Spatial Profiling of Immune Cell Gene Signatures in the Tumor Microenvironment

Complex tissues with high cellular heterogeneity require single cell technologies both at the transcriptomic and spatial level to fully interrogate the cell types within them. Simultaneous detection of multiple markers is critical to obtain meaningful information from patient samples using single cell platforms. Single cell technologies enable precise analysis of heterogenous tissues to elucidate key therapeutic targets and biomarkers. In addition, studying target gene expression with spatial context is vital for understanding the cellular organization and function within the tissue. Recognizing the significance of spatial biology, Nature Methods declared spatially resolved transcriptomics as the method of the year in 2020.

RNAscope™ in situ hybridization (ISH) technology has been used for single molecule detection of RNA transcripts at single cell and sub-cellular resolution in the tissue. The proprietary “double Z” probe design in combination with the advanced signal amplification enables highly specific and sensitive detection of the target RNA. Over the years, the RNAscope technology has evolved to encompass the detection of short RNA targets and splice variants, miRNAs and more recently, DNA targets.

This document demonstrates the capabilities of a multiplexed in situ transcriptomic approach for the spatial mapping of target genes in highly complex and heterogenous FFPE tumor tissues using the RNAscope HiPlex v2 assay.