Single-nucleus RNAseq reveals the renal response to acute pH imbalances

Maintenance of whole-body pH is essential for human health. Renal adaptations to pH imbalances contribute to compensated acid-base disorders and are vital to correcting whole-body pH. However, overstimulation of these adaptive processes can cause renal inflammation and lead to long-term kidney injury. Surprisingly, the acute and chronic effects of pH challenges on the whole kidney are poorly defined. While upregulation of ammoniagenesis in the proximal tubule due to acidosis, and the coordinated secretion of protons from the collecting ducts is a well-documented phenomenon, there is a significant gap in knowledge regarding how the other segments of the nephron respond to an acidosis or alkalosis. Therefore, to determine the cell-specific impact of overt metabolic acidosis and alkalosis on the kidney, we performed single-nucleus RNA sequencing on male and female WT mice following 48-hours of acid-base challenge (280mM NH4Cl (acid), 280mM NaHCO3 (alkali), 280mM NaCl (isosmotic control)). The results of our studies reveal the sex-specific single-cell transcriptional response by the kidney to pH imbalances, including a novel proximal tubule cell cluster we labeled PT S3a that arises de novo following both acidosis and alkalosis. These cells were characterized through gene expression analysis as being distinct from cells that arise during renal injury models like IRI, and ontology pathway analysis identified TNFα signaling as an enriched pathway in PT S3a suggesting that the cluster consists of cells that have experienced a stress-response that could stimulate renal inflammation. Moreover, these cells could be characterized through the expression of the AP-1 transcription factor c-Fos. To determine the long-term fate of these cells, we employed a Fos Targeted Recombination in Active Populations (TRAP2) transgenic mouse model that confirmed the presence of discrete Fos-positive tdTom+ cells in the proximal tubules after acute acidosis. No tdTom+ cells were detected in control mice. In addition, our results reveal a sex-dependent increase in polyamine abundance following pH challenge as determined transcriptionally by snRNAseq and Xenium spatial analysis, and through GC-MS metabolomics (males > females), as well as numerous pH-sensitive transcripts in the kidney including the circadian clock gene Per1, Col27a1 and Plk3. In summary, we have produced the complete single-cell kidney transcriptional response to acute acid-base disturbances, revealing a subset of proximal straight tubule cells that are especially sensitive to pH challenges, and demonstrated the utility of the FosTRAP2 mouse for long-term identification of responsive/injured cells in the kidney, regardless of the injury or challenge model. This abstract was presented at the American Physiology Summit 2026 and is only available in HTML format. There is no downloadable file or PDF version. The Physiology editorial board was not involved in the peer review process.