Sunday, June 25, 2017

Proteomic analysis of human cells grown in bacterial cellulose

A LOT of biological studies of human cells occurs with cells grown in culture. And we can thank cell culture techniques for a huge amount of what we know of how cells work, but it has been no secret that there are some limitations to cell culture techniques. This is a nice open review on limitations -- with a strong title.

Over the last 15 years or so there have been numerous ideas put forward to bridge the gap between cells growing in monolayers in cell culture and cells as they actually exist in human tissues and organs. Growing cells in 3 dimensions is something that has been discussed for years, but -- so far hasn't yielded much in the way of new understandings in biology. Please don't take this as a criticism, I know two great people working hard on this stuff right now who will have stuff out soon, but these complex bioreactors seem to come with their own bevy of complications -- which better technology may soon fix. In the meantime, check this out! 

This is the analysis of a bacterial cellulose gel material that can be used to support growing human cells....and the title gives away some of it...but this material seems to allow cells to develop in a more native type state!

The preparation of the cells to grow within the material seems reasonably straight-forward. (A quick Google search indicates that the material they used may be a commercialized product. Please do not interpret this as an endorsement and see my rapidly expanding list of blog disclaimers if you have questions).

This team goes to great lengths to compare classically grown cells with the ones grown in this bacterial cellulose material, employing immunocytochemistry and global RNA analysis. They also extract peptides and use isobaric tagging technology and do relative quantification with a quadrupole high field Kingdon-style trap system.

Of particular interest to this methods nerd, although a 10-plex isobaric tagging reagent is employed, the instrument is ran at 35,000 resolution, which the authors state is approximately 50,000 resolution in the reporter ion region. This should allow almost baseline separation of all the reporter ions and may compromise just a little on full separation in favor of maximum speed.

The data files and MaxQuant processed files are available at ProteomeXchange here (after the fully edited version of the paper is released; PXD003975). I strongly suggest checking out the supplemental info for the paper. They did a LOT of work here (...okay...maybe I just really like to look at expert level ICC and pretty STRING networks...)

What did all these quantified transcripts and proteins reveal? That this technique might be an easy way to obtain information from cells that more closely reflects the way the cells exist in the human body than growing those cells in plastic plates in 2 dimensions -- and that sounds like a step in the right direction!

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