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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 1

Altered gene expression pattern in AAN tissue identified by multiomics.

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Altered gene expression pattern in AAN tissue identified by multiomics.
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(A) The workflow chart depicts the multiomics experimental design and initial data exploration in this study (n = 6 for each cohort). (B) The volcano plots show the differentially expressed genes or proteins in scRNA-Seq (in silico bulk) (left), bulk RNA-Seq (middle), and mass spec proteomics (right) data sets. The x axis illustrates the log2 fold change (FC), and the y axis indicates as –log10 FDR. The color of scatter point indicates the changed type of differentially expressed genes or proteins (red, up; black, stable; blue, down). (C) The scatter plots show the correlation relationship of DEGs and DEPs’ log2FC between scRNA-Seq (in silico bulk) and RNA-Seq experiments (left), scRNA-Seq (in silico bulk) and mass spec experiments (middle), and bulk RNA-Seq and mass spec experiments (right). Blue line indicates the Deming regression fit. Black dotted horizontal and vertical lines indicate 0 values (no differential expression) for the in silico bulk and mass spec data, respectively. The color of square indicates the changed type of differential expressed genes or proteins (red, upregulate; blue, downregulate). (D) The Venn plots indicate the overlap upregulated as well as downregulated DEG or DEP number across 3 data sets. (E) The bar plot shows the top 5 upregulated and downregulated GO enrichments items of overlap corresponding DEGs or DEPs across 3 data sets. The color of the bar indicates the type of enriched pathways (red, upregulate; blue, downregulate).

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ISSN 2379-3708

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