Metabolomics on cell subpopulations

A new paper just published by Irena Roci in Analytical Chemistry, combining FACS and isotope tracing to analyze the metabolism of complex cell populations. Congrats Irena!

I think this method will be instrumental in many studies to come. Several groups are working in this direction, but Irena’s paper is the first to critically evaluate the methodology, and shows that isotope labeling is an important step to achieve robust results. There are many conceivable applications: subtypes of cultured cells, co-culture models,  selection of cell populations at cell cycle phases or at other states by fluorescent markers …  the list goes on. Now we have a great tool to probe the metabolism of such specific cell populations. Exciting times!  :)

2 thoughts on “Metabolomics on cell subpopulations”

  1. Hi, Prof. Nillson.
    I am a reader from China focused on toxicology and metabolism. Your work which combined the FACS and metabolite profiling was interesting.
    It is a great work with strict design. However, I still have some quesions after read your paper.
    Firstly, the Fig 2 results showed that the sorted cells had a different metabolite profilings compared with the dash groups and it was significant that the difference between sorted and dash was larger than one in sorted and pellet (Fig 2b). And I found that the sorted cell were collected by trypsin treatment. Did you have made a sorted cell sample from directly collected cell by physically methods like the dish group (like using the suspension cell lines) ?
    Another quesion is about the application of this works. I think your works will influence the data analysis and pretreatment steps of relative studies in future. I wondered how your team would analysis the changes after the sorting steps which could influence the accurance of metabolism in sub-celltypes. Did your found any regularity like which kinds of peaks would be more likely influenced during sorting or some mathematics model to evaluate this kind of influence in special chemicals which might be the ones reseachers interested.Did optimizing the sorting steps like changed sheath fluid or control the temperature during FC helped?
    If you don‘t mind, I suggested that your team could release the protocal of this works in some journals published the protocals like nature protocal or JOVE. The standard protocals would limit the difference caused of operation and improved the reproducibility of results.
    Thank you for your group’s works.

  2. Hi Chen,

    Thank you for your interest in our paper.
    The sorted samples were first trypsinized then sorted. For practical reasons we do not scrape the cells before sorting like we do in direct extract. However, as a control for the trypsinization step we have included pellet extracts which can tell if that particular step affects the cell metabolism.
    Regarding the question about the effect of sorting on metabolism, we have seen that sorting procedures affects the metabolism and it is reflected in the peak areas of metabolites. However mass isotopomer fractions of metabolites in isotope labeled samples are not affected in the same way. They reflect the metabolism of cell in the dish and are more reliable for analyzing metabolism of sorted samples.
    Thank you for your suggestion. We are planning to publish our protocol in JOVE and the manuscript is currently under revision. We hope that a video of the protocol will make it easier for the method to be used by other labs.

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