Novel CRISPR-derived ‘base editors’ surgically alter DNA or RNA, offering new ways to fix mutations

Since the start of the CRISPR craze 5 years ago, scientists have raced to invent ever-more-versatile or efficient variations of this powerful tool, which vastly simplifies the editing of DNA. Two studies published in Science and Nature this week broaden CRISPR’s reach further still, honing a subtler approach to modifying genetic material that’s called base editing. One study extends a strategy for editing DNA, whereas the other breaks new ground by base editing its molecular cousin, RNA.

Both open new avenues for genetic research and even curing diseases. “One shouldn’t view base editors as better than CRISPR—they’re just different,” says David Liu, a chemist at Harvard University who pioneered DNA base editing in a paper in Nature last year and co-authored the latest Nature paper. “It’s like, what’s better, a boat or a car?”

CRISPR, adapted from a primitive bacterial immune system, does its handiwork by first cutting the double-stranded DNA at a target site in a genome. Base editing, in contrast, does not cut the double helix, but instead uses enzymes to precisely rearrange some of the atoms in one of the four bases that make up DNA or RNA, converting the base into a different one without altering the bases around it. That ability greatly increases the options for altering genetic material. “It’s a very worthwhile addition and it’s here to stay,” says CRISPR researcher Erik Sontheimer of the University of Massachusetts Medical School in Worcester.

Many human diseases are caused by the mutation of a single base. CRISPR has difficulty correcting these so-called point mutations efficiently and cleanly, so base editing could provide a more effective approach. After Liu’s initial report, a group in China used DNA base editing to correct a disease-causing mutation in human embryos cloned from a patient with a genetic blood disorder.

Conventional CRISPR uses a guide RNA (gRNA) coupled with an enzyme known as a nuclease, most commonly Cas9, that together attach to a specific stretch of DNA bases; the nuclease then snips the double helix. A cellular repair mechanism attempts to rejoin the cut DNA ends, but occasionally inserts or deletes bases, which turns the DNA code into gibberish and can knock out a targeted gene. “Gene editing based on nucleases is very good at inactivating genes,” says CRISPR researcher Feng Zhang of the Broad Institute in Cambridge, Massachusetts.

Yet CRISPR, he notes, “is less efficient at making precise changes.” To fix a point mutation, a CRISPR-Cas9 system must also introduce a strand of “donor” DNA that has the correct base and then rely on a second cellular mechanism called homology-directed repair (HDR). But HDR works poorly unless cells are dividing, which means this strategy doesn’t function in, say, brain and muscle cells that no longer copy themselves. Even in dividing cells, the donor DNA rarely slots into the cut spot.

Getting to the point of mutations

Base editors borrow from CRISPR’s components—guide RNAs (gRNAs) and Cas9 or other nucleases—but don’t cut the double helix and instead chemically alter single bases with deaminase enzymes such as TadA and ADAR.

Base-editing systems, which borrow heavily from CRISPR’s tool kit, readily work in nondividing cells. DNA has four nucleotide bases—A, C, T, and G—and base editing changes one to another. In Liu’s 2016 study, his team fused gRNA with a “dead” Cas9 (dCas9) that cannot cut the whole double helix but still unzips it at the correct spot. To this complex the researchers tethered an enzyme, APOBEC1, which triggers a series of chemical reactions that ultimately change C to T. DNA’s base-pairing rules, which specify that a T on one DNA strand pairs with an A on the opposite strand, govern a subsequent change. The dCas9 was further modified to nick the unedited strand, which gooses the cell’s DNA repair mechanism into converting the G that originally paired with C into an A that pairs with the new T.

That first DNA base editor could not address the most common point mutations associated with human diseases—accounting for about half—which have A•T where there should be G•C. The new editor from Liu’s group can now make this fix. The team again fused gRNA with a dCas9, but there is no known enzyme that can convert A to G in DNA. So the lab developed one from TadA, an enzyme in the bacterium Escherichia coli. The new enzyme converts A to a base called inosine, or I. Either a cellular repair mechanism or the process of the DNA copying itself then changes the I to a G. “The big deal here is engineering the TadA enzyme to do something fairly unnatural,” says George Church of Harvard, who studies CRISPR. “My hat is off to them.”

Zhang’s team created its RNA base-editor system by fusing gRNA with a different dead nuclease, dCas13, and a natural enzyme that converts A to I in RNA. Unlike in DNA, that’s where the changes stop. The I-containing RNA simply performs as if it had a G in that spot.

Because RNA carries the genetic message from DNA to the cell’s proteinmaking factories, or can directly perform acts such as gene regulation, it, too, is an appealing target for therapies. But an RNA only sticks around in a cell for a short time. That means RNA base editors likely would have to be repeatedly administered to work as a therapeutic, which Zhang and his co-authors suggest may make sense for transient conditions, such as localized inflammation.

Although the short-lived nature of RNA makes base editing less attractive for many therapies, Sontheimer sees an upside, too. “In some ways, it’s safer to work on RNA,” he says. Researchers worry that genome editing could accidentally affect the wrong part of the genome—a change that would be permanent with a DNA base editor. “If there’s some degree of off targeting, you’re not permanently etching those mistakes into the underlying genome” with an RNA base editor, Sontheimer says.

Church says base editing should be evaluated “case-by-case” for whether it offers advantages over CRISPR and other technologies that alter nucleic acids. “People make it sound like [changing bases] was not possible before. In fact it was hard or just inefficient,” he notes.

Zhang and Liu stress that it could be several years before base-editing therapies enter clinical trials—and longer until it’s clear whether the strategy offers advantages over existing gene therapies. “It’s both scientifically short-sighted and long-term incorrect to conclude that base editing is going to be a better way to do human genetic therapy,” Liu says. What’s already clear, however, is that powerful alternatives to standard CRISPR are now in the game.

(Source: Science and AAAS,  by Jon Cohen)

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