Metabolic
reprogramming is an emerging cancer hallmark. It was first recognized in 1924
by Otto Warburg, who identified increased glycolysis in cancer cells even in
aerobic conditions. The interest in the link between cancer and metabolism was
re-stimulated with the identification of oncogenes and tumor suppressors that
affect metabolism and the discovery oncogenic mutations in metabolic. System-wide
analyses of breast cancer clinical samples can unravel the network changes that
occur with cancer progression and lead to better understanding of the
mechanisms of metabolic remodeling. Analysis of the protein levels reflect more
accurately the cellular phenotype than mRNA levels, however due to
technological challenges, till today, the majority of expression analyses of
breast cancer clinical samples have been performed on the transcript level.
Technological developments in the proteomic field, such as high-resolution mass
spectrometry combined with accurate quantification techniques can now enable a
global view of cancer proteomes. Stable Isotope Labeling with Amino Acids in
Cell Culture (SILAC) is a metabolic labeling technique that enables accurate
quantification of proteins in mass spectrometry-based experiments. We have
extended the applicability of SILAC to tissue sample with the development of
the super-SILAC technique, in which a mixture of heavy labeled cell lines
serves as an internal standard for tissue quantification. In combination with a
method for extraction of proteins from formalin-fixed paraffin-embedded
tissues, super-SILAC can be used to quantify panels of archived breast cancer
clinical samples. We further combined our results with advanced computational
analysis and metabolic modeling and revealed the global changes in cell growth
and metabolite utilization with cell transformation. This work is the basis for
future analysis, which aims to elucidate the biological significance of these
metabolic alterations.
