Implementation of automated staining in conjunction with spatial analyses

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Project Summary We are in the process of building a facility that will take advantage of emerging spatial transcriptomic and proteomic technologies to study the immune landscape in clinical samples. Originally developed under the aegis of the Mayo Clinic Breast Cancer Translational Genomics initiative, the Spatial Biology facility focuses largely on analysis of solid tumors. Our central objective is to define the fundamental properties that underlie the relationship between clinical phenotype (most commonly therapeutic response) and the number, types, activities, and locations of immune cells within the tumor. It has, however, become increasingly clear that similar features may underlie neurodegenerative diseases of aging; and we have initiated several projects related to the immune landscape of Alzheimer’s disease and neuronal aging in mouse models. Our core technology is NanoString GeoMx, which enables us to interrogate the transcript and/or protein expression profiles of user-defined areas of interest in a single 5-micron formalin-fixed, paraffin-embedded tissue section. We routinely carry out a range of analyses, from digital spatial profiling of multi-plex protein abundance to whole transcriptome analysis. These applications utilize the GeoMx platform, which we have been running since September 2019. We are currently beta testing the NanoString CosMx platform, which provides single cell level resolution for both transcriptomic and proteomic analysis. The Spatial Biology facility is fully operational at this time. The model is something of a hybrid between a collaborative arrangement and a core facility. We play a very active role in experimental design of these spatial biology projects, and we recover costs through a recharge mechanism. The demand for these services has been little short of overwhelming. To date we have analyzed almost 4000 clinical samples. All of these sample were processed manually, including a rather labor-intensive staining procedure that requires the better part of two days. Our goal is to automate this step, thereby providing for increased throughput, experimental consistency, and more efficient use of time for our limited personnel. To this end, we are requesting funds to purchase a Leica Bond RXm autostainer.