Yeah!! Okay -- it's pretty clear to everyone that -- while valuable -- taking cells out of an organism and growing them flat in a plate has some limitations. Some of these limitations can be eliminated by growing cells in a somewhat more normal 3D way (come on -- cells are used to being in contact with other cells on ALL sides...that has to affect some stuff...)
In this great new study a SILAC system is used to compare the same cell lines grown as 2D and 3D cultures to see what is changing. I particularly like the fact they use a cancer fibroblast cell line and some non cancerous more normal skin cells so they can get a better feel for what is normal, what isn't and what is shared when good and evil cells are hugging it out (in matrigel).
The proteomics for the 2D is performed on an Orbitrap XL and the 3D is performed on a Q Exactive. Perseus is used to determine significance between sets and my only minor criticism is that I wish the methods would have elaborated a bit on how the normalization was handled between the instruments (intensity scaling is very different between those two devices) but maybe it is just straight-forward in a program as smart as Perseus.
Downstream analysis is mostly handled by STRING and the plots are nice enough that it reminds me I need to default to that program....
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