Biomarker Discovery with Morphological Context
Changing How Tissue Specimens are Analyzed
Historically, immunohistochemistry and immunofluorescence have been used to assess spatial heterogeneity of proteins and nucleic acids in tissue slices. However, these techniques are of limited utility due to restricted dynamic range, difficult quantitation, and limited multiplexing capability.
NanoString’s GeoMx™ Digital Spatial Profiler* combines standard immunofluorescence techniques with digital optical barcoding technology to perform highly multiplexed, spatially resolved profiling experiments. In a single reaction, the DSP technology performs whole slide imaging with up to four fluorescent stains to capture tissue morphology and select regions of interest for high plex profiling. The ability to perform tissue morphology guided profiling experiments increases the likelihood of capturing rare events often missed by typical grind and bind assays. The DSP chemistry enables spatially resolved high plex profiling of RNA and protein targets on just two serial sample sections. The ability to perform multianalyte analysis enables deep characterization of the sample.
What is Digital Spatial Profiling?
GeoMx Digital Spatial Profiler is a novel platform developed by NanoString. Digital Spatial Profiling is based on nCounter® barcoding technology and enables spatially resolved, digital readout of up to 96 proteins or RNA targets in a multiplexed assay. The assay relies upon antibody or RNA probes coupled to photocleavable oligonucleotide tags. After hybridization of probes to slide-mounted formalin fixed paraffin-embedded (FFPE) tissue sections, the oligonucleotide tags are released from discrete regions of the tissue via UV exposure. Released tags are quantitated in a standard nCounter assay, and counts are mapped back to tissue location, yielding a spatially-resolved digital profile of analyte abundance.
A formalin-fixed, paraffin-embedded (FFPE) or fresh frozen tissue section is stained with a cocktail of standard morphology markers (i.e. fluorescent antibodies) combined with either oligo-tagged antibodies (protein) or oligo-tagged ISH probes (RNA) that contain a photocleavable linker. Regions of interest (ROI) are selected by the user, and Areas of Illumination (AOIs) are identified by the ROI selection (if using geometric) or by morphology markers (if using autosegmentation), where oligos from selected regions are released upon exposure to UV light. The photocleaved oligos are then collected via a microcapillary tube and stored in microplate wells. Finally, the photocleaved oligos from the spatially-resolved ROIs in the microplate are analyzed using standard NanoString nCounter® instruments. Alternatively, the photocleaved oligos can be ported into a standard library preparation workflow for analysis on NGS platforms.
The GeoMx DSP is paired with data analysis software that allows users to easily visualize their data, and lowers their barrier to data interpretation. The data analysis solution will include QC and normalization for reproducibility as well as several data visualization methods for various types of inquiries. The software ties the expression data back to the image, such that selecting a data point within a data visualization automatically highlights, within the image, the ROI from which the expression data was generated.
For Research Use Only. Not for use in diagnostic procedures.