In vivo phosphoproteomics reveals kinase activity profiles that predict treatment outcome in triple-negative breast cancer

Abstract

Triple-negative breast cancer (TNBC) lacks prognostic and predictive markers. Here, we use high-throughput phosphoproteomics to build a functional TNBC taxonomy. A cluster of 159 phosphosites is upregulated in relapsed cases of a training set (n = 34 patients), with 11 hyperactive kinases accounting for this phosphoprofile. A mass-spectrometry-to-immunohistochemistry translation step, assessing 2 independent validation sets, reveals 6 kinases with preserved independent prognostic value. The kinases split the validation set into two patterns: one without hyperactive kinases being associated with a >90% relapse-free rate, and the other one showing ≥1 hyperactive kinase and being associated with an up to 9.5-fold higher relapse risk. Each kinase pattern encompasses different mutational patterns, simplifying mutation-based taxonomy. Drug regimens designed based on these 6 kinases show promising antitumour activity in TNBC cell lines and patient-derived xenografts. In summary, the present study elucidates phosphosites and kinases implicated in TNBC and suggests a target-based clinical classification system for TNBC. ; We are grateful to the Spanish Biobanks integrated within the Spanish Network of National Biobanks for the tumor samples used in our investigations and to the Breast Cancer Group at VHIO for providing study materials. The present study was funded by FIS PI10/00288, FIS PI13/00430, and AECC Scientific Foundation "Beca de Retorno 2010"awarded to MQF; FIS PI11-00832, FIS PI14-00726, and ISCIII PIE15/00068 awarded to RC. I.Z. is a recipient of a La Caixa PhD Fellowship, 2011. S.F. is a recipient of a FPI grant (SEV-2015-0510-16-6). V.S. is supported by the Miguel Servet Program (CP14/00228). This work was also supported by the PRIME-XS project, Grant Agree- ment Number 262067, funded by the European Union Seventh Framework Program and the project Proteins At Work (project 184.032.201), a program of the Netherlands Proteomics Centre financed by the Netherlands Organisation for Scientific Research (NWO). ...