Editorial: Genome Editing Goes Beyond CRISPR with the Emergence of ‘Bridge’ RNA Editing

Therapeutic human gene editing technologies continue to advance, with the endonuclease, clustered regularly interspaced short palindromic repeats (CRISPR) being one of the most rapidly developing technologies [1,2]. As recently as 2020, Charpentier and Doudna were awarded the Nobel Prize in Chemistry for their research on CRISPR and the CRISPR-associated protein 9 (CRISPR-Cas9) DNA editing methods [3,4]. On 16 November 2023, the UK Medicines and Healthcare Products Regulatory Agency (MHRA) was the first to approve a CRISPR-Cas9 gene editing therapy, Casgevy (exagamglogene autotemcel), to treat patients with transfusion-dependent β-thalassemia and sickle cell disease in patients aged ≥12 years with recurrent vaso-occlusive crises [5,6]. This initial regulatory decision was followed on 8 December 2023 by approval from the US Food and Drug Administration (FDA) of both Casgevy and Lyfgenia (lovotibeglogene autotemcel) [7]. On 15 December 2023, the European Medicines Agency (EMA) granted regulatory approval [8].

Advances in CRISPR genome editing have occurred in parallel with, and are probably dependent on, advances in imaging and computing methodologies [9]. A new era is emerging in which individualized or personalized medicine could include the evaluation of genetic disease susceptibility, diagnosis, and treatment [9]. Climate change profoundly affects the epidemiology of human disease, population demographics, and food availability [10,11]. It is important to note that, at this time, CRISPR gene editing technology is being applied to transform animal and plant traits, agricultural research, and animal and plant breeding [9,12]. Developments in CRISPR gene editing for humans, animals, and plants could progress during the next year as an approach to mitigating some of the global effects of climate change [9,12].

CRISPR technology has evolved to mutate specific sites in the genome due to its potential to treat a wide range of human diseases [9]. The future development of modifying CRISPR proteins to edit DNA directly is predicted [9]. Base editors can alter a single DNA base without cutting the DNA, and prime editors can guide RNA to DNA [9]. Ongoing clinical trials are further exploring the potential of these modifications [9]. However, treating some major human diseases may require more advanced genome changes [13,14].

Recently, in 2024, a method of RNA editing called ‘bridge editing’ has been described in bacteria, which is more powerful and has broader applications than CRISPR to reshape the genome [13,15]. The term ‘bridge editing’ is used because the method physically links, or bridges, two sections of DNA and can alter large sections of a genome [13,15]. ‘Bridge editing’ relies on insertion sequence (IS) elements, the simplest autonomous transposable elements in prokaryotic genomes [15]. Hiraizumi and colleagues have identified that components of the IS110 family encode a recombinase and a noncoding ‘bridge’ RNA (bRNA) that confers specificity for target DNA and donor DNA through two programmable loops [15]. Bispecific RNA was shown to confer target DNA and donor DNA specificity to IS110 recombinases for programmable DNA recombination by cryo-electron microscopy [15]. The ‘bridge editing’ system consists of a recombinase protein that combines with a guide RNA, similar to the method of action of the CRISPR Cas9 protein [13,14]. However, in the ‘bridge editing’ system, the guide RNA specifies two DNA sequences; one sequence specifies the genomic target site to be altered, similar to CRISPR, while the other specifies the DNA site to be changed [13,15].

A recent study has investigated the role of a transposable element of DEDD (which encodes the death effector domain-containing protein) [16]. This nucleic acid DNA sequence can change its position within the genome to create or reverse mutations [16]. The IS110 family (IS1111 and IS110) insertion sequence members encode an unusual DEDD transposase type with specific target site selection [16]. The IS1111 group includes identifiable subterminal inverted repeats (sTIR) not found in the IS110 type, but the insertion sequence in both families consists of a noncoding region of significant length [16]. The noncoding region-derived RNA is usually downstream of the transposase gene in the IS1111 type and upstream in the IS110 type, and four IS1111 and one IS110 family members target different sequences [16]. They are used to demonstrate that the noncoding region determines a short seeker RNA (seekRNA), which is essential for the transposition of the IS [16]. Short sequences matching both the upper and lower strands of the target are present in the seekRNA, but their order in IS1111 and IS110 is reversed [16]. Siddiquee and colleagues have recently demonstrated that reprogramming the seekRNA and the donor flank can target different sites [16]. The ‘bridge editing’ system can add, delete, or reverse DNA sequences of almost any length [13,15]. The ‘bridge editing’ system has been studied in bacteria in vitro [13,15]. However, the results of studies in vivo in complex human cells are awaited [13,15]. However, if ‘bridge editing’ succeeds in initial tests in human cells, it will likely undergo clinical trials soon. Ongoing studies support the potential role of ‘bridge’ RNA-guided recombination in gene therapy [16].

Conclusions

‘Bridge’ RNA editing represents a unified mechanism for the three fundamental types of DNA rearrangement required for genome design: inversion, insertion, and excision [13]. Therefore, the IS110 ‘bridge’ recombination system can potentially expand the range and diversity of nucleic acid-guided therapeutic systems beyond RNA interference and CRISPR.