Single-nucleus transcriptomics illuminates sex differences during murine Escherichia coli pyelonephritis

There are profound sex differences in the prevalence and outcomes of urinary tract infections (UTI). While females comprise the majority of infections, males exhibit higher morbidity and mortality with upper-tract UTI. Correspondingly, preclinical modeling has demonstrated that male and androgen-exposed female mice are highly susceptible to severe high-titer pyelonephritis, a phenotype observed in < 20% of females. Here we subject kidneys from female, male, and androgen-exposed female C3H/HeN mice with pyelonephritis and PBS-exposed control mice to single-nucleus RNA sequencing, creating (to our knowledge) the first whole-kidney single-nucleus transcriptomic dataset reflecting an infected state, comprising 248,483 nuclei. We differentiate healthy cell populations from those affected during UTI and show sex-discrepant responses that extend to kidney cell types beyond those directly interacting with bacteria. Female responses to UTI comprise a more limited range of cell types exhibiting significant upregulation of genes within KEGG pathways and pro-inflammatory transcription factor regulons. Meanwhile, males evidence predisposition to injury pathways even with control (saline) inoculation and responded to UTI with less intensity but across more cell types than females. In total, these data illuminate sex-discrepant transcriptional responses and outcomes in renal infection and enable detailed dissection of these responses at the cellular and molecular level.