The title in Nature: “Programmable base editing of A•T to G•C in genomic DNA without DNA cleavage”
A brief description of what was accomplished (a modification of cas9): “We evolved a tRNA adenosine deaminase to operate on DNA when fused to a catalytically impaired CRISPR-Cas9. Extensive directed evolution and protein engineering resulted in seventh-generation ABEs (e.g., ABE7.10), that convert target A•T to G•C base pairs efficiently (~50% in human cells) with very high product purity (typically ≥ 99.9%) and very low rates of indels (typically ≤ 0.1%).“
Translation: they modified the CRISPR associated DNA editing enzyme, cas9, to “deaminate” (remove or otherwise alter the amino groups) in A-T or G-C pairs without breaking the DNA, as cas9 normally would.
This makes single point precision edits possible, but I’m not sure what that implies for the “guide RNA” cas9 needs to know where to make the edits, as I haven’t read the paper in full yet.
I'm definitely getting into hair-splitting territory, but I think it's important to not conflate modifying a protein with fusing two proteins. It would be easy to come away from the GP and think that scientists have the ability to easily change the enzymatic function of Cas9, when in reality they're effectively just connecting a protein to Cas9 and letting it do its thing.
While direct editing of bases will be a really useful tool, I think it's worth pointing out to any alarmists about human editing that our ability to make directed changes far outpaces our knowledge of what changes to make (and our ability to make reasonable guesses about how safe those changes are). Although there are a relative handful of diseases that have a single, protein coding change that's responsible (sickle cell, cystic fibrosis, etc), most diseases are due to multiple variants, many of which are non-coding, interacting with environmental factors and chance (diabetes, obesity, depression). These kinds of tools are incredibly useful in the lab for making advances in understanding disease, but we're a long way off from widespread clinical use, if that is even in the cards.
CRISPR has arrived at a time when we're also making huge advances in bioinformatics and machine learning. When you've got a reliable tool for editing DNA, many biology problems reduce to software problems. The big risks and big opportunities reflect the synergy of multiple technologies. CRISPR alone is a useful curio, but CRISPR plus high-throughput sequencing plus shared genome databases plus ASIC-based machine learning is something else entirely.
It's also worth considering that conventional western standards of ethics and acceptable risk won't necessarily be a constraining factor on the development of genetic engineering over the next few decades.
I'm with you on single base edits being mostly not applicable to humans clinically, but...
"our ability to make directed changes far outpaces our knowledge of what changes to make"
On this point I couldn't disagree more. It's the opposite: our knowledge of what changes to make is years ahead of being able to make those changes. The polygenic scores available for complex traits now, though crude, are within an order of magnitude of what correlations will ever be possible.
For example, the best PGS for educational achievement explains somewhere around ~10% of variance, which corresponds to a correlation of ~32%, and the total heritability is only something like ~75%, meaning the best possible correlation would be ~87%. Anything you can do with a 87% correlation, you can also do with a 32% correlation, and get a proportionately weaker effect.
Of course, there are still many unanswered questions about which SNPs are really causal, and the tradeoffs associated with editing them, but you don't really _need_ this to make edits that are much more likely to help than hurt. As long as you stay within the bounds of what could have happened naturally by chance, the risk really isn't big.
The real problem is that you have to make a _lot_ of edits, and the editing technologies aren't ready for that. I don't know an exact number, but you might be looking at 100s of edits in a single embryo to do anything noticeable. Traditional double-stranded-break CRISPR can't even do 1 edit without usually causing some major damage. Base editing looks better, but still can only do a small proportion of all possible edits.
In conclusion, if you could print an arbitrary human genome, you'd see some pretty sci-fi stuff even today. But we're pretty far off that.
Clinical use is definitely coming, no argument there. What I am arguing is that most people don't have any medical issues that are worth the risks, expense, and ethical considerations of gene editing. I'd also doubt that will change much in the lifetime of anyone alive today.
> our ability to make directed changes far outpaces our knowledge of what changes to make (and our ability to make reasonable guesses about how safe those changes are)
But won't ability to make changes lead to better knowledge of wehat these changes do? E.g. it would make it easier to perform experiments (on non-human species, one would hope) where changes are made and the results studied.
