Molecular profiling of HER2-Related protein networks in formalin-fixed and paraffin-embedded cancer tissues

Mapping tumour cell protein networks in routinely processed clinical samples, such as formalin-fixed and paraffin-embedded (FFPE) breast cancer tissues, will be critical for realizing the promise of personalized molecular therapy as only a subset of patients will respond. The quantification and characterisation of deregulated signalling molecules, including HER2, is a very promising approach for the identification of new suitable therapy targets and for the selection of those patients who will receive the greatest benefit from individualised treatments. In this regard the reverse phase protein array (RPPA) is a powerful technology for quick and simultaneous analysis of many patient samples allowing relative and absolute protein quantifications. Importantly, it requires only limited amounts of routine clinical material (e.g. biopsies). In this article we present a straight forward approach for extract-based determination of protein levels for HER2 and downstream signalling molecules in FFPE cancer tissues in order to define patient subgroups for therapy.