IDRM Spatial Transcriptomics Platform

Relationships between different resident and infiltrating cell types with the cellular matrix are recognized as key components that define tissues. One way to profile individual cells is to use technologies that allow all the genes in each cell to be sequenced so we can determine which genes might regulate how the cell behaves in a tissue of interest, either during health or disease. However, this involves separating out cells from the tissue and so we lose important information as to how cells interact with each other and the local environment. To this end, being able to profile genes within cells whilst they remain intact within tissues is a major advance, as has been pioneered commercially by NanoString with the GeoMx Spatial Profiler. We wish to utilise such a profiler within the Institute of Developmental Biology & Regenerative Medicine (IDRM) at the University of Oxford, and also make it available to colleagues in the Kennedy Institute of Inflammation and Rheumatology (KIR) and Institute of Biomedical Engineering (IBME) on the Old Road Medical Campus and across the wider Medical Sciences and Maths, Physics and Life Sciences Divisions. Specifically, we propose to use the GeoMx Spatial Profiler to provide molecular profiles of neighbouring cells within tissues, and to detect changes in gene or protein expression during tissue/organ development, normal function and in response to injury or disease.

Single cell-omics technologies have revolutionised biology in recent years. The ability to acquire whole transcriptomes or proteomes (global gene and protein expression data) from single cells has provided significant molecular insight into physiological and pathophysiological cell biology and functional heterogeneity across cell types and lineages within normal and diseased tissues. That said, a major limitation is the need to dissociate cells to acquire the sequence data. As such, the loss of spatial resolution and lack of insight into important cell-cell and cell-tissue interactions is a major drawback. The NanoString GeoMx Digital Spatial Profiler addresses this by measuring spatial RNA and protein levels within heterogeneous tissue samples. Combining both multiplexed nucleic acid and protein on the same platform provides the ability to spatially resolve RNA when suitable antibodies do not exist, at a resolution that captures 20 (protein detection) and 100 (RNA detection) cells in situ. We propose that the GeoMx Spatial Profiler will act as a key component of a small -omics research facility within the IDRM, complementing existing scRNA/ATAC-Seq and Codex spatially resolved multiplex immunofluorescence. Candidate genes/proteins identified by the GeoMx Spatial Profiler will be assimilated into a lower throughput Codex profiling of 40+ protein markers in tissue samples at single cell resolution thus ensuring a pipeline from genome/proteome-wide spatial information in tissues down to cohorts of genes/proteins within single resident cells. We will use the GeoMx Spatial Profiler (combined with Codex) to define the molecular signatures in cellular niches in tissues and detect cellular gene/protein expression changes during normal homeostasis, in response to injury or disease and/or therapeutic intervention.