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.
