Saturday, August 31, 2019

An amazing clinical scale proteogenomic study of lung cancer!

This is just a beautiful piece of work demonstrating what proteomics and genomics can do in tandem to really find the true differences in patient samples in diseases that may look -- to traditional assays -- to be the same disease.

I'm going to try and not type much because I can't do this justice. I don't even know what the word squamous means. I'd assume that if there is a squamous then that is a subtype of lung cancer and that these might be enough of a subcategory that we'd treat them the same way. What this huge amount of work shows clearly enough that it even gets through to me, that these aren't the same thing and that if we didn't know that -- and we treated these patients the same way -- we'd get massive differences in treatment response.

Details I do understand:
Start with 108 patient samples that have corresponding clinical, molecular, pathology AND outcome data.
Have someone who understands that experimental design needs to be done up front. Up front. You need to think about this. Maybe get a statistician to say a lot of boring things but help you so that you can draw meaningful data out later.

TMT 6-plex was used with pooled controls and lots of smart statistics to combine all the data.
Combine the output with genomics data you also get on all the patients. (Q Exactive Plus for the TMT. Sorry MS3 nerds. MS2 totally works). DIA is also employed with little tiny 5 Da windows!

Instead of making fun of the other technology (which...I do all the time, of course...look, I realize RNA technologies have value. I just don't think they have 100x the value of protein data, but that's what the outside world spends on the RNA stuff) combine it.

Instead of making fun of how primitive clinical diagnostic assays in the US are because we have to give $99 out of every $100 we spend on healthcare here to corporate money hoarders, use these data to help make sense of the patterns you've found with these modern assays your hospitals could totally afford if we'd recognize that being a billionaire is actually a hoarding disease that is way more gross than having 32 cats in your house.

What can you get if you combine all this? New and more powerful therapeutic opportunities for disease subtypes.

Okay -- I lied -- I was going to type a lot. Check this out: You've developed a great new chemotherapeutic and it goes through all the hurdles to get to human clinical trials. You get a bunch of patients with squamous lung cell cancer -- if you didn't know there were these important subgroups and lumped them all together you could fail that trial! For a drug that could totally and completely help some of the patients in that subgroup!

Awesome study. 100% recommended. Lots and lots of words in it I don't understand, but I'm still really optimistic about it.

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