(Original Image by Terese Winslow, used here in accordance with NCI stated guidelines.)
As you can imagine -- having a tiny messed up chromosome that is part of 2 different chromosomes is in not a good thing for your cells. Major efforts have been made to develop treatments specifically targeting cells that have this event -- with the biggest ones in the 80s-90s finding tyrosine kinase inhibitors that help in some patients, but not others.
Mystery? Yup! Solution? Ultradeep SILAC phosphoproteomics sound like a great place to start!
You can check this paper out in Nature Leukemia here!
Since my faded textbook and Wikipedia supplemented understanding of this BCR-ABL thing isn't the most-in-date thing in the world, there is a lot to learn from this study. This translocation can occur in different places and form two different protein products; p190 and p210. This group artificially created this event in a SILAC murine model and tracked the tyrosine phosphoproteome. They did global un-enriched proteomics as well and the p-Tyr proteome was enriched with PTMScan® Phospho-Tyrosine.
All the proteomics was done on 50cm nanoLC columns with high resolution MS/MS (30,000 resolution) using stepped HCD (32 with 5% steps) as the lone fragmentation method. The bias in the instrument method was toward maximum sensitivity and the higher resolution was used appropriately to optimize the longer fill times employed.
What did they find?
These 2 different variants of the Philadelphia chromosome do completely different things! Yeah, they both kick in phophotyrosine cascades, but initiating in different regions and going down distinct pathways!
"We splotted these 2 patient's chromosomes on a slide and they both definitely have BCR-ABL translocations, but only one responded well nilotinib and we have no idea why...." (Hypothetical situation, I just made up), but maybe this is the hypothetical answer!
This is a solid study that I'm not doing justice at all (did I even mention the global proteomes they did here? You can check them out for yourself. ProteomeXchange PXS005209)