4 ms·

Having worked with this technology, there is a ton of hype. This is NOT easy. First of all you cannot target any sequence; it must match a certain consensus pa

Having worked with this technology, there is a ton of hype. This is NOT easy. First of all you cannot target any sequence; it must match a certain consensus pattern. Second, while cutting is easy (to delete or knock out a gene), introducing a substitution is hard and requires a lot of chance. Third, the process is extremely noisy. You cannot guarantee your edit will occur. Usually you must verify by resequencing, which is actually worse than shRNA. Finally we are far away from full body gene therapy this way, which would involve delivering a CRISPR kit to every cell. In short this is a powerful experimental tool but it is extremely far from freely editing the genome.

untilHellbanned 11y ago
Agreed. Biologist here who uses CRISPR too. Gene therapy is limited by getting the DNA into the right cell and having it only do the genome manipulation you want and nothing more. This was hard before and will continue to be hard. That said, it is an amazing advance. There is good reason for excitement.
deleted 11y ago
[deleted]
defen 11y ago
> Finally we are far away from full body gene therapy this way, which would involve delivering a CRISPR kit to every cell. My layman's understanding of the situation is that the most likely first use of this in humans will be for personal eugenics of one's offspring. Meaning, removing deleterious genes from, or adding beneficial ones to, your sperm or egg cells in a lab and then implanting an embryo.
- OopsCriticality 11y ago
  > My layman's understanding of the situation is that the most likely first use of this in humans will be for personal eugenics of one's offspring. Meaning, removing deleterious genes from, or adding beneficial ones to, your sperm or egg cells in a lab and then implanting an embryo. My non-layman's prediction is that you are quite incorrect. As others are pointing out, successfully using CRISPER/Cas is hardly as trivial or as easy as the media's hype machine (or university PR offices) would like us to believe. Blatantly obvious ethical issues aside, embryos are hard to tamper with, and the odds of successfully achieving multiple edits to the genome are miniscule. I think the most likely first application of the CRISPER/Cas system in human medicine will be in an autologous bone marrow transplant to correct a genetic disorder of the blood, likely sickle-cell anemia.
  - defen 11y ago
    > Blatantly obvious ethical issues aside, embryos are hard to tamper with I'm not suggesting tampering with an embryo - rather, editing the sperm or egg cells. I don't think the ethics is going to stop people when there is a chance of giving your offspring a significant advantage. But like I said, this is purely from an "outside" perspective - I don't know much about the field.
    - OopsCriticality 11y ago
      I'm fairly certain editing sperm or eggs is going to be even more challenging than an embryo---think of the effects of meiosis alone. Contrast your prediction of elective eugenics for offspring with my own for autologous bone marrow transplants for sickle cell anemia: sickle cell is a single point mutation, there's a lot of tissue that we can sequence and work with, you don't need to transform anywhere near 100% of the tissue to get a good therapeutic effect, and we already do cure sickle cell anemia with bone marrow transplants given the right circumstances. All of that is in part why I think you are completely wrong with your prediction.
  - ejlperello 11y ago
