*Purpose: Males with chronic kidney disease (CKD) experience a more rapid decline in kidney function and progression to end-stage kidney disease than females. In vitro studies further support a sexually dimorphic response to kidney injury. The molecular basis for the poor prognosis associated with male sex in CKD remains unclear. Single-cell RNA sequencing enables precise characterization of the transcriptional signature from individual cells. Such sex-specific single cell transcriptional profiles would transform our understanding of the impact of sex on CKD progression.

*Methods: We sequenced single-cell suspensions of 19 pre-implantation kidney biopsies from 9 male and 10 female living kidney donors (10X Genomics). 10 biopsies (5 male, 5 female) underwent CD45+ selection to enhance representation of immune cell populations. Mapping and quantification were performed using the Cellranger software package. Ambient RNA contamination was corrected using SoupX, and doublets removed using DoubletFinder. Normalization and clustering were performed using the Seurat pipeline. Sex-based transcriptional differences were identified using varimax rotational analysis.

*Results: All expected parenchymal populations from both glomerular and tubulointerstitial compartments featured on our map (Fig1A). Striking sex-specific differences in gene expression were identified in proximal tubular (PT) cells, which contributed ~80% of all cells in these healthy kidneys (Fig1B). Interestingly, X/Y-chromosome encoded genes and phenotypic genes (e.g. LRP2) were among these sex-specific genes altered in PT cells. Genes with higher expression in females were associated with important metabolic processes including detoxification, antioxidant processes and the negative regulation of cell death. In contrast, processes related to nonsense mediated decay and the cellular response to stress were enhanced in males.

*Conclusions: We have generated a comprehensive healthy kidney map with novel focus on sex-specific differences in kidney cell populations. Male and female PT epithelial cells display marked changes in genes associated with metabolism and antioxidant activities. These changes might underpin the differences in male and female susceptibility to CKD.

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