Proteomic maps of breast cancer subtypes

Stefka Tyanova, Reidar Albrechtsen, Pauliina Kronqvist, Juergen Cox*, Matthias Mann, Tamar Geiger

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

Abstract

Systems-wide profiling of breast cancer has almost always entailed RNA and DNA analysis by microarray and sequencing techniques. Marked developments in proteomic technologies now enable very deep profiling of clinical samples, with high identification and quantification accuracy. We analysed 40 oestrogen receptor positive (luminal), Her2 positive and triple negative breast tumours and reached a quantitative depth of >10,000 proteins. These proteomic profiles identified functional differences between breast cancer subtypes, related to energy metabolism, cell growth, mRNA translation and cell-cell communication. Furthermore, we derived a signature of 19 proteins, which differ between the breast cancer subtypes, through support vector machine (SVM)-based classification and feature selection. Remarkably, only three proteins of the signature were associated with gene copy number variations and eleven were also reflected on the mRNA level. These breast cancer features revealed by our work provide novel insights that may ultimately translate to development of subtype-specific therapeutics.

Original languageEnglish
Article number10259
JournalNature Communications
Volume7
DOIs
StatePublished - 4 Jan 2016

Funding

FundersFunder number
Israel Center of Research Excellence Program41/11
Israel Cancer Research Fund
Max-Planck-Gesellschaft

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