Assessing Cell-Specific Delivery and Efficacy of Therapeutic Oligonucleotides Using Combined RNAscope Plus and Protein Multiplexing in FFPE Tissue.

ISH/RNAscope is widely used to detect mRNA in tissue sections. The RNAscopePlus assay (Bio-Techne) enables the detection of one siRNA/ASO/miRNA, up to three mRNAs, and one protein for cell-specific analysis of biodistribution and target knock-down. The latest introduction of a protease-free RNAscope workflow allows for the detection of more proteins in the same tissue section by using the tyramide signal amplification (TSA) workflow with heat mediated antibody stripping (or comparable stripping methods). Integrating this automated assay (on Leica BOND Rx) with the PhenoImager HT imaging system and Opal dyes (Akoya Biosciences) creates a powerful tool for high-throughput tissue analysis of oligonucleotides. Furthermore, utilizing the autofluorescent tissue properties acquired by the proprietary filter in the PhenoImager HT allows to train deep learning classifiers for advanced image analysis. The assay is especially valuable in the development of therapeutic oligonucleotides, where biodistribution and efficacy read outs can be attained for a larger set of samples in an automated and streamlined way.