4 ms·

I would add to that that because most cancer causing (single mutation) variants are in the coding space, it ultimately seems reasonable to be able to revert the

by jfarlow 10y ago

I would add to that that because most cancer causing (single mutation) variants are in the coding space, it ultimately seems reasonable to be able to revert the mutations back to wild type with genome editing tools such as Cas9 in the (decade-ish future?). Using small molecules to fight against cancer as the article speaks to really seems like the last vestiges of a 20th century technology, while designing novel genetic tools like immunotherapies are today's superweapon - tomorrow's is just to fix the mutation. All the more reason to pour money into the DNA side of things (sequencing, synthesis, analysis) over the small molecule side of things ('drug development'.

nonbel 10y ago
>"it ultimately seems reasonable to be able to revert the mutations back to wild type with genome editing tools such as Cas9 in the (decade-ish future?)" What are you basing this on? Have you seen a study where they report "modification" in a living organism using this tech? I highly doubt it, due to toxicity. Also see my post above regarding the presence of aneuploidy and chromosomal instability in cancer cells. How is crispr/cas9 going to fix that?
- jfarlow 10y ago
  >What are you basing this on? Logical extension of how the strategies for technologies like Car-T therapies are being developed and delivered. By first targeting an ex-vivo tissue (like T-cells that can be harvested and then re-implanted), you first develop the tools to use genome editing techniques effectively, without significant off-target effects. It's essentially practice for much more useful therapies that can be done in-vivo. Further, the design of the biological 'sensors' in the T-cells are precisely the kinds of sensors you'd need to deliver a payload to and only to a mutation-containing cell. So you would neither need to target an entire organism (rather a tissue, or even a particular cell type), and off target effects from genomic insertion would be curtailed by advances in the technologies surrounding Cas9 itself. For many cancers you wouldn't need to repair the mutation in the entire organism as the cancer is tissue- or cell-specific. You are correct that you would, however, likely need to repair the prior to significant metastasis or loss of stability of the chromosome. At that point fixing a point mutation is not going to help much. All the more reason screening and baselines should start being established now - so that we can even detect a mutation prior to it becoming 'cancerous'. If you know you have a stop codon mutation in your Her2 gene when you're born, it will not be too far off when that stop codon, in particularly sensitive tissues, could be reverted with reasonable safety prior to the development of an (inevitable) cancer. And ultimately that actually cures the the cancer in a way a small molecule can never, from first principles, hope to do.
  - nonbel 10y ago
    This editing procedure is extremely toxic, and I do not believe this is all due to off-target effects. I found this one quickly, where the paper claimed 80% viability when their data showed something more than half of them "go missing" (impossible to tell more from the chart): https://news.ycombinator.com/item?id=12971533 https://news.ycombinator.com/item?id=12971533 Here is actually one where they injected into Drosophila embryos. It looks like to get 10% success rate, they had to kill 50% of the "subjects" (table 1): https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3714591/ https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3714591/ Here is another where you see the more cas9 you inject, the more animals (C. elegans) die (table S1): https://www.ncbi.nlm.nih.gov/pubmed/23979586 https://www.ncbi.nlm.nih.gov/pubmed/23979586
    - jfarlow 10y ago
      Certainly. That is with unaided, wild-type Cas9, 4 years ago. The understanding (and mitigation) of what causes those side-effects is under some of the most comprehensive and intense research as we speak. Searching PubMed for 'Cas9' shows that 2000 papers (of a total of 3200 results) have been written in the last 16 months. And there are other ways to edit genomes - Cas9 is great for research because it's fast, but there are likely less toxic ways to edit a live genome once you have used Cas9 in the lab to figure out what to actually edit. Further, the body is pretty resilient. You don't need viability to be 100% before a therapy could be successful. Chemotherapy kills a whole lot of cells and people survive it.
      - nonbel 10y ago
        Is there a less toxic (but equally effective) cas9 available, or are you saying this is still under research? Sorry, I do not feel like searching around right now.
        jfarlow 10y ago
        Off the top of my head: Entirely new (smaller, thus more engineerable) Cas systems (1 month ago): http://www.nature.com/cr/journal/v27/n3/full/cr201721a.html http://www.nature.com/cr/journal/v27/n3/full/cr201721a.html Variously engineered Cas9 proteins to reduce toxicity the over wild-type protein (two months ago): https://www.ncbi.nlm.nih.gov/pubmed/28179977 https://www.ncbi.nlm.nih.gov/pubmed/28179977 Cas9-Inhibitors to help regulate activity (two months ago) http://www.cell.com/cell/fulltext/S0092-8674(16)31683-X http://www.cell.com/cell/fulltext/S0092-8674(16)31683-X And this doesn't include any ongoing research using other homing nuclease technologies like TALENs and Zn-Fingers that provide an entirely different set of tradeoffs but aren't as sexy, in part because they're harder to use.

