Ingredients for New Kind of DNA Editing Method Are Ready, Say US Scientists

There has been some talk on whether base-editing can replace CRISPR/Cas9. One scientist brushed off the idea: they “are two different genome editing tools, much like scissors and a pencil.”

Scientists from the US have designed high-performance, low-error DNA editors that can selectively transfigure a single DNA building block to another. This technology fills a gap in genome editing that even CRISPR/Cas9 could not, further raising hopes for a world where disease-causing mutations can be corrected without fear.

The building blocks that chain together to make DNA are called nucleotide bases. They come in four types: adenine (A), guanine (G), thymine (T) and cytosine (C). DNA exists in the form of two chains of nucleotides wound in a double helix shape. The second chain is complementary to the first: for every A in the first strand. there is a T in the second and vice-versa. Similarly, for every G in the first strand, there is a C in the parallel strand. The two chains are held together by bonds that pair the As to the Ts and the Cs to the Gs.

The four bases must exist in a specific sequence for the human body to function properly. Most mutations are harmless but a few are responsible for genetic diseases that are largely considered incurable. Therefore, molecular biologists have been on a mission to devise techniques that will allow dangerous mutations to be corrected.

Though most diseases are linked to multiple sections of DNA, there are several that arise due to a mutation in a single base. These point mutations are called single nucleotide polymorphisms (SNPs). With diseases that are caused by SNPs, it’s just a matter of converting the ‘wrong’ base to the ‘right’ base – and this is called base editing.

A complete base editing toolkit should cover techniques to allow correcting all types of SNPs. In other words, we need chemical processes that can turn one nucleotide into any of the other three. Last year, a team of chemical biologists led by David R. Liu from the Broad Institute, at the Massachusetts Institute of Technology, and Harvard University got us halfway there. They described a way to use an existing enzyme that could chemically convert C to T. Since Cs exist as either a C-G base pair or a G-C base pair, this meant that Liu’s technique could correct C-G → T-A as well as G-C → A-T. All that remained to complete this toolkit was a technique that could convert A to G.

Theoretically, this should have been simple to devise. C/T and A/G are chemically quite similar, so all that scientists needed was another enzyme. However, the problem was that there is no enzyme known that can convert a molecule of ‘A’ to a molecule of ‘G’. So Liu and team had to design a solution for this themselves. This week, they announced that they had finally succeeded in developing a new class of adenine base editors (ABEs) that allow A-T → G-C and T-A → C-G transformations.

The ingredients for the toolkit are all finally at hand.

This discovery is a significant step forward because C-G to T-A mutations account for approximately half of all known disease-causing SNPs, including several that are specific to the Indian population. Ramkumar Sambasivan, who studies embryonic development at InStem, Bengaluru, told The Wire that adopting the base editing technology will help advance studies on such SNPs in India.

The ABEs developed by Liu in this new finding work relatively well (about 50% efficiency) in bacterial as well as human cells. More importantly, they do their jobs with minimum collateral damage; for example, off-target mutations are one of the chief concerns about current gene-editing techniques. “These ABEs advance the field of genome editing by enabling the direct installation of all four transition mutations at target loci in living cells with a minimum of undesired byproducts,” they wrote in their paper, published on October 25 in the journal Nature.

To really explore the potential of their newly developed ABEs in disease correction, Liu and team tested them on human cells. The base editors kept their hopes alive. “We used ABE to install two mutations that suppress the effects of some blood diseases such as sickle cell anaemia,” he said. They were also able to correct an iron-storage disorder called hereditary haemochromatosis, commonly caused by a G to A mutation. “These examples demonstrate the potential of ABEs to correct disease-driving mutations, and to install mutations known to suppress genetic disease phenotypes, in human cells,” the scientists concluded.

As with all gene editing discoveries, hurdles both technical and ethical remain. Sambasivan calls this is a great beginning – but reminds us that issues that other researchers are grappling with still persist. “These base-editors have to be delivered correctly to affected cells in the body of patients, or else the base editing has to be done in the dish outside the body and then the ‘corrected’ cells have to be introduced back into patients.” Liu agreed that delivery of these editing agents and verifying safety and efficacy in animal models, as well as in clinical trials, are significant challenges.

There has been some talk on whether base-editing can replace CRISPR/Cas9 – the latter being the gene-editing technology that has taken over the field in the last five years. Liu brushed off the idea. “CRISPR/Cas9 and base editing are two different genome editing tools, much like scissors and a pencil. For some tasks, scissors are the best tool. For other tasks, like correcting a single letter in a cell’s DNA, the pencil is best. So it’s not correct to say that base editing will replace other CRISPR technologies. Rather, they are complementary tools,” he clarified.