Wednesday, February 2, 2022

Inspirational multi-omics of lung cancer recurrence without ever going to a lab bench!


Some of the biggest and most expensive projects in our field are just building big resources. I really like this study despite the statistics and cancer terminology heavy writing (with a lot of probably necessary all capital letters?) because is shows how people can put these to use and find cool biomarkers(?) without leaving their house.  

This group in a beautiful couch burning mountain city (I was there for that one. It was nuts. Turns out that's just what they do there. Find a nickel on the sidewalk? Get the gasoline and the recliner! Beat a historic rival for the first time in 412 years? People will still talk about it almost 20 years later! It wasn't the best day to be wearing my school colors which, as a super bright orange can still be seen by drunk kids even when there is tons of smoke) pulled out the stops and dug into at least 6, maybe 8, cancer resources, including the most recent release of the Cancer Cell Line Encyclopedia Proteomics Project which might have gotten a facelift? It looks super sharp. 

What really stands out here is that this group didn't just fish around looking for what stood out as intense and obviously changing in abundance. They went into these massive resources with what seems like a pretty clear hypothesis that centered on 7 genes previous results from their lab indicate are linked to cancer recurrence. By thinking about how each of these resources, which are human samples, so intrinsically flawed since we can't control all the variables in an actual tumor or tumor cohort resource, in a medically relevant sense they can continually refine their hypotheses. Even if you can't follow their full line of thinking here (which I can't, I've already went to Wikipedia 3 times) it seems like a great story that leverages what information you can get from CCLE and the Achilles KO project to support or shoot down observations from much older microarray and RNASeq analyses of cancer projects.

They do end up going to the bench and doing some western blots to back up what survived from their initial hypothesis and it looks like they're onto something. 

So, if you're out there trudging through your one millionth pulldown experiment because your boss got the money to capture every protein-protein interaction of some sea slug, or (maybe more pertinent) you are doing 46 offline fractions of each tumor and there are two -80C freezers of tumors left to go maybe you should check out this paper. I bet it is easy to stop and wonder if maybe you're doing a lot of work to make a resource that no one will ever use, right? But I think this shows that, if you trudge through and keep doing it right, you might be enabling some smart people out there in the world to do important things with it, and really, is there a better use of that great big noisy vacuum chamber? 

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