Spatial transcriptomics reveals renal ER stress in alcohol-associated kidney injury.

Alcohol misuse damages numerous organs, including the liver, heart, brain, and pancreas. The kidney remains a severely understudied target of alcohol-induced injury despite renal injury being commonly observed in end-stage alcohol-associated liver disease (ALD) patients. A 6-week murine ethanol (1-6% v/v) model for early-stage ALD combined with carbon tetrachloride (CCl4) treatment was utilized to reveal mechanisms of renal injury. This paradigm yields elevated kidney damage markers when compared to ethanol consumption alone, including elevated urinary KIM-1 in 3 weeks. Hypothesis generating tissue spatial analysis was used to explore ethanol-related transcriptomic alterations across kidney morphology. Using a publicly available scRNA-seq dataset, the predominant cell-type specific differences were identified and allowed for the generation of spatially resolved gene clusters. Ethanol + CCl4 increased kidney injury marker gene expression in proximal tubule cells, signifying extensive damage. Overall, a decrease in expression of ethanol metabolizing genes was localized to the renal cortex. Genes associated with the unfolded protein response (UPR) were induced across the kidney and were morphologically associated throughout the nephron. Key mRNAs (Hspa5, Hsp90b1, Ndrg1) and ribosomal transcripts were altered due to ethanol metabolism across proximal tubules. Furthermore, epigenetic alterations in regulatory marks of lysine acetylation or trimethylation are associated with the combination treatment. Collectively, the application of tissue spatial transcriptomics to a well-defined model of alcohol toxicity reveals dynamic morphologic changes in gene expression across renal cell types due to ethanol. Our results indicate ER stress and the UPR are significantly impacted by ethanol metabolism throughout proximal tubules, associating with ethanol-induced renal dysfunction.