CRISPR “Base Editors” Promise to Treat Diseases With Novel DNA, RNA Fixes

The discovery of the CRISPR gene-editing system five years ago began a transformative era in molecular biology, opening up new horizons for researchers in a myriad of fields. Last week, two studies extended CRISPR’s reach by presenting new ways to efficiently and precisely modify genetic material. One report, published in Nature, presents a method for editing DNA without cutting the double helix, while another, in Science, outlines a new approach for editing RNA to repair mutations without permanently altering the genome.

For CRISPR DNA editing, scientists developed a tool called Adenine Base Editor, or ABE, that can directly repair the type of single-letter changes in the human genome that account for about half of human disease-associated point mutations, according to the researchers. The new system can be programmed to target specific base pairs in a genome using a guide RNA and ABE, fused to a modified form of CRISPR-Cas9 to repair mutations that cause a wide range of disorders, including genetic blindness, sickle-cell anemia,  metabolic disorders, and cystic fibrosis.

This new molecular tool can convert the DNA base pair A•T to G•C with high efficiency, without cutting the double helix, and without undesired byproducts, David Liu, Professor of Chemistry and Chemical Biology at Harvard University and a member at the Broad Institute, who lead the research team, said in a news release.

In addition to the system being very efficient compared with other genome editing techniques for correcting point mutations, it also produces virtually no detectable byproducts, such as random insertions, deletions, translocations, or other base-to-base conversions, the team said.

ABE “can rearrange the atoms in a target adenine (A) — one of the four bases that make up DNA — to instead resemble guanine (G), and then tricking cells into fixing the other DNA strand to complete the base pair conversion, making the change permanent,” the researchers said. The A•T base pair thus becomes a G•C base pair.

ABE can fix the misspellings of about half of the 32.000 known disease-causing, single-letter mutations identified by researchers. “We developed a new base editor — a molecular machine — that in a programmable, irreversible, efficient, and clean manner can correct these mutations in the genome of living cells,” Liu said. “When targeted to certain sites in human genomic DNA, this conversion reverses the mutation that is associated with a particular disease.”

In a paper published in Science, researchers announced an RNA-editing system for  altering gene products without making changes to the genome.

Called RNA Editing for Programmable A to I Replacement, or REPAIR, the system can change single RNA nucleotides in mammalian cells in a programmable and precise fashion. REPAIR has the ability to reverse disease-causing mutations at the RNA level, and can also be used in other potential therapeutic and basic science applications.;

“The ability to correct disease-causing mutations is one of the primary goals of genome editing,” said the paper’s senior author, Feng Zhang, a member at the Broad Institute and investigator at the McGovern Institute for Brain Research at MIT. “So far, we’ve gotten very good at inactivating genes, but actually recovering lost protein function is much more challenging. This new ability to edit RNA opens up more potential opportunities to recover that function and treat many diseases, in almost any kind of cell.”

REPAIR can target individual RNA letters, or nucleosides, switching adenosines to inosines (read as guanosines by the cell). Researchers said that, unlike the permanent changes to the genome required for DNA editing, this RNA editing method offers a safer, more flexible way to make corrections in the cell.

“REPAIR can fix mutations without tampering with the genome, and because RNA naturally degrades, it’s a potentially reversible fix,” David Cox, a co-author of the study and a graduate student in Zhang’s lab, said in a news release.

Gene editing of disease is in the early stages of development, but offers tremendous promise. Researchers will no doubt use these new methods to open up new battles in the fight against the many diseases they are capable of addressing, enabled by the use of high-throughput DNA synthesis capabilities such as those from Twist Bioscience.

“One reason these are so exciting is, they show the CRISPR toolbox is still growing,”  Gene Yeo, a chemical engineer at the University of California, San Diego, told STAT. “There are going to be a lot more, and it’s not going to stop anytime soon.”