Can someone help me understand the main differences between CRISPR and traditional genetic engineering that has been done for many years now? My understanding is that we've had technologies to selectively modify DNA for some time, but perhaps it hasn't been as targeted or reliable as CRISPR?
One thing that stands out to me (especially from the radiolab episode) is that it sounds like CRISPR isn't just gene editing in the sense of engineering something in a lab; it's gene editing in an already living organism. If DNA is anything like an organism's "source code", once the code is "shipped" (organism is conceived), traditionally we tend to think of that code as being locked/frozen. It sounds like CRISPR is akin to modifying the code live - "in production", so to speak. Is that a fair analogy?
Edit: to explain, when I say "in an already living organism", I'm referring mostly to a developed, multi-celled organism. I understand that traditional techniques also use living cells, but the radiolab episode makes it sound as if a full-grown adult human may someday get a live "DNA upgrade" - at least to applicable portions of the body - via CRISPR, e.g. to remove a genetic predisposition for developing a particular disease. To me, that would be substantially different (in practical application) from genetically engineering something like a gamete or a single-celled bacteria.
Mostly, CRISPR/Cas9 reduces the cost of getting a custom endonuclease (molecular scissors that cut DNA at particular sequences). It is several orders of magnitude cheaper than alternatives, and it is also incredibly quick to set up! This makes it much easier to try more experiments. Also dCas9 (partly or wholly disabled Cas9) can be used to make the system the basis for multiplex gene targeting experiments that can be used to induce entirely new regulatory networks in one step! Wow!
So there is a lot of good but don't forget your question: haven't we had this for a long time? Yes, the techniques are fundamentally the same as others which have been used for a long time. Endonuclease and homologous repair are standard tools in genome engineering. It just costs much less to design custom endonuclease now. It seems like there is a bit too much hype about CRISPR/Cas9 techniques as genome engineering tools--- we are engineering genomes in exactly the same way as before. The scissors have changed but the glue is still endogenous to the organisms that we are engineering.
To my knowledge there has only been one case in which DNA was shipped as code to be the genome of a dead cell. Maybe someday we will be able to write large genomes. Until then nearly all the editing we do will be in living organisms, as it has been forever (even before CRISPR/Cas9).
Well said. I'll add some scientific esoterica, because it parallels software a little: we've even had custom endonuclease services for a while (TALENS[1]), which serve a very similar function. But they were hard to generate and difficult to work with. Companies like Invitrogen even sold a TALEN-making service, costing in the dozens-of-thousands of dollars to generate a TALEN for preclinical drug discovery use.
Then CRISPR came along. It was like the open-sourced, better-performing alternative to the cumbersome, proprietary software. Switching was a no-brainer, and it has handily become the future, if not the mainstream already.
Right. My own PhD work was on designing custom transcription factors to bind to specific sequences (not even with TALENs- it tried to do full molecular dynamics to predict the binding constant for multiple different DNA sequences, which was absurdly expensive). It would have to be re-engineered once for each sequence; with CRISPR, you just provide a matching template sequence.
But CRISPR/Cas9 is not open source. It is proprietary! A half billion year old natural system has been slightly tweaked and is now owned by the discovering groups. It is free for research use and for commercial purposes might still be quite expensive.
Its makes many more organisms tractable, more accurately.
Previously, transgenics was tough mostly because of the difficulty in inserting sequence in the right place doing the right thing. It would take decades to develop the specific organism-specific tools to really change DNA.
>it's gene editing in an already living organism.
True. The thing about older transgenics, is that it was like using a shotgun to build a birdhouse. It was messy and you broke a lot of things to get the one gene where you wanted it. So you had to do a lot of transformations to get it right, and afterwords there was a lot of genetic cleaning up to do.
With CRISPR you can be extremely specific with your targeting, which means you can do things like "gene therapy", which is "patching" DNA in a live organism.
CRISPR performs pattern matching on the DNA sequence immediately preceding the cut location where new sequences are added. While we have had CTRL-X and CTRL-V for awhile (in the other gene modification techniques you alluded to) CRISPR provides a cursor that allows us to precisely control where the CTRL-V takes place.
As for updating "live" code...that's a flawed, but not completely wrong analogy. Other techniques do rely on modifying the genome before "production", and in that sense CRISPR does enable us to edit DNA in cases that would have been impractical before, but it still basically requires performing the modification on each cell individually -- so there are still practical limits on deploying the technique.
Well, for most microorganisms, traditional genetic engineering is perfectly fine. You just create long homology ends and transform the cell and it works peachy keen. (Ironically, the one organism for which this spectacularly fails is E. coli, requiring the lambda-red system).
For 'higher eukarya' the big problem is you can still do the long homology ends, but a competing process is random insertion. Basically (if my understanding is correct), CRISPR reduces the competing process and makes specific insertion of DNA the dominant result. Sometimes, though, having multiple random insertion is not a huge problem.
One thing that stands out to me (especially from the radiolab episode) is that it sounds like CRISPR isn't just gene editing in the sense of engineering something in a lab; it's gene editing in an already living organism. If DNA is anything like an organism's "source code", once the code is "shipped" (organism is conceived), traditionally we tend to think of that code as being locked/frozen. It sounds like CRISPR is akin to modifying the code live - "in production", so to speak. Is that a fair analogy?
Edit: to explain, when I say "in an already living organism", I'm referring mostly to a developed, multi-celled organism. I understand that traditional techniques also use living cells, but the radiolab episode makes it sound as if a full-grown adult human may someday get a live "DNA upgrade" - at least to applicable portions of the body - via CRISPR, e.g. to remove a genetic predisposition for developing a particular disease. To me, that would be substantially different (in practical application) from genetically engineering something like a gamete or a single-celled bacteria.