Mild dehydration effects on the murine kidney single-nucleus transcriptome and chromatin accessibility

Abstract

Daily we may experience mild dehydration with a rise in plasma osmolality that triggers the release of vasopressin. While the effect of dehydration is well characterized in collecting duct principal cell (CDPC), we hypothesize that mild dehydration (<12 h) results in many kidney cell-specific changes in transcriptomes and chromatin accessibility. Single nucleus (sn) multiome (RNA-ATAC) sequencing and bulk RNA-sequencing of kidneys from male and female mice that were mildly water deprived or not were compared. Water deprived mice had a significant increase in plasma osmolality. The sn-multiome-seq resulted in 19,837 nuclei that were annotated into 33 clusters. In the CDPC Aqp2and Apq3 were greater in the dehydrated mice, but there were novel genes like Grem2 (a cytokine) that were increased compared to ad lib mice. The transcription factor Crem (cAMP Responsive Element Modulator) was greater in the CDPC of dehydrated mice and the Crem DNA motif was more accessible. There were hundreds of sex- and dehydration-specific DEGs throughout the kidney, especially in the proximal tubules and thin limbs. In the male mice DEGs were enriched in pathways related to lipid metabolism, while the female DEGs were enriched in organic acid metabolism. Many highly expressed genes had a positive correlation with increased chromatin accessibility, and mild dehydration exerted many transcriptional changes that we detected at the chromatin level. Even with a rise in plasma osmolality, male and female kidneys have distinct transcriptomes suggesting there may be diverse mechanisms used to remain in fluid balance.

Comprehensive analysis of the endothelin system in the kidneys of mice, rats, and humans

“… ( A ) Unsupervised clustering of 99588 kidney single cells and single nuclei RNA sequenced from C57bl/6J male and female mice from [ 30 , 38 , 40–46 ]. ( B ) Dotplot of the RNA expression of the endothelin related genes across the clusters.…”

“…Using our previously published murine whole kidney [ 38 ] and inner medulla bulk RNA-seq datasets [ 47 ] we determined normalized counts for the ET system ( Figure 7 C,D). In the whole kidney, Ece1 and Ednrb were significantly greater in the female kidney compared with male kidney ( Figure 7 C), while no statistically significant differences in the normalized counts of any of the ET related genes were observed in the inner medulla ( Figure 7 D).…”

“…Following batch correction using the Harmony the final rat dataset was created. Clusters were annotated based upon manual inspection of known kidney cell type markers as previously published [ 33 , 38 , 39 ]. DEGs were determined between male and female rats (regardless of age), or effects of age within a sex (e.g., young male compared with old male) using the FindMarkers function and DESeq2 test.…”

“…The mouse dataset was generated from single cell and single nucleus RNA studies on the kidneys collected during daytime (personal communication); GSE157079 [ 40 ], GSE180420 [ 41 ], GSE182256 [ 42 ], GSE164273 [ 43 ], GSE129798 [ 30 ], GSE193649 [ 44 ], GSE139107 [ 45 ], and GSE119531 [ 46 ]. Additionally, we included our recent ad libitum C57bl6J, male and female, single nucleus RNA sequencing from mice that were euthanized at midnight (GSE232662 [ 38 ]). The count matrixes were imported into Seurat and filtered as explained in the rat analyses except percent.mt < 5 .…”

“…The bulk kidney (GSE232792) and inner medullary RNA-sequencing (GSE195786) datasets were recently published [ 38 , 47 ]. Normalized counts from DESeq2 and adjusted P -values are reported.…”