Wednesday, July 27, 2022

Dysregulated proteins and RNA in Parkinson's lymphoblasts!


I keep going back to this recent study in Proteomes for a couple of reasons

Obviously, if you're going to study Parkinson's you need access to some cerebral spinal fluid or postmortem brain sections, right? Those are so easy to get that there is a guy I know who will provide you with the latter material only under the upfront agreement that he is the senior author on the paper and he gets to pick the author order. You can do a proteomics or a metabolomics study, make every figure, and you might be 7th author. That's the deal. Go get 30 brain sections somewhere else if you don't like it. 

What drew me to this at first was the use of RNASeq and proteomics. Always a draw, and then once I googled what a lymphoblast was (I'd heard of it, give me a break, I just couldn't point it out on a map) then it made me think this group was a little crazy. What do we care about white blood cells for in a neurological disease? 

They find a bunch of differences at both the proteomic and transcript levels. And the talk about how this disease does end up affecting other systems you wouldn't necessarily have thought of. 

The proteomics was on a QE HF and that data was processed by MaxQuant (I'm pretty sure, details have faded a little). More proteins were found altered between healthy and diseases patients than transcripts at the cutoffs they used, which is pretty cool. Chances are only 1 out of 3 of the changing transcripts actually make it to alter a protein anyway, so the less of those to think about the better.

The final reason I kept thinking about this paper was the fact that the data aren't publicly available. Based on the extensive ethics declarations for the study, I had a hunch and I confirmed the senior author that they couldn't get a release from the medical ethics people to make the files available. As much as we have to be proud of as a field for making our data available....

 -- you know, except the few big labs that have decided making a single 1TB zip folder and uploading that still counts as making the data available -- which, it doesn't. If that's you...

PRIDE is amazing but a LOT can happen during an 8 day download. And who has space for a 1,000 GB zip folder that is EVEN bigger after it's unzipped? 

What was I....oh yeah! 

...human samples have a ton of rules and sometimes someone behind a desk somewhere says that .RAW file isn't leaving the lab, and what do you do about that?

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