GeoMx digital spatial profiler: expanding the capabilities of the CVR Virus Genomics and Bioinformatics platform

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The CVR Viral Genomics and Bioinformatics is a team of scientists which use sequencing techniques and computational methods to understand viral infections.Scientists working on genomics and bioinformatics use DNA sequencing to determine the sequence of nucleotides within a DNA molecule. Every organism has a unique sequence of nucleotides, including viruses, and we can use that sequence to understand many aspects of their biology. At the CVR, the Viral Genomics and Bioinformatics team also does RNA sequencing (RNA-seq). This is a type of experiment that measures the expression of genes. In other words, we determine which of the genes encoded by our DNA are turned on or off and at what extent. This is particularly useful to understand how our cells respond when they become infected by viruses, ultimately leading to clues on the mechanisms by which viruses cause disease. We know that tissues are a complex grouping of different cell types, and that each cell type may respond differently to a viral infection. We also know that tissues can have compartments and that spatial information is important during infection. However, the protocols most frequently used by the research community require homogenisation of tissues in a single mixture, containing all the RNA molecules. This means that all the information provided by each individual cell, as well as the spatial context is lost.In this application, we are applying for funds to invest in a new technology that retains the spatial information. With the GeoMx from NanoString, we retrieve RNA-seq information from the tissues while maintaining the spatial context. This is important because it enables us to visualise how different cells or areas of a tissue are turning their genes on and off and overlap that information with images which indicate where in the tissue is the infection taking place or if are there any lesions, amongst other features.Overall, this new instrument will enable us to understand how viruses infect us based on RNA-seq data from different cell types, spatial data and other characteristics of the tissues, enabling a more complete view of infections and how we respond to them.