Tuesday, September 8, 2015

Macrophage S1P Chemosensing -- and an interesting way of integrating genomics and proteomics!

All this next gen sequencing data out there!  How do we leverage all of it to our advantage? We can supplement our databases for mutations and we can cross-reference our quan, but this new paper from Nathan Manes et al., out of

In this new paper at MCP from Nathan Manes et al., out of the CNPU these researchers describe a different twist on integrating next gen sequencing data with LC-MS/MS.

The model is also super interesting. The study investigates osteoclasts, the cells that destroy bone. During normal maintenance osteoclasts break down bone where appropriate and osteoblasts rebuild it. This is a tightly controlled process (involving chemotaxis), but one that is only partially understood. Disregulation of this tight process leads to many different diseases, the most common of which is osteoporosis.

The focus of this study is the use of next gen sequencing technology and mass spec to explore that pathway. As a model they have some mouse cells that function like osteoclasts and they can add the right chemotaxic things to activate them. Cool, right?!?

First they started out with the next gen sequencing following all the normal protocols (they did deep sequencing via Hi-Seq) to get a list of transcripts that were differentially regulated in a significant matter.

Then they went a different direction. They used an in-depth literature search to hunt down proteins that have been implicated in these pathways. Some of this info comes from other quantitative proteomics studies and others come from genomics techniques. Why reproduce data that is already out there for free!  Strong protein candidates were filtered and heavy copies of good peptides were made to develop an absolute quantification method for SRM analysis for these targets.

To wrap it all up they took the results from their next-gen and from their absolute LC-MS quan and compared it (it compares strikingly well!) and then they dumped it all into a cool modeling program called Simmune that they developed that you can check out (and download for free) here!

Great, interesting study on an interesting model that uses some really original thinking and tools.

1 comment:

  1. Ben,

    thanks for your note - very nice to find out that someone liked our paper.