3 ms·

The idea of using CRISPR/Cas to detect tumor-specific mutations that aren't necessarily oncogenic and then kill the cell is not a new one [0, 1, 2]. However, pr

The idea of using CRISPR/Cas to detect tumor-specific mutations that aren't necessarily oncogenic and then kill the cell is not a new one [0, 1, 2]. However, previous studies used Cas9, which just damages the DNA at the target site; this uses Cas12a2, which is far more destructive because it shreds the chromatin in the cell once activated by detecting the target sequence. As with any cancer treatment, it's likely the tumor will evolve resistance. My guess is that cells will find ways to reject the lipid nanoparticles used to deliver the CRISPR/Cas mRNA and associated guide sequence(s), either via modifications to the cell surface (preventing LNP uptake) or via changes to endosomal/lysosomal pathways (causing the mRNA payload to get degraded before it has a chance to be translated into protein). [0] https://pubmed.ncbi.nlm.nih.gov/28575452/ https://pubmed.ncbi.nlm.nih.gov/28575452/ [1] https://www.nature.com/articles/s41598-018-30205-2 https://www.nature.com/articles/s41598-018-30205-2 [2] https://www.nature.com/articles/s41467-020-18875-x https://www.nature.com/articles/s41467-020-18875-x

cyberax 4mo ago
There are some ideas about making it triggerable. So first you load the cells with a protein that is ready to start shredding but is inactive. Then you trigger it with a second compound.
- MontyCarloHall 4mo ago
  This would shorten the timeframe for cells to mutate and acquire resistance mechanisms, but would not address the issue of cells with preexisting (epi)genetic resistance mechanisms that would then be promptly selected for.
  - cyberax 4mo ago
    Yes, and if you shorten the timeframe enough, there's a chance that it can clear all the cancerous cells. You also ideally would use multiple variations of the therapy to further reduce the chance of a pre-existing escape mutation. That's how we deal with HIV. No single HIV therapy (so far) is effective enough to suppress the virus all by itself, but a combination of them provides a barrier that is too high for mutations to jump.
    - MontyCarloHall 4mo ago
      Agreed. Assuming it's ultimately proven to work in vivo, I think the endgame of this therapy is multiple guides targeting multiple mutations along with multiple delivery mechanisms (a formulation-diverse cocktail of LNPs + eVLPs [0]?). Sure, tech like [0] is futuristic and fanciful, but so is the tech of the OP, and both will probably reach in vivo maturity around the same time. [0] https://pmc.ncbi.nlm.nih.gov/articles/PMC8809250/ https://pmc.ncbi.nlm.nih.gov/articles/PMC8809250/
- inglor_cz 4mo ago
  This will also cause problems because too many cells die at once. See the comments in other threads; killing the entire cancer at once is very hard on the body.
  - cyberax 4mo ago
    Tumor lysis syndrome is a thing, but it can be managed. It's far better than the alternative. The new therapies will also likely be applied after surgical resection and/or classic therapies to reduce the bulk of the cancer.
AnimalMuppet 4mo ago
But cancer isn't an organism. Cancer cells in any specific individual may evolve that way, but "human cancers" as a group will not. (The only way they could is by evolving human DNA, but "survival of the fittest" pushes the opposite direction for that.)
- MontyCarloHall 4mo ago
  Nonetheless, we see the exact same resistance mechanisms to the same therapies recur across individuals, e.g. [0]. Convergent evolution is a harsh mistress. [0] https://pmc.ncbi.nlm.nih.gov/articles/PMC2538882/ https://pmc.ncbi.nlm.nih.gov/articles/PMC2538882/
- mikepurvis 4mo ago
  Indeed, there's no "be a better/stronger cancer and spread more effectively to more hosts" the way there is with bacteria or a virus. It's not like the flu where we need a new shot every winter because every winter is a new flu. Once we solve the cancers we know about, they're solved forever, with the one caveat that more people will live longer, so that will increase the window for eventually still ending up dying to one of the cancers that happens to have a non-evolved built in resistance to this or that treatment. Which is a great deal of course, especially if it's a treatment that sounds way less destructive of QoL than chemo, radiation, etc.
  - MontyCarloHall 4mo ago
    >there's no "be a better/stronger cancer and spread more effectively to more hosts" No, but there is "be a better/stronger cancer cell and don't succumb to whatever therapy is killing its neighboring cells." It's exactly akin to how dosing isolated populations of bacteria with antibiotics selects for individual cells that are resistant, which then multiply and dominate [0], just like a tumor. [0] https://www.youtube.com/watch?v=plVk4NVIUh8 https://www.youtube.com/watch?v=plVk4NVIUh8
    - mikepurvis 4mo ago
      Right, but that's within a single host isn't it? Like patient A gets that mutation and succumbs, that sucks, but the stronger cancer cells don't them jump to patient B the way antibiotic-resistant bacteria do. (barring the transmissible cancers article that your sibling comment linked to, but that's not the common case)
strbean 4mo ago
Depending on how the LNPs are designed, would resistance also potentially cripple the cancer cells? Like, it stops surfacing some cholesterol receptor because the drug is being delivered by LNPs that target that receptor, and now the cell is starved for cholesterol? I've heard about drug resistance in bacteria leading to slower growth / reduced virulence. Maybe the same would occur with cancers. A drug that could effectively switch an aggressive cancer into a slow-growing one wouldn't be the worst thing.
- MontyCarloHall 4mo ago
  >Depending on how the LNPs are designed, would resistance also potentially cripple the cancer cells? Yes, if the LNP could be engineered to target an essential surface receptor, which is still a very tough problem. It would also not solve the issue of the payload successfully entering the cell but being subsequently degraded. >I've heard about drug resistance in bacteria leading to slower growth / reduced virulence. Maybe the same would occur with cancers. A drug that could effectively switch an aggressive cancer into a slow-growing one wouldn't be the worst thing. This is essentially how treatment for chronic lymphocytic leukemia happens (hence why it's called "chronic"). People with CLL can stay on BTK inhibitors for decades, often until they die of other natural causes.
  - strbean 4mo ago
    Interesting, thanks for the info! Another question: how does this approach compare to trying to repair the pathogenic variants in the cancer? I asked here about that approach recently and the response was mainly about delivery difficulties: https://news.ycombinator.com/item?id=48285386 https://news.ycombinator.com/item?id=48285386
    - MontyCarloHall 4mo ago
      Even with 100% delivery efficacy, editing efficacy is nowhere near 100%. CRISPR/Cas editors will reliably detect the target sequence but will not reliably edit it in order to repair the mutant allele, whereas CRISPR/Cas12a2 will activate and destroy chromatin ~100% of the time when it detects the target. As is often the case, it's a lot easier to indiscriminately destroy than precisely (re)build.
rolph 4mo ago
turn the stick around and grasp the other end. evolution isnt about generating a response to a challenge, its about differential success. those cells [oncocytes] that have properties conferring resistance carry it as un-utilized baggage, those without said properties make a living without that fetter. the selective factor comes into play when payloaded LNP [in this case] facillitates destruction of "nonresistant" oncocytes and spare the "resistant" the resistance is not generated in response to the challenge, it is already present, and confers survivorship in the face of the administration of the drug.
amluto 4mo ago
Surely a far simpler way to evolve resistance would be a trivial mutation in the p53 transcript that the guide RNA is looking for.
- epihelix 4mo ago
  [dead]
- MontyCarloHall 4mo ago
  In practice, you’d use multiple guides targeting multiple mutations, so that the probability of having/acquiring multiple resistance mutations abrogating every guide from binding would be infinitesimal.
  - amluto 4mo ago
    LNPs have limited capacity, and if the CRISPR/Cas system they’re using requires an exact match, then any additional point mutation or insertion or deletion in the segment being matched would allow the cell to survive. I suppose that approximately 3n extra guide RNAs (where n is the length of the matched sequence) could be added, but that seems a bit messy.
    - MontyCarloHall 4mo ago
      Including additional guides is negligible with respect to the overall LNP capacity, which can contain a few thousand nucleotides. The CRISPR/Cas mRNA is about 5 kilobases total, and each guide is on the order of 100 bases.
hinkley 4mo ago
[dead]

