Abstract
How can we get more information on drug discovery and disease from a single section of tissue? Most tissues are heterogenous with multiple discrete compartments, yet traditional ‘omics technologies take a homogenized snapshot of tissues, resulting in destruction of spatial information and combination of separate molecular signatures into a single entity. This limitation can be overcome by GeoMx Digital Spatial Profiling, which enables high-plex proteomics and transcriptomic analysis of FFPE tissue sections in regions as small as only a few cells. In January 2021 Nature Methods named the NanoString GeoMx platform their method of the year. Here, we showcase some examples of these assays used within projects at the Medicines Discovery Catapult.
GeoMx protein assays consist of a panel of 20-80 antibodies focussed on a specific field of interest, while transcriptomics assays can range from 1,600 RNAs to the whole transcriptome (~18,000 RNAs). This allows for not only profiling of individual regions of interest within the tissues, but also relationships between adjacent regions, such as through ligand-receptor interactions. Additionally, GeoMx data can be used in combination with single-cell RNA-seq datasets in order to spatially deconvolve cell types within tissues, adding the spatial aspect back into single-cell RNA-seq. The RNA assays in particular represent a huge technological leap forward by enabling full transcriptomic profiling of FFPE tissues within a region the size of only a few cells, with a growing list of downstream analysis tools available to further profile FFPE tissues.