I'm more terrified of bioweapons targeted at people with some specific gene and attached to a flu virus. Genocide at a push of a button, orders of magnitude cheaper than a nuclear weapon, no materials other than standard lab equipment needed. Bond villains, rejoice!
Any reason to hope we won't be able to do this for another hundred years? Because CRISPR seems awfully close.
How would you prevent natural mutations from modifying or disabling the target mechanism? If you can't guarantee its integrity, the descendants of your air-born killer virus will be back for you in short order. That, rather than inability to do it, is what will hopefully prevent it.
* In order to get CRISPR to fit inside a virus you have to remove all the viral DNA, so it can't reproduce.
* Even if you could make such a virus, there would be enormous selective pressure to ditch the CRISPR proteins, and there's no pressure maintaining the CRISPR or guide RNA sequence, so it would be inactive pretty quickly
* Race isn't well-defined genetically so it might not even be possible to target a group of interest
* Bombs are cheap and a proven technology
I too have some bad genes that make life pretty challenging at times. This type of tech gives me great hope. I wish I were more qualified to work on it and advance it.
I'm sorry to be trying to take away your hope but I just don't see the path from CRISPR to gene therapy that can cure diseases in adults. CRISPR allows scientists to modify DNA in individual cells in a lab setting. But it doesn't help with mass editing DNA in cells throughout the body. I've heard of experiments where they take white blood cells, edit their DNA, and then reinject them. But there's currently no way to modify the genes in-place in a person's retina for example.
Actually, the retina is one of the few places that gene therapy has been really successful. Adeno associated virus can be injected, and it has a fairly conservative safety profile (for instance, it doesn't normally integrate into the genome).
There is actually a large controversy where one half of people who care think they are non living and the other half of people who care think they _are_ living.
That's extremely far from the truth. The entire CRISPR field is focused heavily on being able to mass edit genes in adults in fact.
The three major CRISPR companies, Berkeley and Broad are all focused on pushing the technology there. It's not a question of if, it's inevitable. They already know it can be done, the challenge is scaling it up and constantly improving the accuracy and the overall command they have of what eg Cpf1 can do (in the case of Broad & Editas).
A very large percentage of all disease occurs in adults after the age of ~30. That is, well after the person is an adult. Take a look at the disease targets that Editas, Intellia and Crispr Therapeutics are pursuing: they're going after adult diseases long-term, including targeting things such as diseases of the liver more near-term (next five years). Most of their initial targets are focused on easier (relative term) editing targets, the retina being a popular target due to the genes there. First they'll learn to crawl, then walk, then run.
You don't have to edit all the genes in the body to cure most genetic diseases.
>"That's extremely far from the truth. The entire CRISPR field is focused heavily on being able to mass edit genes in adults in fact."
It doesn't seem so to me. I've noticed less and less focus on toxicity lately, as if they've given up on that. For example, I took a look at one of the papers[1] from TFA. All they look at is percent of sequences from surviving cells that contained the A->G mutation. They don't report how many cells died during the process to get there.
Also, they see these mutations in the control group too (figure 4 untreated A5 = 99.8), so it seems this may be yet another way to use crispr to select for pre-existing mutants. It's hard to say since no info is provided on the toxicity for this new strategy.
On the other hand, the new strategy may be less toxic since it is only supposed to introduce a single strand break rather than double (ie as opposed to cas9). Reviewers should be on this, not sure why they so consistently drop the ball regarding the role of toxicity in these studies.
Yes, this is correct. We develop from a single cell, and many complex tissues ultimately derive from single cells. A single mammary stem cell can recapitulate the entire breast tissue for example. Bone marrow stem cells are able to produce the entire complement of red and white blood cells. If you can edit these stem cells, you will make a big difference to the patient.
I appreciate the comment. It is certainly better to be realistic about hopes.
I think my hope is really more into something like the Ray Kurzweil cellular-sized nano computers that can be injected into the body to perform various functions. As we understand what causes certain "bugs" in bodies, perhaps an effective solution can be developed.
