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bioRxiv · 10.64898/2026.01.28.702357

Illuminating the renal response to pH stress with single-nucleus RNA sequencing

Xue, J.·Eaton, K.·Alaoui, O. R.·Ponomarova, O.·Brayer, K.·Zaidman, N.
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Abstract

Maintenance of whole-body pH is essential for human health. The kidneys play a crucial role in defending pH homeostasis by excreting excess acid in the urine and returning alkali buffers to the blood. Consequently, renal insufficiency causes serious and harmful effects on pH balance. While a serious and common complication of chronic kidney disease (CKD), pH imbalances themselves appear to be catalysts of kidney injury. 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. The 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. However, there is a significant gap in knowledge regarding how the other segments of the nephron respond to 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 proximal straight tubule cell cluster that arises de novo following both acidosis and alkalosis. We label these proximal tubule cells PT S3a and demonstrate that their transcriptional profile is distinct from other injured PT cells that arise from ischemic injury. These studies lay the foundation for future research into the long-term renal adaptations to pH challenges that may lead to renal insufficiency and the development of CKD.

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Xue, J., Eaton, K., Alaoui, O. R., Ponomarova, O., Brayer, K., Zaidman, N.. 2026-02-01. Illuminating the renal response to pH stress with single-nucleus RNA sequencing. https://doi.org/10.64898/2026.01.28.702357

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