Monday, November 2, 2020

"Single cell" HLA peptidomics by cloning a population?

I'm going to run this by some biologists and MDs today to see if they think this is biologically relevant, or if this is cheating to some extent. 

"Single cell" anything is huge right now, and we've got to be skeptical.  This group just published some decent CyTOF data and got away with calling it single cell somehow and scored Nature Biotech. If you aren't out there trying to find whatever the largest "single cell" in the world is (there is an algae that is over a foot long!) so you can do some damage to this newly emerging field, I'm not sure what side you're on, probably not your own! 

However -- I hope this isn't cheating because, it is reeeeeeeeeeeeeaaaaaaaaaaaallly cool. 

HLA peptides suck. They typically don't have K/R on the ends so they often don't doubly charge (or at least localize to the termini so we have full b/y ion spreads. However, we could absolutely overcome this with high resolution MS/MS IF we have enough signal.

How to get over the signal hurdle? Get a single cell from the tumor and grow a ton of them. Now....I'm going to consult people who know biology, but I'm worried that whatever the presentation is in the tumor vs whatever it is while you're growing out a clonal population on a plate might be very different things. I assume the people who reviewed this considered that, but....ummm....wait. Same journal as the CyTOF IHC "single cell" stuff. So...grain of salt all around. 

Disclaimer: Maybe I just don't understand the CyTOF paper. I'm obviously no expert, but I was very disappointed because there are groups out there doing what I'd consider real single cell metabolism/ metabolomics.


Check out this recent work from the Bamba lab

They go ultra-low flow with fancy cell loading and build a targeted list for 35 metabolites and curves and calculate LOD off good ol' linear regression. 

There is also a great new resource that just came out: 

If you had time to read a whole book you'd probably have time to finish that review you've been working on since 2016. I'm not going to read the whole thing either, but I did get it and the bookmark is at the very back. 

Weird words
Weird words (...did that say microarrays....what the actual f...?..o..urier...?...moving on!) 
Weird words

And then the good stuff! 

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