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Unless I am unaware of something, CRISPR is not yet ready for medical usage. Sure, it is an amazing research tool. But every gene editing trick built on the bac

Unless I am unaware of something, CRISPR is not yet ready for medical usage. Sure, it is an amazing research tool. But every gene editing trick built on the back of this incredibly useful protein (Cas9, that is) has "off-target" effects. These mean that not only do you mutate your target, you cause a whole bunch of other mutations. The future of human genome engineering is almost certainly going to feature CRISPR genes in some capacity, but we just don't have the precision, reliability, and ability to avoid other deleterious mutations yet to do so. Also, as someone working with CRISPR, it isn't quite as easy as it is made to sound. It is relatively easy, but still a lot of work! I guess that is a footnote when it makes the impossible, possible though. We need to keep having these ethics conversations though, so we can use this tool wisely. For further reading I would recommend Jennifer Doudna's "A crack in creation". She is one of the founders of CRISPR as a gene editing tool, and her book is good reading on the topic.

Animats 6y ago
CRISPR isn't quite enough. That's just patching. Direct synthesis of a human sized genome will probably be available at some point. The human genome is about 3 billion base pairs. Largest synthesis so far is 580,000 base pairs. Then we'll need CAD tools. Really good CAD tools.
- vikramkr 6y ago
  Just synthesizing a genome isn't going to get us to designer humans - frankly its already well within the reach of modern technology to synthesize 3 billion bases. You cant just bootstrap from the nucleotide sequence - even in really simple bacteria we have to pop the genome into a pre-prepared genome free cell with the machinery to start working on doing life stuff, and adding the complexity of human epigenetics and a multicellular organism makes that a nonstarter currently. Especially when just editing the genome is so much easier.
  - adrianN 6y ago
    I would be interested in reading some literature about the current problems of plopping a synthesized genome into a vertebrate ovum. Or a simpler multi-cellular species, say C. elegans.
    - vikramkr 6y ago
      This has more to do with the synthesis process itself, but here's a good read [0]. Youll notice most of the problems are around cost and logistics, but if we had the funding of the human genome project, that would be a non issue. I dont know if any articles discussing the epigenetics really exist since the organisms so far are ones where that's not really so much of a problem yet - I don't now of any de novo synthesized efforts in multicellular organisms but perhaps someone has a link (not counting cloning - the epigenetic information is carried along in the transfer). [0] https://www.nature.com/articles/d41586-020-00511-9 https://www.nature.com/articles/d41586-020-00511-9
- dekhn 6y ago
  I can't even imagine why you would want to synthesize and inject a replacement human chromosome (let alone the entire genome). That sounds like a huge waste of time and money, unlikely to achieve any reasonable goal, and prone to far more unintended side effects than localized patching
  - sbierwagen 6y ago
    GWASes have shown that many strongly heritable things that we care about (height, heart attack risk, IQ) are hugely polygenetic, the result of the interaction of thousands of genes: https://en.wikipedia.org/wiki/Genome-wide_association_study#Results https://en.wikipedia.org/wiki/Genome-wide_association_study#... CRISPR is too unreliable and has too many off target effects to move the needle on height. By the time you've made a hundred CRISPR edits to a single genome, you've shot the other chromosomes full of holes. It's only useful for taking out one or two genes, for someone who knows they carry a fatal genetic disease, but still wants to have kids. True designer babies will be done with genome synthesis.
    - dekhn 6y ago
      What you're describing is basically science fiction, far in the future. We have no technology to do what you're describing, nobody is planning on "repairing thousands of genes" to increase somebody's height. I understand it's fun to speculate about this.
      - sbierwagen 6y ago
        Factual statement: "We have no technology to do what you're describing" Correct. We can only assemble synthetic bacteria right now. Synthetic sperm is years away. Synthetic eggs are too complicated, I wonder if they'll ever be made. Synthetic embryos would be true sci-fi stuff, requiring heavy engineering and many breakthroughs. Emotional statement: "nobody is planning on" Human germline engineering inspires strong feelings. I'm sure that the advent of motorized vehicles would have inspired the same strong feelings in horses, if they could have understood what was about to happen to them. Nevertheless.
- anticensor 6y ago
  We will rather need an IDE and decompilers for genetic code.
im3w1l 6y ago
So one thought I had just now: If an asexual organism has both a good and a bad mutation they are intrinsically tied together forever. But with sexual reproduction, chromosome crossover can produce offspring having the good mutation that are also free of the bad one. Maybe we could clean up the off-target mutations using that. Edit: To clarify, I mean somehow inducing crossover in a petri-dish.
