Spatial multi-omic analysis of the tumor microenvironment using high-plex HCR RNA and proteomic immune profiling on the CellScape platform 4057

Abstract Description The tumor immune microenvironment (TiME) accommodates significant transcriptomic and proteomic heterogeneity, and understanding this heterogeneity is key to the development of cancer treatments. Most analytical approaches provide only one type of biological readout and/or lack spatial information needed to decipher TiME complexity. We developed a new spatial multi-omics toolset to comprehensively study the TiME transcriptomic and proteomic readouts with single cell resolution. We used the CellScape™ Precise Spatial Proteomics platform with enhanced photobleaching in cyclic immunofluorescence (EpicIF) technology to detect 12+ RNA targets via HCR™ Gold RNA-FISH and 24+ protein markers via multiplex immunofluorescence (mIF) on the same formalin-fixed paraffin-embedded (FFPE) tissue sample. RNA-FISH target probes were added to the tissue sample after antigen retrieval, and tissues were then mounted in CellScape fluidic chambers to enable on-instrument staining, imaging, and signal removal. The RNA-FISH assay was followed by a 24-plex mIF assay containing antibodies against common immune-oncology biomarkers. Multiomic data from human tonsil, colon and breast tissues showed high conformity between RNA-FISH and mIF assays on the CellScape platform. The combined assay revealed differential biomarker expression profiles associated with immune-regulatory processes in the tumor samples and provided detailed insight into immune and inflammatory processes of the TiME. Topic Categories Tumor Immunology: Cellular Responses and Tumor Microevironment (TIME)