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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 7

Tissue microenvironment remodeling induced by AAI.

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Tissue microenvironment remodeling induced by AAI.
(A) The UMAP visualiz...
(A) The UMAP visualization shows unsupervised single-cell transcriptome clustering, revealing 5 distinct subtypes of stromal cells. GE, Glomerular endothelial; Endo, endothelial; Fibro, fibroblast; MyoFibro, MyoFioblast; Peri, pericytes and vascular smooth muscle cells. (B) The heatmap depicts the cell marker expression of each cell subtype in stromal cell subpopulations. (C) The bar plot shows percentages of group types (upper panel) and sample origin (lower panel) of cells among 5 subtypes, colored according to group types and sample ID, respectively. (D) The violin plots show the relative expression level of cytokines of 5 stromal subtypes in scRNA-Seq data sets, colored according to group types. (E) The bubble plot shows the GO enrichment BP items of the AAN versus Con upregulated DEGs in 5 stromal subtypes. (F) Kidney sections in renal parenchyma with Masson’s trichrome and Sirius red staining (n = 3 per group). Scale bar: 50 μm. (G) Immunofluorescence staining of Hoechst (blue), α-SMA (red), and CD86 (green) in Con and AAN renal tissues (n = 3 per group). Scale bar: 50 μm.

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