McKayDavis 6y ago
> Unless I am unaware of something, CRISPR is not yet ready for medical usage. CRISPR has been used successfully to treat Sickle Cell Anemia in at least one patient. [1] You're spot on though that there are many obstacles to overcome (such as off target effects). CRISPR-Cas is not the answer, but rather just one more tool in the gene editing toolbox, albeit a very powerful one. https://www.npr.org/sections/health-shots/2020/06/23/877543610/a-year-in-1st-patient-to-get-gene-editing-for-sickle-cell-disease-is-thriving https://www.npr.org/sections/health-shots/2020/06/23/8775436...
- ImaCake 6y ago
  Yes, plenty of examples of gene editing in sick adult humans in the literature :) We have done the same with older techniques using zinc finger nucleases (same mechanism, but much more difficult to "program) and also infecting cells with lentivirus (modified HIV) to insert some useful genes. The problem is that none of these has been good enough to implement generally to save lives. Although, the lentivirus infection of T4 killer cells to fight late stage cancers seems to have promise.
sriku 6y ago
I saw a program in which a geneticist described the gene editing precision prior to CRISPR as about 2-3% and after CRISPR as about 50%. That's a big jump, but as you say, what happens in those other 50% cases is of concern too when it comes to humans. Of course, this precision figure can't also be the single metric on which we judge it. However, it's an indicator that we aren't there yet too .. but are certainly moving in the right direction. Supposing we can up the precision to, say, 4 9s - i.e. 99.99%, would that suffice? I don't know enough to say anything, but given the number of cells we typically deal with, the chance of a wrong application proliferating, however small, if it gains an advantage over the intended mutation, what consequences would it have? Disclaimer: I'm curious about this space, but don't know much right now and am just learning up.
- ImaCake 6y ago
  Since you are curious I will try to answer with a bit of a tangent :) But, in short, the real problem is the unintended edits that happen at the same time. Because if you mutate a bunch of stuff in a cell, you will probably end up giving the patient cancer. 99% efficiency is good, but not really essential for many gene therapies. Something Cas9 does really well is find the sequence you program it to look for, and then bind super tightly to it. You can even change your Cas9 so it will no longer break the DNA. Once you do this, Cas9 cannot edit the DNA by itself, but you can add a second enzyme to it that is able to change a single base of DNA from one letter to another. In theory this means you could target a single nucleotide somewhere in the ~3 billion letters of the genome. We call this changed Cas9 "base editor". It is much more refined than the crude DNA breakage of Cas9, since base editor will initiate only one time of edit in the genome (a single letter flipped from A to G or C to T). But it will still have unintended edits! It is pretty trivial to test for these in whole genome sequencing, and it turns out you will get plenty of them. Another problem, which might seem more important, but I think is a much easier fix in the medium term (~10 years). Is that base editor will actually target a region of about 5-6 bases around the intended target and will happily flip those bases too. So you are unlikely to get just your intended mutation. Some of your cells will also get other mutations in the same spot. The reason this is less concerning in the long term is that I think this can be fixed with optimisation of the base editor protein. The off target effects are much more difficult to prevent.
asdff 6y ago
If you actually know the target loci for whatever disease, it's a much more sensible prospect to just put the patient on a drug for life that inhibits whatever that mutation does. If the treatment turns out unsafe, you just take the patient off. With editing the genome you can't really go back if you find out after the fact that you screwed up. CRISPR is a great research tool, but I think in vitro fertilization is fine enough for catching congenital diseases.
- ImaCake 6y ago
  This is a good point, it can be hard to predict what gene does what. Most genes that have been targetted for gene therapies tend to be the singular and known source of a genetic disease. Something like the sodium transporter mutation in cystic fibrosis. If you fix it, it is clear what will happen; you will clear out the disease. Most diseases are not so simple and we are still getting to grips with even mapping the mutations scattered across the genome and the global human population that are relevant to certain diseases. I think when you dont have a single genetic cause, but a mix of various genetic factors instead, then the drug route is optimal. For exactly the reasons you stated.
- Nasrudith 6y ago
  In vitro fertilization isn't anywhere close to ubiquitous let alone screening. Genetic editing isn't cheap either but it is only needed for patients with problems instead of literally everybody born. Technically the issue may or may not be drug "additive" and inhibitable like "stop making this protein" but "start making this with your blood cells".

