Background: Molecular changes associated with the initiation of the epithelial to mesenchymal transition
(EMT) program involve alterations of large proteome-based networks. The role of protein products mapping
to non-coding genomic regions is still unexplored.
Objective: The goal of this study was the identification of an alternative protein signature in breast cancer cellular
models with a distinct expression of EMT markers.
Methods: We profiled MCF-7 and MDA-MB-231 cells using liquid-chromatography mass/spectrometry (LCMS/
MS) and interrogated the OpenProt database to identify novel predicted isoforms and novel predicted proteins
from alternative open reading frames (AltProts).
Results: Our analysis revealed an AltProt and isoform protein signature capable of classifying the two breast
cancer cell lines. Among the most highly expressed alternative proteins, we observed proteins potentially associated
with inflammation, metabolism and EMT.
Conclusion: Here, we present an AltProts signature associated with EMT. Further studies will be needed to define
their role in cancer progression.