ac5b03040_si_006.xlsx (551.42 kB)
Triomics Analysis of Imatinib-Treated Myeloma Cells Connects Kinase Inhibition to RNA Processing and Decreased Lipid Biosynthesis
dataset
posted on 2015-11-03, 00:00 authored by Susanne
B. Breitkopf, Min Yuan, Katja P. Helenius, Costas A. Lyssiotis, John M. AsaraThe combination of metabolomics,
lipidomics, and phosphoproteomics
that incorporates triple stable isotope labeling by amino acids in
cell culture (SILAC) protein labeling, as well as 13C in
vivo metabolite labeling, was demonstrated on BCR–ABL-positive
H929 multiple myeloma cells. From 11 880 phosphorylation sites,
we confirm that H929 cells are primarily signaling through the BCR–ABL–ERK
pathway, and we show that imatinib treatment not only downregulates
phosphosites in this pathway but also upregulates phosphosites on
proteins involved in RNA expression. Metabolomics analyses reveal
that BCR–ABL–ERK signaling in H929 cells drives the
pentose phosphate pathway (PPP) and RNA biosynthesis, where pathway
inhibition via imatinib results in marked PPP impairment and an accumulation
of RNA nucleotides and negative regulation of mRNA. Lipidomics data
also show an overall reduction in lipid biosynthesis and fatty acid
incorporation with a significant decrease in lysophospholipids. RNA
immunoprecipitation studies confirm that RNA degradation is inhibited
with short imatinib treatment and transcription is inhibited upon
long imatinib treatment, validating the triomics results. These data
show the utility of combining mass spectrometry-based “-omics”
technologies and reveals that kinase inhibitors may not only downregulate
phosphorylation of their targets but also induce metabolic events
via increased phosphorylation of other cellular components.