Go to The Journal of Clinical Investigation
  • About
  • Editors
  • Consulting Editors
  • For authors
  • Publication ethics
  • Publication alerts by email
  • Transfers
  • Advertising
  • Job board
  • Contact
  • Physician-Scientist Development
  • Current issue
  • Past issues
  • By specialty
    • COVID-19
    • Cardiology
    • Immunology
    • Metabolism
    • Nephrology
    • Oncology
    • Pulmonology
    • All ...
  • Videos
  • Collections
    • In-Press Preview
    • Resource and Technical Advances
    • Clinical Research and Public Health
    • Research Letters
    • Editorials
    • Perspectives
    • Physician-Scientist Development
    • Reviews
    • Top read articles

  • Current issue
  • Past issues
  • Specialties
  • In-Press Preview
  • Resource and Technical Advances
  • Clinical Research and Public Health
  • Research Letters
  • Editorials
  • Perspectives
  • Physician-Scientist Development
  • Reviews
  • Top read articles
  • About
  • Editors
  • Consulting Editors
  • For authors
  • Publication ethics
  • Publication alerts by email
  • Transfers
  • Advertising
  • Job board
  • Contact
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
View: Text | PDF
Research Article Cell biology Nephrology

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

  • Text
  • PDF
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

×

Figure 6

Activated macrophage cells induce inflammatory damage in the AAN.

Options: View larger image (or click on image) Download as PowerPoint
Activated macrophage cells induce inflammatory damage in the AAN.
(A) Th...
(A) The UMAP visualization shows unsupervised scRNA-Seq clustering, revealing 5 distinct subtypes of myeloid cells. Macro M1, macrophage M1; Macro M2, macrophage M2; Macro Pro, macrophage proliferation; Mono, monocytes. (B) The heatmap depicts the cell marker expression of each cell subtype in myeloid 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 plot shows the relative expression levels of key cytokines of 3 macrophage subtypes in scRNA-Seq data sets, colored according to group types. (E) The expression of proinflammatory factors IL-1β and TNF-α proteins by Western blotting and quantitative statistics correspond to groups. The P value was calculated by 2-tailed t test. *P < 0.05, **P < 0.01. (F) Monocle trajectory inference traces a path of pesudotime (top left), and label with the cell state (top right), group types (bottom left), and macrophage subtypes (bottom right). (G) The heatmap reveals the relative gene expression level of 5 clusters at 2 branches (from state1 to state2, and state1 to state3) based on branched expression analysis modeling (right), combined with the upregulative GO enriched items of each cluster (left).

Copyright © 2026 American Society for Clinical Investigation
ISSN 2379-3708

Sign up for email alerts