NanoString Integrated Spatial Biology Platform

The goal of this equipment bid is to build upon recent advances in molecular pathology made within our local and international collaborative environment to develop a greater understanding of tissue heterogeneity through an integrated platform for high-plex profiling of both RNA and proteins in a spatially resolved manner. Recognising that cellular processes such as development, aging, neoplasia, inflammation are necessarily spatially heterogeneous, the additional power to understand these processes and their dysfunction at a spatially resolved, single cell level will be transformative is translating our research into even more impactful clinical and environmental applications. To do this we have requested support for two pieces of equipment to constitute a single Spatial Biology Platform. This technology is currently the field leader in analysing formalin fixed paraffin embedded tissue, the ideal complementary equipment for probing tissue from our adjacently located tissue bioresource and sequencing facility. This equipment provides state of the art technology to spatially profile the transcriptome and protein markers in different regions, biological compartments, or specific cell types in any heterogeneous tissue. This platform will therefore have wide applicability across biomedical and translational research in the broad University of Aberdeen Bioscience community and more widely through our already established international collaborations. This capability alongside developed expertise and a linked training portfolio will provide opportunities to enhance and expand international collaborations and networks to improve the clinical and environmental impact of our research.

GeoMx digital spatial processor (DSP) is a spatial sequencing platform developed by NanoString Technologies. The technology is based on the nCounter barcoding technology to enable spatially resolved, digital characterisation of proteins or mRNA in a highly multiplexed assay. The assay relies upon antibody or RNA probes coupled to photocleavable oligonucleotide tags. After binding of probes to slide-mounted formalin fixed paraffin-embedded (FFPE) or frozen tissue sections, the oligonucleotide tags are released from discrete regions of the tissue via UV exposure. Released tags are quantified in an nCounter assay, providing cost-effective automated solution for multiplex sequencing analysis of (protein or mRNA) targets. The simple workflow requires just 15 minutes hands-on time and produces highly reproducible data, requiring no amplification or technical replicates in ~24 hours. An alternative quantification of released tags is to use next generation whole transcriptome sequencing (already available in our core facility - although this is more expensive and takes slightly longer, it does provide a more comprehensive dataset - access to both provides more experimental breadth for diverse user needs). Counts are mapped back to tissue location, yielding a spatially resolved digital profile of analyte abundance.