Combining xenium in situ spatial transcriptomics and imaging mass cytometry on a single tissue section

Spatial imaging technologies provide an expansive view of tissue microenvironments through high-plex profiling of protein and molecular targets in situ. Imaging mass cytometry (IMC; Standard BioTools) is a trusted method for defining immune phenotypes based on up to 40 protein targets, whilst Xenium in situ spatial transcriptomics (Xenium; 10x Genomics) is an emerging platform that can measure up to 5000 mRNA markers simultaneously. Although these platforms can reveal valuable insights on their own, there is an increasing need to analyse samples using a multi-omics approach to further our understanding of complex biological processes. To address this, we have assessed a novel dual-platform workflow that combines Xenium and IMC on a single formalin-fixed paraffin-embedded tissue section to enable the spatial profiling of both mRNA and protein targets at single-cell resolution. The feasibility of the workflow was determined by comparing the staining quality of IMC performed after Xenium to that of IMC performed alone on an adjacent tissue section, confirming that Xenium has little to no negative impact on subsequent IMC protein staining. Although the location of transcripts picked up by Xenium correlated with the corresponding proteins picked up by IMC at a global scale, discrepancies between the two technologies were apparent at the single-cell level. This is to be expected, as biologically transcript expression does not always correlate with protein, and both platforms have their own technical limitations. However, when we analyse T cells identified by both technologies, as opposed to T cells identified by Xenium or IMC alone, it produces the most biologically meaningful results at both the transcript and protein level for specific T cell markers. These results highlight how integration of the two platforms, identifying the presence of both RNA and protein, can foster a more comprehensive view of cellular landscapes and provide a greater depth of functional capabilities and cellular interactions.