Molecular Portrait of Breast-Cancer-Derived Cell Lines Reveals Poor Similarity with Tumors

Breast-cancer-derived
cell lines are an important sample source
for cancer proteomics and can be classified on the basis of transcriptomic
analysis into subgroups corresponding to the molecular subtypes observed
in mammary tumors. This study describes a tridimensional fractionation
method that allows high sequence coverage and proteome-wide estimation
of protein expression levels. This workflow has been used to conduct
an in-depth quantitative proteomic survey of five breast cancer cell
lines matching all major cancer subgroups and shows that despite their
different classification, these cell lines display a very high level
of similarity. A proteome-wide comparison with the RNA levels observed
in the same samples showed very little to no correlation. Finally,
we demonstrate that the proteomes of in vitro models of breast cancer
display surprisingly little overlap with those of clinical samples.