Credit: S. Harris/Springer Nature Limited
The future of genome editing technology just began its long journey to full drug approval. The base editor, a new therapeutic designed to permanently change a single letter in a patient’s genetic code at a specific location, is now in phase I of clinical trials in New Zealand for the treatment of familial hypercholesterolemia. The central innovation of base editors is rather than disrupt both strands of DNA, base editors only need to nick one strand to perform precisely. By correcting DNA at a single base location, this technology will create new opportunities to silence, mend, modulate and upregulate genes.
VERVE-101, a liver-targeted PCSK9-silencing base editor, is the product of a collaboration between Verve Therapeutics and Beam Therapeutics. According to MedLine Plus, the PCSK9 gene provides instructions for making a protein that helps regulate the amount of cholesterol in the bloodstream, so silencing this gene reduces the body's cholesterol. The phase 1b trial for the drug started on July 12 of this year, with a goal to enroll 40 patients and present interim data next year.
The base editor is the latest of a surge of zinc-finger nucleases, TALENS, and CRISPR-Cas9-based gene editors to begin clinical trials. CRISPR-Cas9 is the most well-known of these technologies, a natural bacterial defense mechanism now re-engineered for genome editing. Zinc-finger nucleases are artificial proteins also isolated from bacteria that fuse a zinc finger DNA-binding domain to a DNA-cleavage domain, allowing them to cleave DNA sequences at sequence-specific sites. This produced DNA fragments with a known sequence at each end. TALENS (transcription activator-like effector nucleases) are very similar, with a DNA-cleaving nuclease fused to a DNA-binding domain, but it's DNA-cleaving nuclease is non-specific.
Base editors have a slightly different makeup. Like CRISPR-Cas9, they require a guide RNA (gRNA) of about 20 base pairs that anchors the nuclease to the right spot on the genome next to its target. Base editors, like CRISPR-Cas9, need teh Cas9 protein to unwind and nick the DNA strand. For base editors however, this Cas-9 protein is modified to only nick one strand. The last component of the base editor is also unique: a deanimase enzyme that changes the base of interest. At the moment, the deanimase is limited to two types of changes (C to T and A to G). However, "the four edits that these can collectively make — by editing either DNA strand — can address over 60% of known pathogenic single-point mutations", says Harvard researcher and Beam co-founder David Liu.
Seems simple, right? Just switching one base at a time can still do a lot. But as with anything in science, it's never that simple.
Drug delivery is a major challenge. At the moment, the dominant delivery methods for these technologies are liver-targeted and ex vivo. Liver-targeted delivery involves packaging the biotech molecule in such a way that the liver will recognize and absorb the payload. Ex vivo refers to a medical procedure in which an organ, cells, or tissue are taken from a living body for a treatment or procedure, and then returned to the living body. Given that these are the options, it's no surprise that "we’re spending now almost as much, if not more, time innovating on the delivery side as on the payload side" says John Evans, CEO of Beam Therapeutics.
As with any gene-editing technology, off-target activity is also a concern. These genome-editing technologies rely on something called a guide RNA that anchors the machinery to the correct spot on the DNA. For reasons that researchers are still trying to understand, the CRISPR machinery will sometimes miss the intended DNA sequence and instead latch onto a different place in the genome. Editing at this "off-target" location can then have unintended and unknown consequences outside of the researchers' control.
Additionally, errors occur when our cells attempt to repair the cut DNA strands. Usually, the in-cell repair team is pretty good at the job. These repair errors happen more often with the standard "cutting" genome editors, like the unmodified CRISPR-Cas9, because they nick both strands of DNA. This gives the in-cell repair team a bigger job and less direction to perform it, so they have to improvise more.
I worked on a short rotation project around CRISPR, with the goal of creating better guide RNAs that would minimize this off-target activity. I can personally attest to how slippery the concept of a "good" guide is because there are so many sequences in the human genome that are identical, luring the editors away from their intended homes. This news is exciting because the technology is simpler and promises more effective, precise functionality.
Thanks for reading! This is my first article, and in order to get the feel of science news writing, it was heavily insprired by the Nature article Base editors hit the clinic.
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