Center for Quantitative Biology: A focus on "omics", from organisms to single cells Supplement 2

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Project Summary / Abstract Macrophages and granulocytes (e.g., neutrophils) are considered key players in the pathogenesis of glomerular kidney injury, glomerulonephritis (GN). However, the intra-renal mechanisms and sub-cellular specificity by which these myeloid cells cause glomerular injury are not known. This large gap in knowledge stems from the limitations in approaches to capture and profile these highly heterogeneous cells. For example, neither normal density (NDN) nor low-density neutrophils (LDN), both implicated in GN, are not captured in scRNAseq studies of kidneys and urine due to the loss of these cells by sample freezing. Given their heterogeneity and importance in disease, implementing technologies that define myeloid populations in GN kidneys and how they interact with renal structural cells is critical for understanding their pathogenic role. Our spatial transcriptomic data reveal macrophages, NDNs, and LDNs in GN kidneys, with unique and shared spatial organizations. Using DNA methylation (DNAm) data from urine cells, we capture both macrophages and granulocytes in GN urine. The overall objectives in this proposal are to: (i) define myeloid populations in GN kidneys, (ii) identify pathogenic interactions between macrophages vs. granulocytes with renal structural cells, and (iii) implement urine DNAm assay to profile myeloid cells in GN. The central hypothesis is that glomerular interactions with LDNs reflect LN immunopathology and worse kidney function and that urine DNAm will allow a less invasive approach to evaluate the pathogenic myeloid populations. The hypothesis will be tested with two specific aims: 1) Define macrophage and granulocyte populations and their communication pathways with structural cells in GN kidneys and 2) Quantify and define kidney infiltrating myeloid populations in urine using DNAm. In Aim 1, single-cell spatial transcriptomics will be used to define in situ myeloid heterogeneity in GN kidneys by integrating bulk RNA-seq-derived transcriptomic signatures of sorted subpopulations. Pathogenic interactions with glomerular, interstitial, and tubular endothelial and epithelial structures will be defined. In Aim 2, macrophages and granulocytes will be quantified in urine using unique DNAm signatures in relation to kidney function. This research is innovative because it will propose molecular and cellular pathways involved in glomerular injury as well as introduce a novel approach to detect pathogenic cell populations via non-invasive urine analyses. This research is significant because it is expected to provide a scientific rationale for targeting specific myeloid populations in GN.