Combined multi-gene analysis at the RNA and protein levels in single FFPE tissue sections

Novel approaches of individualized medicine require rapid analyses of comprehensive multi-gene expression patterns both at the RNA and protein levels. Optimally these analyses are achieved with minimal amounts of tissues, which are derived from routine procedures of clinical diagnostics. We demonstrate the parallel analyses of gene expression of six different genes at the RNA and protein levels in two consecutive sections of routinely processed FFPE tissues. This was achieved by combination of multi-epitope-ligand cartography (MELC) and fully automatically magnetic bead-based RNA extraction and subsequent qRT-PCR analysis. Our work provides proof-of-principle that comprehensive analyses of multi-gene expression patterns can be achieved by the combination of these two high content technologies. This may provide new perspectives for the determination of pathogenic gene expression in the framework of individualized medicine. •MELC is a high content immunohistochemical approach at the single cell level.•Automatically extracted RNA of single rountinely FFPE-processed tissue sections is suitable for qRT-PCR.•We present successful combination of the technologies in single consecutive sections.•Our technology provides new impact for high content screenings in molecular medicine.