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GNPS - Integrated metabolomics and proteomics reveal networks associated with end-stage kidney disease

ABSTRACT: Integrated metabolomic and proteomic profiling of end stage kidney disease patients undergo hemodialysis

INSTRUMENT(S): Orbitrap Exploris 480

ORGANISM(S): Homo Sapiens (ncbitaxon:9606)

SUBMITTER: Andrew Emili

PROVIDER: MSV000091579 | GNPS | Tue Mar 28 13:13:00 BST 2023

REPOSITORIES: GNPS

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Project description:Background: Pyroptosis plays a critical role in eliminating pathogens and facilitating tissue repair; however, sustained pyroptosis-driven inflammation accelerates kidney injury and disease progression. Thus, elucidating the mechanisms governing pyroptosis is essential for developing effective therapies for inflammatory kidney diseases such as acute kidney injury (AKI), which currently lacks specific treatment options. Methods: Changes in tubular epithelial cells following drug-induced AKI were assessed using single-cell RNA sequencing, immunohistochemistry, and immunofluorescence. Mechanistic insights were obtained through RNA sequencing, genomic manipulation, transcriptomic profiling, luciferase reporter assays, co-immunoprecipitation, and Western blotting. Tubular epithelial cell fate was further evaluated using transgenic mouse models and pharmacological interventions. Results: We identified activating transcription factor 4 (ATF4) as a key regulator of inflammation in drug-induced AKI. As the master regulator of the integrated stress response, ATF4 was markedly upregulated in renal tubules and positively correlated with kidney dysfunction in both human and murine AKI models. The specific deletion of ATF4 in tubular epithelial cells significantly ameliorated kidney dysfunction, inflammation, and mitochondrial apoptosis, whereas ATF4 activation exacerbated these pathological features. Mechanistically, ATF4 suppression inhibited STAT1 phosphorylation and disrupted its interaction with GBP2, thereby attenuating NLRP3 inflammasome activation, preventing tubular epithelial cells' pyroptosis, and improving kidney function. Notably, inhibition of ATF4—either pharmacologically using our prioritized integrated stress response antagonist ERMT1 or through engineered nanobiologics-mediated silencing of tubular epithelial cells—significantly reduced renal inflammation and injury. Conclusions: ATF4 promoted pyroptosis in drug-induced AKI through STAT1–GBP2 signaling.

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GNPS - Integrated metabolomics and proteomics reveal networks associated with end-stage kidney disease

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