The 4th Immuno-Oncology World Congress

Spatial biology has transformed our understanding of the tumor microenvironment (TME) by enabling the study of tissue composition and intercellular interactions at a single-cell level while preserving spatial context. Combining the detection of spatial markers, such as RNA and protein targets, can provide valuable insights into unique infiltrating immune cell populations and their activation states. 

Here, we propose a novel approach that combines RNAscope™ and sequential immunofluorescence (seqIF™) protocols for simultaneously detecting RNA and protein targets. The integrated same-slide multiomics protocol is automated on the COMET™ platform, an advanced tissue staining and imaging platform with precise temperature control and full workflow automation, ensuring optimal efficiency and reproducibility. 

We developed an integrated protocol for the automated detection of a 12-plex RNA panel, followed by consecutive cycles of seqIF™, with two protein markers detected per cycle. We included antibodies to detect infiltration of T cells, B cells, macrophages, and other immune cells in combination with RNA probes for key biomarkers such as chemokines and cytokines. Combining RNA and protein codetection, we gained extensive insights into the TME molecular landscape, uncovering co-expression patterns and relationships between RNA and proteins within individual cells. 

Our results demonstrate the successful implementation of the combined RNAscope and seqIF™ protocols on COMET™. Preserving spatial context and intercellular relationships, this approach offers a more holistic understanding of the TME molecular landscape and the complex cellular interactions exhibited by different cell populations. Multiomics analysis will open new perspectives for personalized medicine and the discovery of novel therapeutic targets.