Lectin Chromatography/Mass Spectrometry Discovery Workflow Identifies Putative Biomarkers of Aggressive Breast Cancers

We used a lectin chromatography/MS-based approach to
screen conditioned
medium from a panel of luminal (less aggressive) and triple negative
(more aggressive) breast cancer cell lines (n = 5/subtype).
The samples were fractionated using the lectins Aleuria aurantia (AAL) and Sambucus nigra agglutinin (SNA), which
recognize fucose and sialic acid, respectively. The bound fractions
were enzymatically N-deglycosylated and analyzed
by LC–MS/MS. In total, we identified 533 glycoproteins, ∼90%
of which were components of the cell surface or extracellular matrix.
We observed 1011 glycosites, 100 of which were solely detected in
≥3 triple negative lines. Statistical analyses suggested that
a number of these glycosites were triple negative-specific and thus
potential biomarkers for this tumor subtype. An analysis of RNaseq
data revealed that approximately half of the mRNAs encoding the protein
scaffolds that carried potential biomarker glycosites were up-regulated
in triple negative vs luminal cell lines, and that a number of genes
encoding fucosyl- or sialyltransferases were differentially expressed
between the two subtypes, suggesting that alterations in glycosylation
may also drive candidate identification. Notably, the glycoproteins
from which these putative biomarker candidates were derived are involved
in cancer-related processes. Thus, they may represent novel therapeutic
targets for this aggressive tumor subtype.