The state of the art in genome editing just got reset yesterday.
You’ve probably heard a lot about CRISPR and all of its potential for curing diseases and making better crops. But if you haven’t gotten around to reading much about it yet, don’t worry, because it’s just been surpassed by something called “prime editing”.
This will be the No. 1 story in biotechnology circles for the foreseeable future. It’s the biggest thing since … well, CRISPR.
Prime editing won’t cure genetic diseases all by itself (so let’s not get too sprazzy in the comments), but in the battle against these diseases, I’m telling you, Harvard/Broad Institute professor David Liu just hit postdoc Andrew Anzalone with an 80-yard touchdown pass.
Science magazine had this to say:
Fyodor Urnov, scientific director at the Innovative Genomics Institute in Berkeley, California, reviewed the paper for Nature and says it brought “one of those ‘yay, science!’ kind of moments.” Prime editing “well may become the way that disease-causing mutations are repaired,” he says. But, he adds, it’s too soon to be sure. The technique “just showed up this year.”
NPR chimes in with some fun quotes too:
"Prime editing is really a step — and potentially a significant step — towards this long-term aspiration of the field in which we are trying to be able to make just about any kind of DNA change that anyone wants at just about any site in the human genome," Liu says. [...]
"Prime editing may be a game changer," says Maria Jasin, a molecular biologist at the Memorial Sloan-Kettering Cancer Institute.
"It is a moment to stand up and cheer," agrees Fyodor Urnov, a geneticist at the University of California, Berkeley.
"For gene editors this feels a little bit like a new Avenger has joined our team. Someone who brings a super power that is needed for the field. Excited would be an understatement," Urnov says.
Here’s the basic difference between CRISPR and prime editing. Let’s say you’re typing up a document and you make a little mistake:
Sometimes when a cell replicates DNA, it makes little mistakes, too, and they can be more than just embarrassing.
If you use CRISPR to correct a mistake like this, and let’s say you try it three times, here’s what you might get:
And there’s the frustration with CRISPR. Sure, it gets rid of the bad word, but you’re never quite sure what it’s going to replace it with. You can certainly destroy the function of a gene this way, but that’s about all you can do.
Prime editing, though, will get it right, and seldom give you any surprises. You will get your “paradigm shift”.
That’s obviously important for therapeutic applications, where there isn’t much room for error.
Some diseases are caused by frustratingly simple and well-known mutations. For example, change ONE LETTER in your entire genome from A to T (in the gene that encodes hemoglobin), and you now have sickle cell anemia:
You can’t use CRISPR to take a random sledgehammer to hemoglobin to try and fix this problem. If you knock out hemoglobin, you’re toast.
If we could only change that one stupid letter somehow!
The Liu team used prime editing to make this precise change (from T back to A) in a real human cell, within a sickle cell hemoglobin gene, and it worked! They successfully made several other edits to disease-causing genes as well. In fact, they estimate that 89% of known genetic disease variants could be corrected with prime editing.
Delivering the prime editing machinery to the right cells within a real human being is a challenge, of course. There are many parts to this. The thing to remember here is that previously we didn’t have the machinery to do this at all.
But now we do.
This goes way beyond therapeutics, too. If you can make specific changes in a genome, you can do things like this, and you can do it without years and years of breeding:
A lot of characteristics in plants (fruit size, color, pest resistance, herbicide resistance, drought resistance, etc.) have known mutations in known genes. The problem up to now is that there’s been no way to introduce them into your variety without years of breeding. Or, if you’re an orange grower who’s intrigued by a well-characterized tomato trait? Well, too bad. Can’t breed tomatoes and oranges.
But prime editing allows this kind of thing. You know what change you want to make, so you can just make it and see what it does. The best part is that you wind up with plants that are non-GMO. There are no foreign genes, just changes to the plant’s own genes that could have occurred naturally but that would have taken you a zillion years to isolate.
CRISPR doesn’t allow any of this. All CRISPR can do is wreck things.
But let’s not bash CRISPR too much. Bacteria invented CRISPR, and it’s a godsend for defending themselves against viruses and other nasty invaders. Bacteria collect snippets of DNA they don’t recognize, and they pin those onto a little bulletin board of WANTED photos (the CRISPR array). They make RNA out of each offending DNA snippet and attach that RNA to a killer protein called Cas9 that has one mission: go cut up DNA! Because the RNA was copied from offending DNA, it will only bind to that offending DNA sequence. The RNA “guides” the killer protein to that specific DNA sequence, wherever it may be in the cell, and Cas9 takes it out. The invader is foiled.
Cas9 cuts DNA in half! Whack! Brutal! But all the bacteria want is to chop up their enemies.
If you chop up DNA in an animal or plant cell using Cas9, though, you’re leaving it to the cell to figure out how to repair it, which it usually does, but by haphazardly shoving it back together, plus or minus a few letters. In the end, you get what you get. Shiglyt.
Prime editing makes a few key changes. First of all, it uses a half-inactive version of Cas9 that only cuts one strand of the DNA. We just want to unzip it, not snap it in half! That type of Cas9 is called a “nickase” because it “nicks” the DNA:
We still have our guide RNA attached to Cas9 so we can find the DNA target. But we add two things: another piece of RNA that spells out the new sequence we want to insert, and a protein called RT (Reverse Transcriptase, not Russia Today!) that makes DNA from an RNA template. So the RT uses our extra piece of RNA to make the DNA we want to insert, and in a complicated little ballet, the new DNA replaces the old. The cell repairs the whole thing, but mostly without any haphazard nonsense.
If you are into molecular biology at all, you’ll want to know a little more, so I’d recommend especially Figure 1c in the paper, which is too tiny below, but you see that it lays out the mechanism better than I can attempt to explain here:
So what’s David Liu up to now?
In September, he cofounded a company called Prime Medicine that has licensed the technology from the Broad Institute to develop treatments for genetic disease.
If that company has phones yet, I promise they are ringing off the hook.
Liu unveiled the technology at a genome editing conference ten days ago at the Cold Spring Harbor Laboratory, in front of a rapt audience of nearly 400 scientists. He closed his talk by saying, “I’m really looking forward to seeing what Andrew comes up with in the second year of his postdoc!”