title: Proteomic maps of breast cancer subtypes.
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.
authors.affiliation: Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried 82152, Germany.|Computational Systems Biochemistry, Max Planck Institute of Biochemistry, Martinsried 82152, Germany.
authors.forename: Stefka
authors.initials: S
authors.lastname: Tyanova
authors.affiliation: Department of Biomedical Sciences, University of Copenhagen, Copenhagen 2200, Denmark.
authors.forename: Reidar
authors.initials: R
authors.lastname: Albrechtsen
authors.affiliation: Department of Pathology, University of Turku, 20520 Turku, Finland.
authors.forename: Pauliina
authors.initials: P
authors.lastname: Kronqvist
authors.affiliation: Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried 82152, Germany.|Computational Systems Biochemistry, Max Planck Institute of Biochemistry, Martinsried 82152, Germany.
authors.forename: Juergen
authors.initials: J
authors.lastname: Cox
authors.affiliation: Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried 82152, Germany.
authors.forename: Matthias
authors.initials: M
authors.lastname: Mann
authors.affiliation: Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried 82152, Germany.|Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv-Yafo 6997801, Israel.
authors.forename: Tamar
authors.initials: T
authors.lastname: Geiger
mesh_terms: D001943:Breast Neoplasms / Q000145:classification* / Q000378:metabolism*; D005260:Female; D015972:Gene Expression Regulation, Neoplastic / Q000502:physiology*; D006801:Humans; D040901:Proteomics / Q000379:methods*; D059467:Transcriptome