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Here's a silly idea I had this morning:

  1. Sequence a bunch of normal patient cells.
  2. Sequence a bunch of tumor cells from a biopsy.
  3. Find a DNA sequence that we're reasonably certain exists in the cancer cells but doesn't exist in normal cells.
  4. Create a guide DNA that matches the sequence identified in (3).
  5. Send in a nuclease dead cas9 which stops cell replication through an AAV to all the cells anywhere in the vicinity of the tumour. It specifically binds only to the DNA in the cancer cells, and therefore disables DNA replication only for those cells. Then, target the now-stagnant tumour using conventional chemotherapy.
  6. Alternatively, send in a CRISPR dead cas that induces apoptosis upon binding to the target strand, though this seems harder to pull off.

Would something like this work? If so, has this been attempted? If not, what specific step is impossible?

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  • $\begingroup$ Related: frontiersin.org/articles/10.3389/fonc.2020.604948/full $\endgroup$
    – acvill
    Oct 4, 2021 at 16:34
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    $\begingroup$ “Fools rush in where angels fear to tread” Pope. And this is a question and answer site about problems in biology. $\endgroup$
    – David
    Oct 4, 2021 at 18:55
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    $\begingroup$ @David, I'm sure I don't know what you mean by that. If one of these steps is impossible, you can just tell me in an answer instead of quoting aphorisms. $\endgroup$ Oct 4, 2021 at 19:49
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    $\begingroup$ The negative response you have received is probably because this is an opinion-based question since it is asking about a hypothetical situation. From the help center, avoid asking subjective questions where … you are asking an open-ended, hypothetical question: “What if ______ happened?” We expect answers to be based on verifiable facts and references, along with subject-related expertise. This also seems under researched (demonstration of prior research is expected). Please see the tour and consult the help center starting with How to Ask for details on what is appropriate for this site. $\endgroup$
    – tyersome
    Oct 16, 2021 at 22:02
  • $\begingroup$ why would the crispr dead cas inhibit DNA replication? is there some work demonstrating that cas does this rather alarming thing, as opposed to being kicked off by the highly efficient replication machinery? $\endgroup$ Oct 19, 2021 at 19:40

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There are a lot of assumptions implicit in the system you describe, all of which need to be addressed prior to any serious discussion of your method's feasibility.

  1. Sequence a bunch of normal patient cells.
  2. Sequence a bunch of tumor cells from a biopsy.
  3. Find a DNA sequence that we're reasonably certain exists in the cancer cells but doesn't exist in normal cells.

Depending on the tumor stage, its constituent cells may have a great amount of genomic heterogeneity.1,2 How do you know your biopsy will capture all the distinguishing variation?

  1. Create a guide DNA that matches the sequence identified in (3).
  2. Send in a nuclease dead cas9 which stops cell replication through an AAV to all the cells anywhere in the vicinity of the tumour. It specifically binds only to the DNA in the cancer cells, and therefore disables DNA replication only for those cells. Then, target the now-stagnant tumour using conventional chemotherapy.

What proportion of distinguishing mutations do you expect to have a structure that can be differentially targeted by a dCas9 effector? Are SNPs easily distinguished without off-target effects in healthy cells? Is the purpose of using dCas9 to mitigate off-target effects, as opposed to Cas9, for which off-target effects would be more severe (binding vs. cutting)? Can you provide a citation describing the process by which dCas9 binding prevents replication? Is it trivial to design and deliver a pool of AAV vectors that express a guide for each of your targets? Considering the cost (time and money) of your proposed treatment, can you provide a citation asserting that tumor growth stagnation prior to chemotherapy has an added benefit over chemotherapy alone?

  1. Alternatively, send in a CRISPR dead cas that induces apoptosis upon binding to the target strand, though this seems harder to pull off.

Again, please provide a citation describing the mechanism by which dCas9 association induces apoptosis.


References

  1. Turajlic S, Sottoriva A, Graham T, Swanton C. Resolving genetic heterogeneity in cancer. Nat Rev Genet. 2019 Jul;20(7):404-416.
  2. Navin N, Krasnitz A, Rodgers L, Cook K, Meth J, Kendall J, Riggs M, Eberling Y, Troge J, Grubor V, Levy D, Lundin P, Månér S, Zetterberg A, Hicks J, Wigler M. Inferring tumor progression from genomic heterogeneity. Genome Res. 2010 Jan;20(1):68-80.
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