by jfarlow 10y ago

nonbel 10y ago

>"it ultimately seems reasonable to be able to revert the mutations back to wild type with genome editing tools such as Cas9 in the (decade-ish future?)" What are you basing this on? Have you seen a study where they report "modification" in a living organism using this tech? I highly doubt it, due to toxicity. Also see my post above regarding the presence of aneuploidy and chromosomal instability in cancer cells. How is crispr/cas9 going to fix that?

jfarlow 10y ago
>What are you basing this on? Logical extension of how the strategies for technologies like Car-T therapies are being developed and delivered. By first targeting an ex-vivo tissue (like T-cells that can be harvested and then re-implanted), you first develop the tools to use genome editing techniques effectively, without significant off-target effects. It's essentially practice for much more useful therapies that can be done in-vivo. Further, the design of the biological 'sensors' in the T-cells are precisely the kinds of sensors you'd need to deliver a payload to and only to a mutation-containing cell. So you would neither need to target an entire organism (rather a tissue, or even a particular cell type), and off target effects from genomic insertion would be curtailed by advances in the technologies surrounding Cas9 itself. For many cancers you wouldn't need to repair the mutation in the entire organism as the cancer is tissue- or cell-specific. You are correct that you would, however, likely need to repair the prior to significant metastasis or loss of stability of the chromosome. At that point fixing a point mutation is not going to help much. All the more reason screening and baselines should start being established now - so that we can even detect a mutation prior to it becoming 'cancerous'. If you know you have a stop codon mutation in your Her2 gene when you're born, it will not be too far off when that stop codon, in particularly sensitive tissues, could be reverted with reasonable safety prior to the development of an (inevitable) cancer. And ultimately that actually cures the the cancer in a way a small molecule can never, from first principles, hope to do.
- nonbel 10y ago
  This editing procedure is extremely toxic, and I do not believe this is all due to off-target effects. I found this one quickly, where the paper claimed 80% viability when their data showed something more than half of them "go missing" (impossible to tell more from the chart): https://news.ycombinator.com/item?id=12971533 https://news.ycombinator.com/item?id=12971533 Here is actually one where they injected into Drosophila embryos. It looks like to get 10% success rate, they had to kill 50% of the "subjects" (table 1): https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3714591/ https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3714591/ Here is another where you see the more cas9 you inject, the more animals (C. elegans) die (table S1): https://www.ncbi.nlm.nih.gov/pubmed/23979586 https://www.ncbi.nlm.nih.gov/pubmed/23979586
  - jfarlow 10y ago
    Certainly. That is with unaided, wild-type Cas9, 4 years ago. The understanding (and mitigation) of what causes those side-effects is under some of the most comprehensive and intense research as we speak. Searching PubMed for 'Cas9' shows that 2000 papers (of a total of 3200 results) have been written in the last 16 months. And there are other ways to edit genomes - Cas9 is great for research because it's fast, but there are likely less toxic ways to edit a live genome once you have used Cas9 in the lab to figure out what to actually edit. Further, the body is pretty resilient. You don't need viability to be 100% before a therapy could be successful. Chemotherapy kills a whole lot of cells and people survive it.
    - nonbel 10y ago
      Is there a less toxic (but equally effective) cas9 available, or are you saying this is still under research? Sorry, I do not feel like searching around right now.
      - jfarlow 10y ago
        Off the top of my head: Entirely new (smaller, thus more engineerable) Cas systems (1 month ago): http://www.nature.com/cr/journal/v27/n3/full/cr201721a.html http://www.nature.com/cr/journal/v27/n3/full/cr201721a.html Variously engineered Cas9 proteins to reduce toxicity the over wild-type protein (two months ago): https://www.ncbi.nlm.nih.gov/pubmed/28179977 https://www.ncbi.nlm.nih.gov/pubmed/28179977 Cas9-Inhibitors to help regulate activity (two months ago) http://www.cell.com/cell/fulltext/S0092-8674(16)31683-X http://www.cell.com/cell/fulltext/S0092-8674(16)31683-X And this doesn't include any ongoing research using other homing nuclease technologies like TALENs and Zn-Fingers that provide an entirely different set of tradeoffs but aren't as sexy, in part because they're harder to use.