A robust experimental and computational framework analysis at multiple resolutions, modalities and coverages

We assessed the utilities of integrating four advanced sequencing and multiplex imaging technologies to study cancer-immune cell interactions. These four technologies include single-cell RNA sequencing and Spatial Transcriptomic (both measuring over >20,000 genes), RNA In Situ Hybridization (multiplex 4-12 genes) and Opal multiplex protein staining (4-9 proteins). We evaluated the approach to discover and validate cell-cell interaction in situ through in-depth analysis of two types of cancer, basal cell carcinoma (BCC) and squamous cell carcinoma (SCC), which account for over 70% of skin cancer cases.