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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 3

Proximal tubule–specific damage response to AAI.

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Proximal tubule–specific damage response to AAI.
(A) The UMAP visualizat...
(A) The UMAP visualization shows unsupervised scRNA-Seq clustering (up) and split into Con and AAN groups (down), revealing 3 distinct subtypes of PT cells. PT-S, proximal tubules subgroup; PCT, proximal convoluted tubules; PST, proximal straight tubules. (B) The violin plot shows the expression levels of respective selected markers across 3 cellular subtypes. The y axis shows the log-scale normalized reads count. (C) The bar plot shows the percentages of group types (upper panel) and sample origin (lower panel) of cells among 3 subtypes, colored according to group types and sample IDs, respectively. (D) The UMAP plot represents the PT cells colored by cell subtypes with Velocyto projection. (E) The bar plot shows percentages of cell cycle phase (G1, G2M, and S phase) of cells among 3 subtypes in the Con and the AAN groups. (F) The Venn plot represents the intersect and union number upregulated DEGs among 3 proximal tubules subtypes. (G) The bubble plot shows the top 10 GO enriched pathways of overlap upregulated DEGs among 3 cellular subtypes upon AAI treatment. (H) The split-violin plots show the distribution of enrichment scores of 10 GAVA hallmark pathways between the Con (green) and the AAN (red) groups. Data are shown as mean ± SD. (I) The heatmap depicts the relative activity scores of the top 10 regulons within different cellular subtypes, group types, and sample IDs.

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ISSN 2379-3708

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