Saturday, June 25, 2016

PRM assays show that oncogenic KRAS and BRAF reprogram metabolism!

In all this newfound interest the world has in metabolomics/metabolism these days, this awesome new paper from Josiah Hutton et al., is a breath of fresh air!

In the study they compare tumors that have both wild-type (WT) and mutant KRAS. They do some nice global analysis on the QE Plus and add some nice data to the huge pile of KRAS proteomics data out there.

Where this paper differentiates itself is that they go after the metabolome of these difference cells. Instead of extracting the metabolites themselves and trying to infer what they are (which is hard cause lots of those things have the same exact masses -- thank goodness the mZcloud and high res NIST libraries keep getting better!!) they do something I don't think I've seen before.

They use parallel reaction monitoring (PRM) to quantify the proteins that are most key to central metabolism. The PRMs give them absolute certainty that they're looking at the right proteins as well as the sensitivity to see statistically significant changes (that...the global proteomics data wasn't quite sensitive enough to conclude!) and they end up with this awesome heatmap I stole and put at the top.

I can't recall now, but I think they PRM'ed 73 different metabolism proteins. I wouldn't change a thing in the methods as they described them. (Though I'm just a tiny bit confused about what source they are using on the QE Plus...looks like nanoflow rates, but described as micro, probably just a difference in what the authors and I consider the proper term for the flow rate. Again completely minor observation.)

Totally sharp paper. I hope we see a lot more of this kind of work going forward!!

Everybody here in Maryland is talking about the NCI proteomics moonshot initiative. I would like to officially cast my vote for targeted pathway quantification (and mutation confirmation) via sensitive and high certainty PRMs being a central component of the initiative!!  This paper would sure make a nice template!

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