cyberax 4mo ago

There are some ideas about making it triggerable. So first you load the cells with a protein that is ready to start shredding but is inactive. Then you trigger it with a second compound.

MontyCarloHall 4mo ago
This would shorten the timeframe for cells to mutate and acquire resistance mechanisms, but would not address the issue of cells with preexisting (epi)genetic resistance mechanisms that would then be promptly selected for.
- cyberax 4mo ago
  Yes, and if you shorten the timeframe enough, there's a chance that it can clear all the cancerous cells. You also ideally would use multiple variations of the therapy to further reduce the chance of a pre-existing escape mutation. That's how we deal with HIV. No single HIV therapy (so far) is effective enough to suppress the virus all by itself, but a combination of them provides a barrier that is too high for mutations to jump.
  - MontyCarloHall 4mo ago
    Agreed. Assuming it's ultimately proven to work in vivo, I think the endgame of this therapy is multiple guides targeting multiple mutations along with multiple delivery mechanisms (a formulation-diverse cocktail of LNPs + eVLPs [0]?). Sure, tech like [0] is futuristic and fanciful, but so is the tech of the OP, and both will probably reach in vivo maturity around the same time. [0] https://pmc.ncbi.nlm.nih.gov/articles/PMC8809250/ https://pmc.ncbi.nlm.nih.gov/articles/PMC8809250/
inglor_cz 4mo ago
This will also cause problems because too many cells die at once. See the comments in other threads; killing the entire cancer at once is very hard on the body.
- cyberax 4mo ago
  Tumor lysis syndrome is a thing, but it can be managed. It's far better than the alternative. The new therapies will also likely be applied after surgical resection and/or classic therapies to reduce the bulk of the cancer.

AnimalMuppet 4mo ago

But cancer isn't an organism. Cancer cells in any specific individual may evolve that way, but "human cancers" as a group will not. (The only way they could is by evolving human DNA, but "survival of the fittest" pushes the opposite direction for that.)

