Detection of infiltrating fibroblasts by single-cell transcriptomics in human kidney allografts

Background: Single cell RNA sequencing (scRNA seq) provides unique opportunity to study cell types and cell states at a hitherto unavailable level of precision. We tested the hypothesis that scRNA seq and computational analysis of human kidney allograft biopsies will reveal new cell types and cell states and yield insights to personalize the care of transplant recipients. Methods: We selected 3 kidney biopsies from 3 individuals for scRNA seq using the 10x Chromium Single Cell platform; (i) HK: native kidney biopsy from a living kidney, (ii) AK1: allograft kidney biopsy with transplant glomerulopathy, fibrosis, and worsening kidney function but with undetectable circulating anti-HLA antibodies, and (iii) AK2: allograft kidney biopsy after successful treatment of active antibody mediated rejection but with persistent circulating donor specific anti HLA antibodies. Results: We generated 7,217 high-quality single cell transcriptomes. Taking advantage of the recipient donor sex mismatches, we determined that in the AK1 biopsy with fibrosis, more than half of the kidney allograft fibroblasts were unexpectedly recipient derived and therefore likely migratory and graft infiltrative, whereas in the AK2 biopsy without fibrosis, all the fibroblasts were donor derived. Furthermore, tubular progenitor cells that overexpress profibrotic extracellular matrix genes potentially contributing to fibrosis, were enriched in AK1 biopsy. Eight months after successful treatment of antibody mediated rejection, AK2 biopsy contained endothelial cells that expressed mRNA for T cell chemoattractant cytokines. In addition to these key findings, our analysis revealed unique cell types and cell states in the kidney. Conclusions: Altogether, single cell transcriptomics complemented histopathology and yielded novel mechanistic insights for individualizing the care of transplant recipients.