic modification tool, is emerging as a focus in the realm of genetic disease therapy. We provide a comprehensive overview of the fundamental principles and delivery methods of cytosine base editors (CBE), adenine base editors (ABE), and RNA base editors, with a particular focus on their applications and recent research advances in the treatment of genetic diseases. We have also explored the potential challenges faced by base editing technology in treatment, including aspects such as targeting specificity, safety, and efficacy, and have enumerated a series of possible solutions to propel the clinical translation of base editing technology. In conclusion, this article not only underscores the present state of base editing technology but also envisions its tremendous potential in the future, providing a novel perspective on the treatment of genetic diseases. It underscores the vast potential of base editing technology in the realm of genetic medicine, providing support for the progression of gene medicine and the development of innovative approaches to genetic disease therapy.

Keywords: adenine base editors; base editing; cytosine base editors; delivery strategies; genetic diseases.

FIGURE 1

A brief history of the development and application of the CRISPR/Cas system. (A) Provides a concise overview of the timeline of key events in the development of the CRISPR/Cas system. (B) Summarize the main applications and clinical trials of the CRISPR/Cas9 system in the field of genetic diseases.

FIGURE 2

The advancements and mechanisms of base editing technologies. (A) Evolution of DNA base editing (2016–2023): This section maps the significant developments and innovations in base editing technology from 2016 to 2023. (B) Mechanisms of ABE (left), CBE (center), and the latest deaminase-free glycosylase-based guanine base editor (gGBE, right): A common feature of these editors is the inclusion of their respective Cas9 variants and sgRNA. ABE utilizes variants of adenine deaminase (like TadA), converting A into inosine (I), which is typically read as G during DNA repair or replication, thus achieving A-to-G conversion. CBE employs cytosine deaminases (such as APOBEC1) or its variants to deaminate C into U. During DNA repair or replication, U is usually read as T, enabling C-to-T conversion. The guanine base editor (gGBE) employs N-methylpurine DNA glycosylase (MPG) to recognize and remove G from the DNA strand, and the resulting apurinic/apyrimidinic (AP) site are subsequently repaired through translesion synthesis (TLS) or DNA replication, culminating in G-to-C or G-to-T transversions.

FIGURE 3

The principle of RNA base editors and the multifunctionality of base editors. (A) Mechanism of RNA base editors. This section expounds the mechanism of RNA base editing, achieving A-to-I and A-to-U edits. The REPAIR system employs a fusion of dCas13 with the catalytic domain of ADAR deaminase to facilitate programmable A-to-I replacement. Through specifically designed guide RNAs (gRNAs), the dCas13-ADAR complex is directed to precise sites on RNA molecules. In this context, capitalizing on the induced AC mismatch between the target mRNA and the gRNA of Cas13b, the catalytic domain of ADAR subsequently converts A at the targeted site into I. In the RESCUE system, an enhanced version of ADAR2 can convert C to U. Leveraging induced CC or CU mismatches between the target mRNA and the gRNA of Cas13b, the ADAR2 variant achieves targeted deamination of cytosine on mRNA. (B) The multifunctionality of base editors. Base editing technology, in addition to correcting mutated genes, can be used for a variety of other applications. These include editing RNA splicing receptors, conducting functional screening of single nucleotide variants, and regulating gene expression, among others.

FIGURE 4

Delivery strategies of gene editing systems. This figure details the various methodologies employed in the delivery of editors in forms such as mRNA, plasmids, or ribonucleoprotein (RNP) complexes. The delivery mechanisms are classified into several categories: viral vector delivery, physical delivery method, nonviral delivery, and emerging delivery strategies.

FIGURE 5

Comprehensive overview of base editing applications and strategies in genetic disease treatment. It includes an overview of major diseases that are being targeted with base editing technology, as well as the strategies employed for their treatment, both in vivo and ex vivo.

FIGURE 6

The application of base editing in treating genetic diseases. (A) Duchenne muscular dystrophy (DMD): The absence of axon 51 leads to a premature stop codon in exec 52. Base editing induces exec slapping at either non 50 or 52 to construct a correct open reading frame, thereby improving or restoring muscle function. (B) Inherited retinal disease (IRD): For IRD, base editors are employed to precisely target and cared specific mutations vnthin retinal genes. The goal is to restore normal retinal function or to halt further degeneration of the retina. (C) Genetic heanng loss (HL): The application of base editing technology in correcting gene detects causing hearing loss, with the goal of restoring or preserving auditory function. (D) Sickle cell disease (SCD): Base editing modifies the pathogenic protein into benign variants like HbS to HbG-Makassar, to treat red blood cell disorders. (E–I) For phenyketonuria (PKU), familial hypercholesterolemia (FH), dilated cardiomyopathy (DCM), CD3δ severe combined immunodeficiency (CD3δ SCID), and spinal muscular atrophy (SMA): The figure illustrates the utilization of base editing in targeting specific mutations associated with these diseases. The applications are diverse, ranging from restoring liver metabolic functions, reducing cholesterol levels, preventing cardiovascular diseases, to preserving cardiac, immune, and muscle functions.