High-plex Multiomic Analysis in FFPE at Subcellular Level by Spatial Molecular Imaging

Abstract

Abstract The Spatial Molecular Imaging platform (CosMx TM SMI, NanoString Technologies, Seattle, WA) utilizes high-plex in-situ imaging chemistry for both RNA and protein detection. This automated instrument provides 1000’s of plex, at high sensitivity (1 to 2 copies/cell), very low error rate (0.0092 false calls/cell) and background (∼0.04 counts/cell). The imaging system generates three-dimensional super-resolution localization of analytes at ∼2 million cells per sample, four samples per run. Cell segmentation is morphology-based using antibodies, compatible with FFPE samples. Multiomic data (980 RNAs, 108 proteins) were measured at subcellular resolution using FFPE tissues (non-small cell lung (NSCLC) and breast cancer) and allowed identification of over 18 distinct cell types, 10 unique tumor microenvironments, and 100 pairwise ligand-receptor interactions. Over 800,000 single cells and ∼260 million transcripts data are released into the public domain allowing extended data analysis by the entire spatial biology research community.