Gain of cysteine missense mutations in both disease and healthy(?) human tissues?!?

 

In shotgun proteomics we generally do our best to ignore cysteines - and especially the super important PTMs that they tend to carry. We reduce the cysteines (losing the PTMs and anything else, like drugs that might bind to them) and then we put in harsh binding chemicals to make sure those cysteines never do anything remotely biological ever again. We assume those 2 reactions occured with 100.0000000000% efficiency, and we move on. 

Chemoproteomics people, however, tend to be very intersted in the drugs that bind to active things like cysteines so they have to use other approaches. And....maybe the coolest discoveries of this awesome new paper weren't a surprise while doing some chemoproteomics, but I felt like there was an air of increasing surprise (there was for me!) as I read through it! 

The paper isn't a short read because this team did a lot. On the mass spec front, cysteine pull-downs and whole proteomes (which did employ reduction/alkylation) were analyzed on an Orbitrap Eclipse with a nanoLC system. TMT was also used at times.

On the genomics front, cell lines were sequenced and the variant call files were integrated into the database search using a 2 step process with MSFragger through command line. I'm not sure if this was just their typical way of doing things or whether integrating the normal FASTA with the processed peptide variants and controlling FDR the way they did required some fine tuning that is easier to set up outside of the GUI. 

These cancer cell lines largely suffer from problems repairing mismatch errors in their DNA. (Deficient in MisMatch Repair, or dMMR). Makes sense, right? Cancer is often a DNA disease. Errors propagate until you've created renegade cells that do whatever they want. Missense mutations typically end up changing one amino acid to another. Why would new cysteines be the most likely outcome?  

From a pure codon perspective, it doesn't seem like the most likely outcome! If you are randomly altering bases in DNA you'd think Leucing or Arginine (6 codons each) would be the most likely random occurence, right? Cysteines are only 2. (Stolen from Wikipedia)

...but we're talking about the selective pressure of cancer cells....does having more cysteines infer some sort of an advantage? Beyond me to think about, but it sure is weird. 

Where is gets weirder is that it looks like missense mutations are also found in the healthy human data they evaluated as well.....again....beyond this blogger to really think about - but it should go as yet another of this huge pile of reasons to question our current ability to target every human protein. 

As an aside, I found myself reading between the lines of this one more than I should have, but I could imagine someone doing chemoproteomics of cysteine binding drugs (maybe because I spent a lot of time on sotorasib the last few years) and then finding 800 peptides it bound to that had no presence in any human FASTA database. It sure would justify the time they put into this great thought-provoking study!