Immunophenotyping by Spatial Biology.

Studying the transcriptome and the proteome of cells is essential for gaining a detailed understanding of cellular behavior, development, drug action, and disease progression. Spatial biology emerges to advance our ability to study the expression of molecules within tissues while preserving their natural spatial context. These cutting-edge technologies enable the mapping of thousands of individual cells in their original environment by detecting the location and biological quantity of cellular contents, such as RNAs and proteins. Here, we present a protocol to combine spatial transcriptomics (Xenium) and spatial proteomics (PhenoCycler-Fusion) within 8 days on the same tissue section to successfully study the expression of hundreds of RNAs and tens of proteins simultaneously. The combination of these two technologies and consequent integration of the two data layers together with high-resolution H&E images allows for the extraction of a maximum of information from a single tissue section. Application of this protocol and the resulting integrated data will help researchers to understand complex biological processes and disease mechanisms, supporting more nuanced research in molecular biology and pathology.