Animats 6y ago

CRISPR isn't quite enough. That's just patching. Direct synthesis of a human sized genome will probably be available at some point. The human genome is about 3 billion base pairs. Largest synthesis so far is 580,000 base pairs. Then we'll need CAD tools. Really good CAD tools.

vikramkr 6y ago
Just synthesizing a genome isn't going to get us to designer humans - frankly its already well within the reach of modern technology to synthesize 3 billion bases. You cant just bootstrap from the nucleotide sequence - even in really simple bacteria we have to pop the genome into a pre-prepared genome free cell with the machinery to start working on doing life stuff, and adding the complexity of human epigenetics and a multicellular organism makes that a nonstarter currently. Especially when just editing the genome is so much easier.
- adrianN 6y ago
  I would be interested in reading some literature about the current problems of plopping a synthesized genome into a vertebrate ovum. Or a simpler multi-cellular species, say C. elegans.
  - vikramkr 6y ago
    This has more to do with the synthesis process itself, but here's a good read [0]. Youll notice most of the problems are around cost and logistics, but if we had the funding of the human genome project, that would be a non issue. I dont know if any articles discussing the epigenetics really exist since the organisms so far are ones where that's not really so much of a problem yet - I don't now of any de novo synthesized efforts in multicellular organisms but perhaps someone has a link (not counting cloning - the epigenetic information is carried along in the transfer). [0] https://www.nature.com/articles/d41586-020-00511-9 https://www.nature.com/articles/d41586-020-00511-9
dekhn 6y ago
I can't even imagine why you would want to synthesize and inject a replacement human chromosome (let alone the entire genome). That sounds like a huge waste of time and money, unlikely to achieve any reasonable goal, and prone to far more unintended side effects than localized patching
- sbierwagen 6y ago
  GWASes have shown that many strongly heritable things that we care about (height, heart attack risk, IQ) are hugely polygenetic, the result of the interaction of thousands of genes: https://en.wikipedia.org/wiki/Genome-wide_association_study#Results https://en.wikipedia.org/wiki/Genome-wide_association_study#... CRISPR is too unreliable and has too many off target effects to move the needle on height. By the time you've made a hundred CRISPR edits to a single genome, you've shot the other chromosomes full of holes. It's only useful for taking out one or two genes, for someone who knows they carry a fatal genetic disease, but still wants to have kids. True designer babies will be done with genome synthesis.
  - dekhn 6y ago
    What you're describing is basically science fiction, far in the future. We have no technology to do what you're describing, nobody is planning on "repairing thousands of genes" to increase somebody's height. I understand it's fun to speculate about this.
    - sbierwagen 6y ago
      Factual statement: "We have no technology to do what you're describing" Correct. We can only assemble synthetic bacteria right now. Synthetic sperm is years away. Synthetic eggs are too complicated, I wonder if they'll ever be made. Synthetic embryos would be true sci-fi stuff, requiring heavy engineering and many breakthroughs. Emotional statement: "nobody is planning on" Human germline engineering inspires strong feelings. I'm sure that the advent of motorized vehicles would have inspired the same strong feelings in horses, if they could have understood what was about to happen to them. Nevertheless.
anticensor 6y ago
We will rather need an IDE and decompilers for genetic code.

im3w1l 6y ago

So one thought I had just now: If an asexual organism has both a good and a bad mutation they are intrinsically tied together forever. But with sexual reproduction, chromosome crossover can produce offspring having the good mutation that are also free of the bad one. Maybe we could clean up the off-target mutations using that. Edit: To clarify, I mean somehow inducing crossover in a petri-dish.

