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Khavari et al. recently demonstrated that a significant fraction of one of the major forms of skin cancer (cutaneous squamous cell carcinomas) are associated with a mutated KNSTRN gene (a protein associated with the kinetochore). They identify a specific region of the gene as being a hotspot for UV induced mutation and suggest that these mutations may be an early event in the development of this type of skin cancer.(1)

Abstract from their nature paper (paywalled):

Here we report the discovery of recurrent mutations concentrated at an ultraviolet signature hotspot in KNSTRN, which encodes a kinetochore protein, in 19% of cutaneous squamous cell carcinomas (SCCs). Cancer-associated KNSTRN mutations, most notably those encoding p.Ser24Phe, disrupt chromatid cohesion in normal cells, occur in SCC precursors, correlate with increased aneuploidy in primary tumors and enhance tumorigenesis in vivo. These findings suggest a role for KNSTRN mutagenesis in SCC development.(2)

My question: Scientists could theoretically alter the nucleotide sequence of the KNSTRN gene to remove the mutation hotspot, potentially lowering the incidence of this type of skin cancer. But are there any downsides to doing so? Are there any cases where a UV mutatable hotspot has shown to have some useful function in a cell or organism?

Thanks!

  1. http://www.sciencedaily.com/releases/2014/09/140907181722.htm

  2. http://www.nature.com/ng/journal/vaop/ncurrent/full/ng.3091.html

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Short-wave UV light (UVB and UVC) causes transition mutations at dipyrmidine sequences (ref.). In the work presented on KNSTRN quoted by the OP the authors report that 19 from a panel of 100 squamous cell carcinomas (SCC) contained a mutation in KNSTRN (and furthermore three of these contained no other mutation across the six genes that were analysed (Fig. 1b)). Normalising for ORF length this makes it the 3rd most recurrent mutated gene. It would seem therefore that it a fairly important mutagenic target. In a broadened set of SCCs they found a total of 29 KSTRN mutations, and of these 13 were Ser24Phe (TCC>TTC) mutations, which they refer to as a 'hotspot'.

Accepting the arguments in the answer from @Chris it is still interesting to consider how one might remove such a hotspot. The normal amino acid at this position is a serine. Here is the human codon useage for ser, obtained from here:

TCT 14.6%

TCC 22.0%

TCA 15.0%

TCG 6.0%

AGT 11.9%

AGC 19.4%

It would seem therefore that it would be theoretically possible to edit the Ser24 codon from the UV-sensitive TCC to AGC, essentially eliminating this 'hotspot'.

This, of course, doesn't answer the question - are there downsides to this? I already selected a synonymous codon with a similar frequency of useage so that shouldn't be a problem. However here is an example of a synonymous codon substitution which has an effect upon splicing of the LMNA gene resulting in muscular dystrophy, and the paper cites several other examples of this. (I haven't actually checked to see where the Ser24 codon lies in relation the exon-intron boundaries in the KNSTRN gene.) No doubt there are other mechanisms by which my proposed edit could have unwanted effects. It would have to be tested carefully, and so we come back around to a cost-benefit analysis - would it be worth developing this editing idea (even if it were feasible as a therapy) given that there are clearly many paths to SCC not involving this specific mutation.

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  • $\begingroup$ This is a good point. In addition to maintaining the same amino acid and taking care to avoid splice site junctions, you'd have to consider if there were any protein, DNA or RNA interacting sequences encoded in the region of interest. If the region were in a non-coding transcript it could also be problematic. Anything else? $\endgroup$ – replicase Sep 16 '14 at 2:26
  • $\begingroup$ The region can also contain regulatory regions (also when this inside a gene) which you probably mess up with. $\endgroup$ – Chris Sep 16 '14 at 5:39
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This is actually a bad idea for severeal reasons: First it is not a good idea to tamper with genes, especially not with ones which are involved in the regulation of mitosis and the correct segregation of sister chromatids. Remember that a one amino acid exchange because of a C to T transition causes the problems with SCC? Into what do you want to change the sequence anyway?

Then this is not the only mutation linked to SCC - mutations in TP53 and CDKN2A are more important here. And even if you manage to change the sequences here which are the causative reason for SCC there are other mutations that will then occur. Simply by chance. It is probably a good idea to target the mutant KNSTRN protein with a treatment as this is already done for other proteins (although these are usually enzymes), but changing it will most likely not only not work but cause other problems as well.

Another problem (even when you use a synonymous codon which does not lead to an amino acid exchange) is that you can disrupt genetic regulatory regions. Not all of these regions are located in the promoters of genes, quite a number of them are found inside of genes. Here even a single nucleotide exchange can prevent a transcription factor from binding to its recognition site. A prominent example for the is the HERC2/OCA2 polymorphism where a single nucleotide polymorphism in HERC2 alters a transcription factor binding site and thus alters the expression of OCA2.

The solution here is pretty easy: Avoid prolonged exposure to UV light whenever possible.

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  • $\begingroup$ This is generally true, but for the specific regions in question, transgenic mice could be used to test these hypotheses, assuming the same effect held in mice. $\endgroup$ – shigeta Sep 10 '14 at 19:38
  • $\begingroup$ The problem with mice is that they usually don't develop skin cancers. You need to use mice with other defects as well and this makes the model much weaker. $\endgroup$ – Chris Sep 10 '14 at 19:57
  • $\begingroup$ sure, though I think its far from saying that this is not a testable hypothesis, and that they will try to do so. $\endgroup$ – shigeta Sep 10 '14 at 20:10
  • $\begingroup$ The problem with mutations is that this will cause severe problems when we change the code like this. So you have to think about cell type specific knock-ins (probably inducable) and then see what the outcome is. This is surely interesting in terms of basic research, but I don't see any practic use for it (which is no reason to not analyze this). $\endgroup$ – Chris Sep 10 '14 at 20:14
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    $\begingroup$ fair enough, @Chris! $\endgroup$ – shigeta Sep 10 '14 at 20:24

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