Not all reference samples are equal in single-cell transcriptomics of human kidney tissue

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Abstract

Identifying mechanisms of kidney disease commonly involves comparing diseased samples to healthy reference tissues; however, the effects of variability in tissue procurement, storage, and donor characteristics remain underexplored. In this study, we systematically evaluated three reference tissue types—tumor nephrectomy (TN), pre-transplant biopsies from living donors (LD), and percutaneous biopsies from healthy control volunteers (HC)—to determine their impact on differential gene expression across three diabetic kidney disease (DKD) states. We observed distinct injury markers, cell state proportions, and gene signatures associated with procurement method, sex, and donor age. Adjustment for these confounding factors significantly influenced pathway analysis results. Specifically, correcting for age and sex eliminated significant enrichment of interferon gamma response in the diabetes mellitus–resilient (DM-R) versus HC comparison. Processes related to biological aging were enriched in older reference tissues, potentially confounding disease-specific interpretations. Importantly, tumor necrosis factor signaling via nuclear factor-κB remained enriched in LD and TN samples relative to HC, even after accounting for confounders. These results underscore the critical importance of selecting appropriate control tissues and rigorously adjusting for confounding variables to reliably discern the molecular mechanisms underlying kidney diseases.

Authors

Rajasree Menon, Paul L. Kimmel, Edgar A. Otto, Lalita Subramanian, Christopher L. O'Connor, Bradley Godfrey, Cathy Smith, Fadhl Alakwaa, Celine C. Berthier, Minnie M. Sarwal, E. Steve Woodle, Laura Pyle, Ye Ji Choi, Patricia Ladd, John R. Sedor, Sylvia E. Rosas, Sushrut S. Waikar, Abhijit S. Naik, Ricardo Melo Ferreira, Michael T. Eadon, Markus Bitzer, Petter Bjornstad, Jeffrey B. Hodgin, Matthias Kretzler