Vizgen SITC Poster 2023: Investigating cancer and immune cell interactions in the tumor microenvironment with MERFISH
Introduction
In situ profiling of cancer tissue with spatial genomics technologies enables researchers to map and catalog various cancer cell subtypes, as well as their interactions with the immune system and the surrounding landscape of stroma, fibroblasts, and vasculature in complex biological tissue. The Vizgen MERSCOPE® Platform is built on Multiplexed Error-Robust Fluorescence in situ Hybridization (MERFISH) technology and enables the measurement of RNA expression for hundreds of genes with sub-cellular resolution in intact FFPE and frozen tissue sections.1 Here, we use the MERSCOPE Platform with the Predesigned Immuno-oncology Panel* to spatially profile a set of 16 tumor tissue samples from 8 different human cancers. By using this 500-gene panel to assess cancer type-specific genes, select immune genes, proto-oncogenes, and tumor suppressor genes, we spatially profiled the gene expression of cell types across the tumor samples. We were able to resolve common cancer and somatic cell clusters across tissue and sample donor backgrounds. To more deeply assess the landscape of tumor cell expression within these tumors, we re-clustered the pan-tumor cancer clusters and demonstrated a robust recapitulation of tissue-specific signatures of cancer. We then compared the spatial neighborhoods of the cancer clusters to those of somatic cell clusters and quantified the effective overlap between pairs of clusters to evaluate the effective colocalization of various cell types across all 16 human tumor tissue samples. Our results demonstrate that different avenues of carcinogenesis can generate similar immuno-oncological interactions across very different cancer types.
*RUO only, not approved for diagnostic or therapeutic purposes.