Cell Surface Proteomics Reveals RAS druggable targets!

RAS mutants are bad news in cancer. KRAS drives something like 90% of pancreatic cancer cases --and I'm sure I don't need to tell you the most common ending of that story. Scientists around the world have been looking for RAS inhibitors for decades and a lot of modern chemotherapies have resulted from this work -- just...well...none of them really target this mutation.

Maybe it is time to flip the switch and look at this a different way!

In this study these authors start with an exploratory look at the cell surface of SILAC labeled cell lines that are KRAS wild-type and induced mutant strains. The cell surface proteome is enriched in this way (as I understand it)

1) Live cells are incubated with a compound that modifies the glycopeptide/proteins on the cell surface.
2) The modified cells are washed of unused glycoprotein modifying compound and flash frozen
3) The cells are thawed with protease inhibitors and a slurry of some sort of avidin that binds to the modified glycoprotein surface
4) The proteins that aren't bound are washed off the beads and the proteins that are still stuck are subjected to on-bead digestion.

If this sounds like a glycoprotein enrichment protocol -- I think it is. The trick, I guess is that since you are only modifying glycoproteins while the cell is still alive that you aren't modifying the ones on the inside of the cell.

5) The proteins are treated with PNGase that cleaves the glycans off the peptides.  (My first thought is -- wait -- can you modify this so you can keep the glycans on it? Or did you chemically modify it so that the glycans now wouldn't provide you with much/any useful information). I'm going to ask the authors a bit later today.

Here the SILAC membrane enriched peptides are analyzed with a Q Exactive Plus and the peptide ID and quantification all appears to have been done in ProteinProspector.  And this is when the paper goes kinda crazy. This group doesn't stop anywhere near here.

Proteomics is the smallest part of this study. The validation is the biggest part. CRISPR, phage displays, ELISAs, and Antibody Drug Conjugate (ADC) killing assays(!!) are the star of this study. Proteomics just tells them where to look.

Even I have to admit that the story here is that they end up showing cell surface targets that appear on KRAS mutant cell lines that they can target with antibodies and kill the cells. We're talking real potential therapeutic targets for KRAS mutant cells. I'd say I'd hope that some pharma companies will jump on this and start developing ADCs right now -- but, come on, you know people have this paper in hand and are working on these right now somewhere! 

I think it is fair to point out that this SILAC study confirmed the findings and pointed to very similar cell surface targets as this larger global label free proteomic analysis of a similar model.

Hopefully this is just the tip of the iceberg to finding all the ADCs to selectively kill all the cancer cells!