    My take is that we will see it used on cell therapies like CAR-T. Id point out that Novartis and Intellia have signed a deal to this effect - see link below. Immunotherapy is likely a clear win for this kind of genome editing technology. Any sort of ex vivo modification and repatriation of cells (like bone marrow transplants) are a good fit. Personal eugenics is extremely unlikely in the West. It is also very far away because of this regulatory burden. Id just point out that there are cases where you might find this kind of thing permissible. For instance the other day a friend of mine who went through IVF with his wife said "imagine if we had one good embryo from three rounds of IVF, and that one embryo had cystic fibrosis - would you really be comfortable stopping me from repairing that?" I found it hard to say "yes we should stop that". But I also recognise that if we allow that, its only a small leap to allow anyone to edit anything they want, for whatever reason. Drawing the lines will be tough. For the deal I mentioned: http://www.xconomy.com/boston/2015/01/07/cart-crispr-1st-of-its-kind-biotech-deal-from-novartis-intellia/ http://www.xconomy.com/boston/2015/01/07/cart-crispr-1st-of-...
dave_sullivan 11y ago
Question for anyone working with CRISPR... What's the current state of the art for using computers to model or simulate how a gene change will impact the rest of an organism? Separate but related, if you were to collect data on that sort of thing during an experiment, how would you? I assume there's quite a bit of variation depending on experiment goal... Is imaging technology to the point where you can record what happens as video?
- scottish-alien 11y ago
  Your questions aren't specific for people working with CRISPR, but more generally relate to gene-editing. Unfortunately, molecular biology and genetics are immensely complex, once you start looking in to them. There very rarely is a 1:1 correlation between one gene and one single function of impact on the entire organism (even for single celled organisms). Moreover, in many cases loss of one gene can be compensated by the function of one or multiple different protein(s). To be fair, I haven't looked up any literature on computer models of how the change of one a single gene would influence the whole organism. However, that is a very complicated question. The closest analogy I can give you is "are there computer models how changing a resistor/capacitor will impact the quality of the picture of my TV?" Frankly, it's often hard to tell how the (novel) change of a single gene will influence a single cell! Regarding your second question: the data you want to collect is always related to the question your asking about the gene at hand. "How does loss of gene X impact cognitive capacity" would obviously require a completely different experimental set-up than asking "Which functional role does gene X fulfil in the immune system". Sorry I can't give a more satisfying answer. On a slightly related note, this article gives some insight on how biologists think and go about their experimental design and recording what they learn: http://math.arizona.edu/~jwatkins/canabiologistfixaradio.pdf http://math.arizona.edu/~jwatkins/canabiologistfixaradio.pdf
- pak 11y ago
  This is actually something one of my thesis committee members worked on. http://www.cell.com/abstract/S0092-8674(12)00776-3 http://www.cell.com/abstract/S0092-8674(12)00776-3 In silico whole cell models are an extremely new concept, and his study demonstrated its capabilities for one small bacterium. Needless to say, we have a long way to go before we can make top-down simulations of multicellular organisms, much less one as complex as a human. There are many people trying to generate "good enough" simulations for certain human diseases though, by modeling interactions between genes and biomolecules among a few tissues within the relevant organ system. With regard to your second question, there are many "omics" assays that can now capture e.g. every mRNA, every protein, etc. at a given timepoint but you have to kill the cells. Fluorescence microscopy can work for "movie-like" time resolution on a live cell but you have to label the cellular elements with stains or antibodies and you can only utilize so many of those simultaneously on a single sample (1-5 is typical).
ccvannorman 11y ago
astazangasta, what did you do in this sector? I am moving into this space and get a foothold -- specifically I want to work on 3-D simulations for cells and gene manipulation.. :-] (coming from game development)

