Comprehensive single-cell transcriptional profiling defines shared and unique epithelial injury responses during kidney fibrosis

• Published in: Cell metabolism 2022-12, Vol.34 (12), p.1977-1998.e9
• Main Authors: Li, Haikuo, Dixon, Eryn E., Wu, Haojia, Humphreys, Benjamin D.
• Format: Article
• Language: English
• Subjects: acute kidney injury; Animals; cell differentiation; chronic kidney disease; Fibrosis; Kidney; lipid droplet; lipid metabolism; Lipids; Lipolysis; Mice; PLIN2; single-cell combinatorial indexing; tissue regeneration
• ISSN: 1550-4131; 1932-7420; 1932-7420
• DOI: 10.1016/j.cmet.2022.09.026

The underlying cellular events driving kidney fibrogenesis and metabolic dysfunction are incompletely understood. Here, we employed single-cell combinatorial indexing RNA sequencing to analyze 24 mouse kidneys from two fibrosis models. We profiled 309,666 cells in one experiment, representing 50 cell types/states encompassing epithelial, endothelial, immune, and stromal populations. Single-cell analysis identified diverse injury states of the proximal tubule, including two distinct early-phase populations with dysregulated lipid and amino acid metabolism, respectively. Lipid metabolism was defective in the chronic phase but was transiently activated in the very early stages of ischemia-induced injury, where we discovered increased lipid deposition and increased fatty acid β-oxidation. Perilipin 2 was identified as a surface marker of intracellular lipid droplets, and its knockdown in vitro disrupted cell energy state maintenance during lipid accumulation. Surveying epithelial cells across nephron segments identified shared and unique injury responses. Stromal cells exhibited high heterogeneity and contributed to fibrogenesis by epithelial-stromal crosstalk. [Display omitted] •sci-RNA-seq3 transcriptionally profiles 309,666 cells from 24 kidneys without batch effects•Two injured proximal tubule cell states with distinct metabolic profiles revealed•Transiently activated lipid metabolism and PLIN2+ lipid droplets appear in early IRI•Nephron epithelia possess both shared and segment-specific injury and repair responses Li et al. profile the full time courses of mouse kidney fibrogenesis using single-cell combinatorial indexing RNA sequencing. They describe diverse injury states of proximal tubular cells, including one cell state with enhanced lipid metabolism at an early phase of ischemia-induced injury. This single-cell atlas defines kidney epithelial injury responses in fibrosis.