MontyCarloHall 4mo ago
Nonetheless, we see the exact same resistance mechanisms to the same therapies recur across individuals, e.g. [0]. Convergent evolution is a harsh mistress. [0] https://pmc.ncbi.nlm.nih.gov/articles/PMC2538882/ https://pmc.ncbi.nlm.nih.gov/articles/PMC2538882/
mikepurvis 4mo ago
Indeed, there's no "be a better/stronger cancer and spread more effectively to more hosts" the way there is with bacteria or a virus. It's not like the flu where we need a new shot every winter because every winter is a new flu. Once we solve the cancers we know about, they're solved forever, with the one caveat that more people will live longer, so that will increase the window for eventually still ending up dying to one of the cancers that happens to have a non-evolved built in resistance to this or that treatment. Which is a great deal of course, especially if it's a treatment that sounds way less destructive of QoL than chemo, radiation, etc.
- MontyCarloHall 4mo ago
  >there's no "be a better/stronger cancer and spread more effectively to more hosts" No, but there is "be a better/stronger cancer cell and don't succumb to whatever therapy is killing its neighboring cells." It's exactly akin to how dosing isolated populations of bacteria with antibiotics selects for individual cells that are resistant, which then multiply and dominate [0], just like a tumor. [0] https://www.youtube.com/watch?v=plVk4NVIUh8 https://www.youtube.com/watch?v=plVk4NVIUh8
  - mikepurvis 4mo ago
    Right, but that's within a single host isn't it? Like patient A gets that mutation and succumbs, that sucks, but the stronger cancer cells don't them jump to patient B the way antibiotic-resistant bacteria do. (barring the transmissible cancers article that your sibling comment linked to, but that's not the common case)

strbean 4mo ago

Depending on how the LNPs are designed, would resistance also potentially cripple the cancer cells? Like, it stops surfacing some cholesterol receptor because the drug is being delivered by LNPs that target that receptor, and now the cell is starved for cholesterol? I've heard about drug resistance in bacteria leading to slower growth / reduced virulence. Maybe the same would occur with cancers. A drug that could effectively switch an aggressive cancer into a slow-growing one wouldn't be the worst thing.

MontyCarloHall 4mo ago
>Depending on how the LNPs are designed, would resistance also potentially cripple the cancer cells? Yes, if the LNP could be engineered to target an essential surface receptor, which is still a very tough problem. It would also not solve the issue of the payload successfully entering the cell but being subsequently degraded. >I've heard about drug resistance in bacteria leading to slower growth / reduced virulence. Maybe the same would occur with cancers. A drug that could effectively switch an aggressive cancer into a slow-growing one wouldn't be the worst thing. This is essentially how treatment for chronic lymphocytic leukemia happens (hence why it's called "chronic"). People with CLL can stay on BTK inhibitors for decades, often until they die of other natural causes.
- strbean 4mo ago
  Interesting, thanks for the info! Another question: how does this approach compare to trying to repair the pathogenic variants in the cancer? I asked here about that approach recently and the response was mainly about delivery difficulties: https://news.ycombinator.com/item?id=48285386 https://news.ycombinator.com/item?id=48285386
  - MontyCarloHall 4mo ago
    Even with 100% delivery efficacy, editing efficacy is nowhere near 100%. CRISPR/Cas editors will reliably detect the target sequence but will not reliably edit it in order to repair the mutant allele, whereas CRISPR/Cas12a2 will activate and destroy chromatin ~100% of the time when it detects the target. As is often the case, it's a lot easier to indiscriminately destroy than precisely (re)build.

rolph 4mo ago

turn the stick around and grasp the other end. evolution isnt about generating a response to a challenge, its about differential success. those cells [oncocytes] that have properties conferring resistance carry it as un-utilized baggage, those without said properties make a living without that fetter. the selective factor comes into play when payloaded LNP [in this case] facillitates destruction of "nonresistant" oncocytes and spare the "resistant" the resistance is not generated in response to the challenge, it is already present, and confers survivorship in the face of the administration of the drug.

amluto 4mo ago

Surely a far simpler way to evolve resistance would be a trivial mutation in the p53 transcript that the guide RNA is looking for.

epihelix 4mo ago
[dead]
MontyCarloHall 4mo ago
In practice, you’d use multiple guides targeting multiple mutations, so that the probability of having/acquiring multiple resistance mutations abrogating every guide from binding would be infinitesimal.
- amluto 4mo ago
  LNPs have limited capacity, and if the CRISPR/Cas system they’re using requires an exact match, then any additional point mutation or insertion or deletion in the segment being matched would allow the cell to survive. I suppose that approximately 3n extra guide RNAs (where n is the length of the matched sequence) could be added, but that seems a bit messy.
  - MontyCarloHall 4mo ago
    Including additional guides is negligible with respect to the overall LNP capacity, which can contain a few thousand nucleotides. The CRISPR/Cas mRNA is about 5 kilobases total, and each guide is on the order of 100 bases.

hinkley 4mo ago

[dead]