untilHellbanned 11y ago

Agreed. Biologist here who uses CRISPR too. Gene therapy is limited by getting the DNA into the right cell and having it only do the genome manipulation you want and nothing more. This was hard before and will continue to be hard. That said, it is an amazing advance. There is good reason for excitement.

deleted 11y ago

[deleted]

defen 11y ago

> Finally we are far away from full body gene therapy this way, which would involve delivering a CRISPR kit to every cell. My layman's understanding of the situation is that the most likely first use of this in humans will be for personal eugenics of one's offspring. Meaning, removing deleterious genes from, or adding beneficial ones to, your sperm or egg cells in a lab and then implanting an embryo.

OopsCriticality 11y ago
> My layman's understanding of the situation is that the most likely first use of this in humans will be for personal eugenics of one's offspring. Meaning, removing deleterious genes from, or adding beneficial ones to, your sperm or egg cells in a lab and then implanting an embryo. My non-layman's prediction is that you are quite incorrect. As others are pointing out, successfully using CRISPER/Cas is hardly as trivial or as easy as the media's hype machine (or university PR offices) would like us to believe. Blatantly obvious ethical issues aside, embryos are hard to tamper with, and the odds of successfully achieving multiple edits to the genome are miniscule. I think the most likely first application of the CRISPER/Cas system in human medicine will be in an autologous bone marrow transplant to correct a genetic disorder of the blood, likely sickle-cell anemia.
- defen 11y ago
  > Blatantly obvious ethical issues aside, embryos are hard to tamper with I'm not suggesting tampering with an embryo - rather, editing the sperm or egg cells. I don't think the ethics is going to stop people when there is a chance of giving your offspring a significant advantage. But like I said, this is purely from an "outside" perspective - I don't know much about the field.
  - OopsCriticality 11y ago
    I'm fairly certain editing sperm or eggs is going to be even more challenging than an embryo---think of the effects of meiosis alone. Contrast your prediction of elective eugenics for offspring with my own for autologous bone marrow transplants for sickle cell anemia: sickle cell is a single point mutation, there's a lot of tissue that we can sequence and work with, you don't need to transform anywhere near 100% of the tissue to get a good therapeutic effect, and we already do cure sickle cell anemia with bone marrow transplants given the right circumstances. All of that is in part why I think you are completely wrong with your prediction.
- ejlperello 11y ago
  My take is that we will see it used on cell therapies like CAR-T. Id point out that Novartis and Intellia have signed a deal to this effect - see link below. Immunotherapy is likely a clear win for this kind of genome editing technology. Any sort of ex vivo modification and repatriation of cells (like bone marrow transplants) are a good fit. Personal eugenics is extremely unlikely in the West. It is also very far away because of this regulatory burden. Id just point out that there are cases where you might find this kind of thing permissible. For instance the other day a friend of mine who went through IVF with his wife said "imagine if we had one good embryo from three rounds of IVF, and that one embryo had cystic fibrosis - would you really be comfortable stopping me from repairing that?" I found it hard to say "yes we should stop that". But I also recognise that if we allow that, its only a small leap to allow anyone to edit anything they want, for whatever reason. Drawing the lines will be tough. For the deal I mentioned: http://www.xconomy.com/boston/2015/01/07/cart-crispr-1st-of-its-kind-biotech-deal-from-novartis-intellia/ http://www.xconomy.com/boston/2015/01/07/cart-crispr-1st-of-...

dave_sullivan 11y ago

Question for anyone working with CRISPR... What's the current state of the art for using computers to model or simulate how a gene change will impact the rest of an organism? Separate but related, if you were to collect data on that sort of thing during an experiment, how would you? I assume there's quite a bit of variation depending on experiment goal... Is imaging technology to the point where you can record what happens as video?

scottish-alien 11y ago
Your questions aren't specific for people working with CRISPR, but more generally relate to gene-editing. Unfortunately, molecular biology and genetics are immensely complex, once you start looking in to them. There very rarely is a 1:1 correlation between one gene and one single function of impact on the entire organism (even for single celled organisms). Moreover, in many cases loss of one gene can be compensated by the function of one or multiple different protein(s). To be fair, I haven't looked up any literature on computer models of how the change of one a single gene would influence the whole organism. However, that is a very complicated question. The closest analogy I can give you is "are there computer models how changing a resistor/capacitor will impact the quality of the picture of my TV?" Frankly, it's often hard to tell how the (novel) change of a single gene will influence a single cell! Regarding your second question: the data you want to collect is always related to the question your asking about the gene at hand. "How does loss of gene X impact cognitive capacity" would obviously require a completely different experimental set-up than asking "Which functional role does gene X fulfil in the immune system". Sorry I can't give a more satisfying answer. On a slightly related note, this article gives some insight on how biologists think and go about their experimental design and recording what they learn: http://math.arizona.edu/~jwatkins/canabiologistfixaradio.pdf http://math.arizona.edu/~jwatkins/canabiologistfixaradio.pdf
pak 11y ago
This is actually something one of my thesis committee members worked on. http://www.cell.com/abstract/S0092-8674(12)00776-3 http://www.cell.com/abstract/S0092-8674(12)00776-3 In silico whole cell models are an extremely new concept, and his study demonstrated its capabilities for one small bacterium. Needless to say, we have a long way to go before we can make top-down simulations of multicellular organisms, much less one as complex as a human. There are many people trying to generate "good enough" simulations for certain human diseases though, by modeling interactions between genes and biomolecules among a few tissues within the relevant organ system. With regard to your second question, there are many "omics" assays that can now capture e.g. every mRNA, every protein, etc. at a given timepoint but you have to kill the cells. Fluorescence microscopy can work for "movie-like" time resolution on a live cell but you have to label the cellular elements with stains or antibodies and you can only utilize so many of those simultaneously on a single sample (1-5 is typical).

ccvannorman 11y ago

astazangasta, what did you do in this sector? I am moving into this space and get a foothold -- specifically I want to work on 3-D simulations for cells and gene manipulation.. :-] (coming from game development)