Wednesday, January 11, 2023

Normalize and integrate your organ-on-a-chip proteomics and metabolomics!


Organ-on-a-chip technology can allow a better representation of in vivo conditions than 2D cell culture can. It clearly isn't as easy as 2D cell culture, but it can also be a good bit easier to scale than animal models. I didn't know it until I read this paper, but the US EPA plans to stop animal testing in their research plans in a few years and these technologies will likely play a big role.

If you are jumping into this field and want to fully characterize your drug (or in this case -- CHEMICAL WEAPON) on your simulated organs with both proteomics and metabolomics, what would you do? I'd just do what this group does!

Hey! I know some of these people...including Wait, that can't be the kid I know. Common name. 

What they do is grow human hepatocytes in scaffold bioreactors to get them to grow into 3D cell cultures. It doesn't look like any funny gelatin things are employed here (whew....all I can see when they grow cells in gels is...their gel monomers...). They take some control little organs and some other ones they treat with "VX" which, according to Google is something like a CHEMICAL WEAPON.

Since they're making tons of these little "organs" they appear to keep their digestions and extractions in plate to keep them scalable. Apparently, though, the size of the "organs" are tough to normalize and since you've got these cells all stuck on scaffolding you can't exactly weigh them. You have to basically lyse them where they are. Proteomics normalization? That's okay, we basically know how to do that (though I'd follow their directions here to make sure that buffers necessary for the "organs" don't interfere with the quan). 

Normalizing the small molecule/metabolomics input? I have no idea how I'd to that. You can normalize the TICs, etc., but that is for relatively small variability. You don't have to load too many samples for LFQ proteomics with vastly different loads on accident to discover the limitations of normalizing at the TIC level, right? What this group comes up with is a rapid method to quantify their metabolomics based on something that reminds me of the name of one of these people...


Joint pathway analysis (!!!) for the metabolomics and proteomics was done in Metaboanalyst, cause apparently it does that now

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