Abstract
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.
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Data availability
Gene expression data have been submitted to the Gene Expression Omnibus (GEO) under accession number GSE296327, and Illumina reads have been submitted to NCBI’s Short Read Archive (SRA) under NCBI bioproject PRJNA1182331. Additional source data behind the figures in the paper are available online26 as Supplementary Data 1–10. Any remaining information can be obtained from the corresponding authors upon reasonable request.
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Acknowledgements
This work was funded by National Institutes of Health grants R01-DK126697 (to DAH and AME) and R01-AI158418 (to DAH), and by the Children’s Discovery Institute through the WashU Center for Cellular Imaging (CDI-CORE-2019-813). We acknowledge Joshua Gould, Lucas van Dijk, Mark Young, Nathan McGuire, and Patrick McGuire for assistance with analysis; and Lisa McLellan for IF images schematized within Fig. 7.
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T.N.H., A.L.M., A.M.E., and D.A.H. designed research; T.N.H., C.A.C., and A.L.M. performed research experiments; T.N.H., A.L.M., H.W., and C.G. performed data analysis and visualization; B.D.H., A.L.M., and D.A.H. reviewed data analyses; T.N.H. and A.L.M. drafted the manuscript; B.D.H., A.M.E., and D.A.H. edited and finalized the manuscript and figures; T.N.H., A.L.M., C.A.C., A.M.E., and D.A.H. completed revision experiments and responses to reviewers.
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D.A.H. serves on the Board of Directors of BioVersys AG (SIX: BIOV) and has received funding for unrelated research work from BioAge Laboratories and Pfizer. All other authors declare no competing interests.
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Hreha, T.N., Manson, A.L., Collins, C.A. et al. Single-nucleus transcriptomics illuminates sex differences during murine Escherichia coli pyelonephritis. Commun Biol (2026). https://doi.org/10.1038/s42003-026-09946-8
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DOI: https://doi.org/10.1038/s42003-026-09946-8
