Jan. 16, 2025 – The breakthrough discovery of a powerful new gene editing tool called bridge RNAs has the potential to significantly advance gene therapy and usher in a new frontier in genome design, researchers say.
Discovered by a team of scientists at the Arc Institute and led by Patrick Hsu, PhD, a University of California, Berkeley, assistant professor of bioengineering, bridge RNAs provide precise control over large-scale DNA rearrangements and make the editing process possible in a single step.
While the technology could potentially lead to new therapeutic approaches to treat heart disease and cancer one day, its biggest application may be for genetic disorders. If it can be copied accurately in human cells, the RNA programmability of this new biological mechanism could eventually allow complex gene editing that could cure genetic diseases that carry hundreds or thousands of genetic mutations,
“Not only can you treat every patient with one therapy for one genetic disease, we can easily reprogram that insertion with a different gene to go to another site, for another genetic disease, and cure everybody for that genetic disease,” said Connor Tou, a biological engineering PhD student at the Massachusetts Institute of Technology who co-authored a piece in Nature discussing the Arc Institute discovery. If this technology works as well as researchers hope it will, “it’s almost like a kind of holy grail.”
A New Game Changer Decades in the Making
Gene or genome editing is when a DNA sequence in a living cell is changed. Three decades ago, the first generation of “programmable biology” was discovered with RNA interference (RNAi). Short RNA sequences could be used to target and shut down specific genes.
The second generation came along about a dozen years ago, with the discovery of CRISPR, which stands for clustered regularly interspaced short palindromic repeats. It is an immune system used by microbes to help protect themselves and a powerful molecule and tool that allows genes to be “edited” directly. This was a game changer. What would have taken years and years of research and development could now be done in a matter of days.
“The analogy a lot of people like to use is, instead of having to rebuild the computer every single time, you just upload new software,” said Tou.
A CRISPR-linked protein could find and target a precise location in DNA to “edit” by acting like scissors and making a cut. The genetic sequence around that location could then be changed by adding a new DNA fragment, for example. Once a cut is made, it is a multistep, imperfect process of cellular DNA repair. CRISPR can be used to make other types of edits too, such as increasing or decreasing the effects of a gene temporarily. Regardless of the type of editing, the process generally remains limited to small-scale changes.
The discovery of bridge RNAs simplifies the editing mechanism dramatically, making it much more scalable, cheaper, and easier to design.
How Does a Bridge RNA Work?
RNAi and CRISPR rely on the same basic biological mechanism involving non-coding guide RNAs – short sequences of RNA that behave as a guide and programmed to recognize where to go in the target DNA. They can be reprogrammed to retarget different parts of the genome for editing. The drawback for both of these systems is that they cut, damage, or destroy their DNA or RNA targets to complete their tasks. Hsu’s team suspected there were many other non-coding RNAs that could be programmable and perform more complex tasks, and be better at doing them than existing gene editing techniques.
“We started thinking: Could there be essentially recombination technologies that allow you to do cut and paste in a single step?” Hsu said in a podcast interview with Eric Topol, MD, director and founder of the Scripps Research Translational Institute. When his team began investigating, the researchers discovered a new type of guide RNA that acts like a bridge between the target, donor, and recombinase enzyme. In a test tube, they were able to target and insert DNA without needing any DNA repair.
The system comes from the insertion sequence 110 (IS110) family – one of many types of small, mobile pieces of DNA, or “jumping genes,” capable of cutting and pasting themselves to move between different locations within a microbial genome. It differs from CRISPR technology not only for its ultra precision, but particularly for its programmability. The bridge RNA folds into two loops; each loop can be programmed independently of one another, with one binding to the element itself and the other binding to the target DNA site. The process seamlessly recombines the two DNA strands without causing any unwanted breaks in the DNA – a major limitation in existing technologies. Hsu’s team was able to achieve a 60% success rate when inserting a desired gene (insertion efficiency) for an E. coli gene, and 94% specificity, reflecting the accuracy with which it was able to correctly identify the location and edit the target DNA.
“It’s as if the bridge RNA were a universal power adapter that makes IS110 compatible with any outlet,” UC Berkeley bioengineering graduate student Nicholas Perry, co-author of the study that announced the discovery, said in a news release.
What Could This Mean for the Future of Medicine?
CRISPR has shown promise in curing certain types of diseases, with the first therapy approved for sickle cell disease in 2023. But this inherited blood disorder is caused by a single mutation. Compare that with a disease like cystic fibrosis, which is caused by more than 2,000 mutations in what is known as the CFTR gene.
“You can imagine, in theory, we could go and correct every single one, but it takes a drug 10 years to get through the [FDA]. And so, you can imagine, creating hundreds or thousands of different gene editing drugs for every single mutation is very impractical, right?” Tou said. Instead of focusing on individual mutations, the easier strategy, he explained, would be to replace the faulty gene with a healthy copy at the CFTR locus – the fixed, physical region of a chromosome.
“That’s kind of the biggest application, is to be able to use integration technologies like bridge recombinases … to be able to integrate a healthy copy of the gene into programmed, desired sites.”
Despite the incredible potential of bridge RNAs, researchers like Tou note there are still some uncertainties, including how well bridge RNA would carry out instructions and how well human cells would respond to those instructions, particularly at a low dose. Unlike CRISPR, bridge recombinases are not immune systems, so they are not as efficient at what they do.
The greatest uncertainty and risk, in Tou’s view, is specificity, or how accurately bridge RNAs can identify the correct location, particularly in a large genome like human cells. These bridge RNAs are shorter than those for CRISPR, so in a complex genome, there could be many sites with the same short sequence of base pairs, he explained. If the guide identifies the wrong target region, significant, unintentional, and even harmful errors involving large deletions or inversions could result. Much like a password, multiple sites might share the same short sequence, but only a few or just one region might match a longer group of base pairs.
“Do you want the ease of bridge recombinase programmability at some expense of specificity, or do you want something that's a little more complicated, but … is much more specific?” Tou said of the current trade-off between CRISPR and bridge RNA. “It has a lot of promise, but there’s also obviously some things to be seen still in the field.”