TGFβ family imaging - Simultaneous quantification of RNA levels (RNAscope) and protein levels (IF) in cancer tissue

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Project Description

Transcriptomic analysis of normal human and cancer cells revealed that the transforming growth factor β (TGFβ) signaling pathway regulates the expression of about 2,000 genes, including protein-coding and non-coding RNAs. Our group uses functional cell-based assays to confirm the regulation of such genes by TGFβ signaling and the function of such genes in cancer biology. We also focus on expression analysis of these genes at the protein and RNA level in fixed tumor tissues. Using in situ analysis (classical immunohistochemistry, multiplex immunofluorescence on the Akoya/Polaris system, in situ proximity ligation, RNAscope) whereby one of these techniques or pairwise combinations are applied, we aim at investigating whether there are correlations in the expression levels of a give gene (RNA or protein level) to a marker of TGFβ signal transduction, usually a key protein of the TGFβ signaling cascade, i.e. phospho-Smad2 or phospho-Smad1. More specifically, using tumor images from individual experiments or in the form of a tissue microarray (TMA), we aim at generating quantifications by measuring the RNA1-positive cells and the pSmad2-positive cells and perform a statistical correlation test in order to ask whether RNA1-positive cells positively or negatively correlate with pSmad2-positive cells.

Image: Green: RNAscope signal of RNA1; red: mIF signal of phospho-Smad2; blue: DAPI. A tumor core plus a magnified detail are shown.