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Kidney Week

Abstract: FR-PO384

Integrative Omics Reveal Molecular Signatures of Endoplasmic Reticulum Stress in Tubular Epithelial Cells

Session Information

  • CKD: Mechanisms - II
    November 08, 2019 | Location: Exhibit Hall, Walter E. Washington Convention Center
    Abstract Time: 10:00 AM - 12:00 PM

Category: CKD (Non-Dialysis)

  • 2103 CKD (Non-Dialysis): Mechanisms


  • Yi, Dan, Northwestern University, Chicago, Alabama, United States
  • Radmanesh, Behram Sarosh, Northwestern University, Chicago, Alabama, United States
  • Liu, Esther, Northwestern University, Chicago, Alabama, United States
  • Lin, Jennie, Northwestern University Feinberg School of Medicine, Chicago, Illinois, United States

Over the past decade, dysregulated and prolonged endoplasmic reticulum (ER) stress has been observed in acute kidney injury and chronic kidney disease (CKD). However, how ER stress contributes to disease pathophysiology in the kidney remains unclear. Here we take an unbiased approach to identify potential modulators of ER stress pathways in human proximal tubular epithelial cells.


We performed bulk RNA sequencing (RNA-seq) and untargeted LC-MS metabolite profiling on HKC-8 proximal tubular epithelial cells cultured with and without 2.5 uM of tunicamycin, an inducer of ER stress. Single-cell RNA-seq (scRNA-seq) was performed on kidney organoids differentiated from induced pluripotent stem cells, grown to day 25, and treated with tunicamycin.


RNA-seq revealed 2912 differentially expressed genes after 4 hours and 2436 differentially expressed genes after 24 hours of tunicamycin treatment. These genes were enriched for pathways relevant to inflammatory response (P < 0.001), Wnt signaling (P=0.015), protein processing in the ER (P=0.022), and extra-cellular matrix receptor interaction (P=0.04). A subset of the most highly differentially expressed genes were validated in tubular cells profiled in scRNA-seq of tunicamycin-treated 3D kidney organoids. Thirty genes differentially expressed in HKC-8 cell ER stress were also genes at kidney trait loci identified in recent genome-wide association studies; these genes are involved in cellular differentiation (PAX8) and fibrosis pathways (ACVR2A, SMAD3, TRIB1). Although network analyses identified known ER stress protein ATF4 as the main upstream transcriptional regulator, ATF4 target genes comprised only a small fraction of the differential expression gene set. Our metabolite profiling revealed decreased 2-HG (FC -2.25, P=0.021) and a-KG (FC -1.63, P=0.002) levels in ER stress: these metabolites are known epigenetic modulators, with implications for differential methylation activated by ER stress. Decreased abundance of these metabolites is also consistent with the commensurate increase in PHGDH expression (FC 2.87, P<0.001).


Taken together, these results demonstrate pervasive injury-relevant and ER stress induced transcriptional changes in kidney cells, with potential modulation by genetic variation and intermediate metabolites.


  • Other NIH Support