Interrogating The Biology Of Human Lupus Nephritis Using Single Cell Resolution Spatial Transcriptomics - Abstract Despite recent FDA approval of new therapies to treat lupus nephritis, most patients fail to achieve clinical remission with standard-of-care treatment. This is particularly important for pediatric patients who exhibit a higher risk for developing lupus nephritis and have a longer potential to accrue kidney damage. This emphasizes the need for greater understanding of the pathophysiology of lupus nephritis, with the expectation that this knowledge will inform the development of effective, targeted therapies for lupus nephritis. To date, pre-clinical studies have typically used animal models to identify immune pathways driving disease, but these efforts have been plagued by limited correlation with clinical benefit in humans. For this reason, the ability to directly analyze human kidney tissue from lupus nephritis patients is of significant importance. Over the past 5 years, single cell RNA-Seq (scRNA-Seq) has been used to study many immune-mediated kidney diseases, from IgA nephropathy to lupus nephritis. However, there are many limitations to standard droplet-based scRNA-Seq protocols. First, tissue dissociation can induce an artifactual transcriptional stress response and all spatial context of the data is lost. Second, several important kidney cell types (such as podocytes, rare immune populations) are sensitive to tissue dissociation and thus under-sampled by scRNA-Seq. Finally, current scRNA-Seq protocols require immediate processing of fresh kidney biopsy tissue, a major limitation for rare disorders such as childhood-onset lupus nephritis. This application leverages a major technical advance to perform spatial transcriptomic analysis at single cell resolution on archived kidney biopsy tissue. In Aim 1, we will use the GeoMX Digital Spatial Profiler (Nanostring, Inc.) to quantify whole transcriptome gene expression in affected vs. unaffected glomeruli from pediatric patients with Class III and Class IV lupus nephritis. In Aim 2, we will perform single cell spatial transcriptomics on primary and validation cohorts of pediatric lupus nephritis using the new single cell resolution CosMx Spatial Molecular Imager (Nanostring, Inc.). Finally, in Aim 3, we will compare the immune and renal stromal transcriptional signatures of lupus nephritis with other glomerulonephritides to identify shared and unique pathways in SLE. In addition to advancing our understanding of lupus nephritis pathophysiology, we anticipate that these efforts will generate a spatially-resolved cell atlas of human lupus nephritis that will be an important resource for investigators in academia and industry.
