1002 Single cell transcriptomics in kidney tissue from African American patients enrolled in the accelerating medicines partnership (AMP) implicates tubular cells in the pathogenesis of APOL1 associated lupus nephritis

BackgroundThe G1 and G2 risk variants (RVs) in Apolipoprotein L1 (APOL1) associate with chronic kidney disease (CKD) and may contribute to poorer outcomes for African American (AA) patients with lupus nephritis (LN). While the pathogenetic mechanism for APOL1 related CKD remains unknown, most studies focus on glomerular injury. This study leveraged the multi- center LN AMP to evaluate APOL1 RV associated clinical phenotypes and identify whether these genetic variants influence the transcriptomic landscape in kidney cells.MethodsLN patients were consecutively enrolled in AMP at the time of a clinically indicated renal biopsy and followed for one year. Dissociated biopsies were passed through a droplet- based single-cell RNA sequencing (scRNAseq) pipeline that included quality control of sequenced libraries. Genotypes for APOL1 RVs were identified by sanger sequencing for all AA patients enrolled with available DNA.ResultsIn total, 104 AA patients were genotyped; 47 (45.2%) carried zero APOL1 RVs, 45 (43.3%) one RV, and 12 (11.5%) two RVs. RVs did not associate with baseline anti-dsDNA or complement levels, biopsy class/activity/chronicity, GFR or proteinuria (figure 1A-G). While there was a trend toward decreased GFR at one year by gene variant dosage, there was no association with changes in proteinuria (figure 1F-H). ScRNAseq yielded 88383 high quality cells in patients with zero RVs (n=30), 72288 one RV (n=28), and 28694 two RVs (n=11) spanning nine parenchymal cluster types (figure 2A). Independent of genotype, APOL1 expression was highest in podocyte, endothelial and ascending thin limb (ATL) cells (figure 2B). Median APOL1 expression was significantly higher in cells with one or two RVs in the ATL cluster but this association was not seen in podocytes or endothelial cells (figure 2C). Single cell pathway analysis revealed that the ATL cluster demonstrated greater pathway level variation between cells with two RVs vs zero than any other cluster, with the most distinguishing related to interferon signaling (increased), antigen presentation (increased), and mitochondrial function (decreased) (figure 2D). The ATL damage associated gene, lipocalin-2 (LCN2), was expressed at significantly higher levels in cells carrying two RVs (figure 2E). Likewise, the proportion of ATL cells double positive for APOL1 and LCN2 was higher in patients with two RVs (figure 2F). While it did not reach significance, the percentage of ATL cells expressing APOL1 more strongly co