McKayDavis 6y ago

> Unless I am unaware of something, CRISPR is not yet ready for medical usage. CRISPR has been used successfully to treat Sickle Cell Anemia in at least one patient. [1] You're spot on though that there are many obstacles to overcome (such as off target effects). CRISPR-Cas is not the answer, but rather just one more tool in the gene editing toolbox, albeit a very powerful one. https://www.npr.org/sections/health-shots/2020/06/23/877543610/a-year-in-1st-patient-to-get-gene-editing-for-sickle-cell-disease-is-thriving https://www.npr.org/sections/health-shots/2020/06/23/8775436...

ImaCake 6y ago
Yes, plenty of examples of gene editing in sick adult humans in the literature :) We have done the same with older techniques using zinc finger nucleases (same mechanism, but much more difficult to "program) and also infecting cells with lentivirus (modified HIV) to insert some useful genes. The problem is that none of these has been good enough to implement generally to save lives. Although, the lentivirus infection of T4 killer cells to fight late stage cancers seems to have promise.

sriku 6y ago

I saw a program in which a geneticist described the gene editing precision prior to CRISPR as about 2-3% and after CRISPR as about 50%. That's a big jump, but as you say, what happens in those other 50% cases is of concern too when it comes to humans. Of course, this precision figure can't also be the single metric on which we judge it. However, it's an indicator that we aren't there yet too .. but are certainly moving in the right direction. Supposing we can up the precision to, say, 4 9s - i.e. 99.99%, would that suffice? I don't know enough to say anything, but given the number of cells we typically deal with, the chance of a wrong application proliferating, however small, if it gains an advantage over the intended mutation, what consequences would it have? Disclaimer: I'm curious about this space, but don't know much right now and am just learning up.

ImaCake 6y ago
Since you are curious I will try to answer with a bit of a tangent :) But, in short, the real problem is the unintended edits that happen at the same time. Because if you mutate a bunch of stuff in a cell, you will probably end up giving the patient cancer. 99% efficiency is good, but not really essential for many gene therapies. Something Cas9 does really well is find the sequence you program it to look for, and then bind super tightly to it. You can even change your Cas9 so it will no longer break the DNA. Once you do this, Cas9 cannot edit the DNA by itself, but you can add a second enzyme to it that is able to change a single base of DNA from one letter to another. In theory this means you could target a single nucleotide somewhere in the ~3 billion letters of the genome. We call this changed Cas9 "base editor". It is much more refined than the crude DNA breakage of Cas9, since base editor will initiate only one time of edit in the genome (a single letter flipped from A to G or C to T). But it will still have unintended edits! It is pretty trivial to test for these in whole genome sequencing, and it turns out you will get plenty of them. Another problem, which might seem more important, but I think is a much easier fix in the medium term (~10 years). Is that base editor will actually target a region of about 5-6 bases around the intended target and will happily flip those bases too. So you are unlikely to get just your intended mutation. Some of your cells will also get other mutations in the same spot. The reason this is less concerning in the long term is that I think this can be fixed with optimisation of the base editor protein. The off target effects are much more difficult to prevent.

asdff 6y ago

If you actually know the target loci for whatever disease, it's a much more sensible prospect to just put the patient on a drug for life that inhibits whatever that mutation does. If the treatment turns out unsafe, you just take the patient off. With editing the genome you can't really go back if you find out after the fact that you screwed up. CRISPR is a great research tool, but I think in vitro fertilization is fine enough for catching congenital diseases.

ImaCake 6y ago
This is a good point, it can be hard to predict what gene does what. Most genes that have been targetted for gene therapies tend to be the singular and known source of a genetic disease. Something like the sodium transporter mutation in cystic fibrosis. If you fix it, it is clear what will happen; you will clear out the disease. Most diseases are not so simple and we are still getting to grips with even mapping the mutations scattered across the genome and the global human population that are relevant to certain diseases. I think when you dont have a single genetic cause, but a mix of various genetic factors instead, then the drug route is optimal. For exactly the reasons you stated.
Nasrudith 6y ago
In vitro fertilization isn't anywhere close to ubiquitous let alone screening. Genetic editing isn't cheap either but it is only needed for patients with problems instead of literally everybody born. Technically the issue may or may not be drug "additive" and inhibitable like "stop making this protein" but "start making this with your blood cells".