Large-Scale Analysis of Breast Cancer-Related Conformational Changes in Proteins Using SILAC-SPROX

Proteomic methods for disease state
characterization and biomarker
discovery have traditionally utilized quantitative mass spectrometry
methods to identify proteins with altered expression levels in disease
states. Here we report on the large-scale use of protein folding stability
measurements to characterize different subtypes of breast cancer using
the stable isotope labeling with amino acids in cell culture and stability
of proteins from rates of oxidation (SILAC-SPROX) technique. Protein
folding stability differences were studied in a comparison of two
luminal breast cancer subtypes, luminal-A and -B (i.e., MCF-7 and
BT-474 cells, respectively), and in a comparison of a luminal-A and
basal subtype of the disease (i.e., MCF-7 and MDA-MB-468 cells, respectively).
The 242 and 445 protein hits identified with altered stabilities in
these comparative analyses included a large fraction with no significant
expression level changes. This suggests thermodynamic stability measurements
create a new avenue for protein biomarker discovery. A number of the
identified protein hits are known from other biochemical studies to
play a role in tumorigenesis and cancer progression. This not only
substantiates the biological significance of the protein hits identified
using the SILAC-SPROX approach, but it also helps elucidate the molecular
basis for their disregulation and/or disfunction in cancer.