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Integrated single-cell transcriptomics and proteomics reveal cellular-specific responses and microenvironment remodeling in aristolochic acid nephropathy
Jiayun Chen, Piao Luo, Chen Wang, Chuanbin Yang, Yunmeng Bai, Xueling He, Qian Zhang, Junzhe Zhang, Jing Yang, Shuang Wang, Jigang Wang
Jiayun Chen, Piao Luo, Chen Wang, Chuanbin Yang, Yunmeng Bai, Xueling He, Qian Zhang, Junzhe Zhang, Jing Yang, Shuang Wang, Jigang Wang
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Research Article Cell biology Nephrology

Integrated single-cell transcriptomics and proteomics reveal cellular-specific responses and microenvironment remodeling in aristolochic acid nephropathy

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Abstract

Aristolochic acid nephropathy (AAN) is characterized by acute proximal tubule necrosis and immune cell infiltration, contributing to the global burden of chronic kidney disease and urothelial cancer. Although the proximal tubule has been defined as the primary target of aristolochic acids I (AAI), the mechanistic underpinning of gross renal deterioration caused by AAI has not been explicitly explained, prohibiting effective therapeutic intervention. To this point, we employed integrated single-cell RNA-Seq, bulk RNA-Seq, and mass spectrometry–based proteomics to analyze the mouse kidney after acute AAI exposure. Our results reveal a dramatic reduction of proximal tubule epithelial cells, associated with apoptotic and inflammatory pathways, indicating permanent damage beyond repair. We found the enriched development pathways in other nephron segments, suggesting activation of reparative programs triggered by AAI. The divergent response may be attributed to the segment-specific distribution of organic anion channels along the nephron, including OAT1 and OAT3. Moreover, we observed dramatic activation and recruitment of cytotoxic T and macrophage M1 cells, highlighting inflammation as a principal contributor to permanent renal injury. Ligand-receptor pairing revealed that critical intercellular crosstalk underpins damage-induced activation of immune cells. These results provide potentially novel insight into the AAI-induced kidney injury and point out possible pathways for future therapeutic intervention.

Authors

Jiayun Chen, Piao Luo, Chen Wang, Chuanbin Yang, Yunmeng Bai, Xueling He, Qian Zhang, Junzhe Zhang, Jing Yang, Shuang Wang, Jigang Wang

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Figure 4

Segment-specific reparative responses to AAI.

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Segment-specific reparative responses to AAI.
(A) The UMAP visualization...
(A) The UMAP visualization shows unsupervised scRNA-Seq clustering, revealing 6 distinct subtypes of segment epithelial except PT cells. DLH, descending loop of Henle; ALH, ascending loop of Henle; DCT, distal convoluted tubule; CD-IC, collecting duct intercalated cell; CD-PC, collecting duct principal cell; Podo, podocyte. (B) The heatmap depicts the cell marker expression of each cell subtype in the segment epithelial subpopulation. (C) The bar plots show the percentages of group types (upper panel) and sample origin (lower panel) of cells among 6 subtypes, colored according to group types and sample ID, respectively. (D) The visualization shows the scatter plot of log2FC value in both upregulated and downregulated DEGs (middle), combined with the bar plot of downregulated (left) and upregulated (right) top 5 enriched GO items’ –log10(P value) in each subtype. FC, fold change; DEGs, differentially expressed genes; GO, gene ontology. (E) The heatmap shows the 10 hallmarks gene set enriched scores of PT subtype cells and other segment epithelial cells. (F) The heatmap shows the gene expression level of organic anion transporters and organic cation transporters of PT subtype cells and other segment epithelial cells. (G) The UMAP plot represents the expression level of kidney injury markers and repair markers in renal epithelial cells. (H) Representative immunofluorescence staining of Hoechst (blue), Ki67 (green), and Lrp2 or Aqp1 (red) in the Con and the AAN groups (n = 3 per group). Scale bar: 50 μm.

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