Background Lupus nephritis is a potentially fatal autoimmune disease, whose current treatment is ineffective and often toxic. In 2014, the National Institute of Health (NIH), industry and non-profit organizations joined their efforts with the AMP project, whose goal is to identify new diagnostic and therapeutic targets through a better understanding of the mechanisms by which individual cell types contribute to autoimmune tissue damage.

Methods To gain insights into disease mechanisms, we analyzed kidney samples from lupus nephritis patients and healthy controls using single-cell RNA-seq. Renal biopsies from 24 LN patients and 10 pre-transplant living donors (LD) were acquired across a distributed research network using a single, uniform pipeline developed by the AMP network. In brief, biopsies were cryopreserved and shipped to a centralized processing site for tissue dissociation. A total of 3541 leukocytes and 1621 epithelial cells were sorted from LN kidney samples. 438 leukocytes and 572 epithelial cells were sorted from LD biopsies. The transcriptome of those LN single tissue-infiltrating cells were assessed using single cell RNA-seq.

Results Our analysis revealed 21 subsets of leukocytes active in disease, including multiple populations of myeloid, T, NK and B cells, demonstrating both pro-inflammatory and resolving responses. We found evidence of local activation of B cells correlated with an age-associated B cell signature, and of progressive stages of monocyte differentiation within the kidney. A clear interferon response was observed in most cells. Two chemokine receptors, C×CR4 and C×3CR1, were broadly expressed, pointing to potential therapeutic targets. Gene expression of immune cells in urine and kidney was highly correlated, suggesting urine may be a surrogate for kidney biopsies.

Conclusions Our results provide a first comprehensive view of the complex network of leukocytes active in lupus nephritis kidneys. Results from this Phase 1 study identified LN active cells and pathways that can be used to guide the development of novel therapies. Analyses at a bigger scale (n=200 LN) in Phase 2 will allow to correlate patterns and signatures of infiltrating cells with those of intrinsic renal cells, particularly the epithelial cells that make up 90% of renal cells and that are prone to hypoxic damage and cellular stress. It will accelerate the discovery of new therapeutic targets and identification of biomarkers to guide therapeutic decisions in LN and integrate the treatment effect.

Funding Source(s): Funding was provided through grants from the National Institutes of Health (UH2-AR067676, UH2-AR067677, UH2-AR067679, UH2-AR067681, UH2-AR067685, UH2-AR067688, UH2-AR067689, UH2-AR067690, UH2-AR067691, UH2-AR067694, and UM2-AR067678).