Forgot to add that I expect to see ads for "Company XYZ is hiring node developers to write robust and reliable javascript for our nano-computer platform" because of course the nano-bots will run javascript :-)
Is it enough to edit the genes or is there a need to activate some kind of regenerative process? The body is regenerating all the time but larger changes might require rebuilding from the ground up?
The very earliest targets are ideally large gene punch-out targets, using Cas9. For example that's what Editas is targeting with their first retina program.
To deal with complex, higher order genetic diseases (which is also where the money will be in the field) you'll have to be able to do inserting of healthy replacement genes. Cas9 is not very good at that as of now, it's like using a mallet to tie a fishing line. There is an immense amount of effort going into trying to shoehorn Cas9 into being better at that. Other options such as Cpf1 (and possibly one day CasX/CasY from Berkeley) have been shown to be far superior at more advanced editing.
It depends on when the gene normally expresses. Some genetic disorders result in incorrect development of organs, which means that gene therapy alone will never resolve the issue. Organ donation or surgery plus gene therapy might be a possible cure for some such disorders, though. But if a condition just results in producing too much of a hormone or something like that it could be addressed with just gene therapy.
I love the answer Gene Roddenberry gave regarding a bald TNG captain.
At a press conference about Star Trek: The Next Generation, a reporter asked Star Trek creator Gene Roddenberry about casting Patrick Stewart, commenting that "Surely by the 24th century, they would have found a cure for male pattern baldness." Gene Roddenberry had the perfect response.
I don't really understand it. Is it because they have fixed it to not become bald in the first place (so no cure needed), or is he just saying no one cares about it?
The solution to hair loss, in the next 20-30 years, will be cloning and implantation. Right now they do that from the parts of your head that are resistant to hair loss, using eg the FUE (Follicular Unit Extraction) approach. The obvious step from here is to clone your resistant hair follicle/s, then implant. If we can use a bioreactor to grow various organs on scaffolds now, we're going to be able to clone follicles sooner than later. I'd be surprised if some labs aren't already on this. At scale this will also be a cost-effective approach and extremely safe, it'll make gene editing as a means to combat hair loss pointless for a very, very long time.
A very very different treatment of related issue:
Warning - this is not from any peer reviewed authority.
Also contains things which people will not agree.
Systems, even mechanical systems, have a tendency to harmonize or synchronize. If you put a bunch of metronomes on a moving platform they will start to synchronize. If you put a bunch of people on a swinging bridge their footsteps will synchronize. http://www.redorbit.com/news/science/1112749056/synchronized...
If you start a trend, people will follow it. If you give people the ability to modify their DNA people will start copying each other, reducing gene pool diversity. What may seem like a trendy gene modification could quickly turn out to be disadvantageous, or even deadly. Imagine if everyone found it cool to possess the skinny gene. Skinny genes are currently very popular, especially among hipsters, but what if a worldwide famine comes? Of course it can become crazier than that, as there are trends with injecting cement into posteriors, plastic surgery on faces, injecting toxins into faces, huffing glue...
Even countries with socialized medicine have that. If you're rich and Canadian, you're not going to wait eight months for your procedure, you have other options that money provides. The same is true in most socialized medicine nations. There is almost always a superior therapy or doctor available somewhere in the world if you can afford it.
How are we claiming to be able to precisely edit DNA when we can’t even properly sequence it all yet - from just a couple days ago: [https://news.ycombinator.com/item?id=15534325]?
A brief description of what was accomplished (a modification of cas9): “We evolved a tRNA adenosine deaminase to operate on DNA when fused to a catalytically impaired CRISPR-Cas9. Extensive directed evolution and protein engineering resulted in seventh-generation ABEs (e.g., ABE7.10), that convert target A•T to G•C base pairs efficiently (~50% in human cells) with very high product purity (typically ≥ 99.9%) and very low rates of indels (typically ≤ 0.1%).“
Translation: they modified the CRISPR associated DNA editing enzyme, cas9, to “deaminate” (remove or otherwise alter the amino groups) in A-T or G-C pairs without breaking the DNA, as cas9 normally would.
This makes single point precision edits possible, but I’m not sure what that implies for the “guide RNA” cas9 needs to know where to make the edits, as I haven’t read the paper in full yet.