A multi-omics landscape of programmed cell death in acetaminophen-induced acute kidney injury

Acetaminophen (APAP) overdose is a known cause of acute kidney injury, yet the underlying molecular mechanisms remain incompletely understood. In this study, we conducted integrated transcriptomic, proteomic, and phosphoproteomic analyses of kidney tissues from mice with early-stage APAP-induced nephrotoxicity and corresponding controls. A total of 884 genes related to 13 distinct forms of programmed cell death (PCD)-including alkaliptosis, apoptosis, autophagy, cuproptosis, disulfidptosis, entotic cell death, ferroptosis, lysosome-dependent cell death, necroptosis, netotic cell death, oxeiptosis, parthanatos, and pyroptosis-were systematically evaluated. Gene set variation analysis was employed to assess the activity of these pathways in APAP-injured kidneys. Moreover, phosphokinase profiling and in vivo inhibition of protein kinase B (AKT) and extracellular signal-regulated kinase were performed to identify potential therapeutic strategies. Pathway enrichment across transcriptomic and proteomic datasets consistently pointed to drug metabolism-particularly cytochrome P450-as a central player. Transcriptomic profiling highlighted six PCD pathways-alkaliptosis, cuproptosis, disulfidptosis, lysosome-dependent cell death, netotic cell death, and pyroptosis-as notably activated in response to APAP exposure. Proteomic analysis further revealed enrichment of eight PCD pathways, including alkaliptosis, apoptosis, entotic cell death, ferroptosis, necroptosis, netotic cell death, oxeiptosis, and pyroptosis. Therapeutically, in vivo inhibition of AKT significantly alleviated renal injury, as demonstrated by improved histopathology, reduced neutrophil gelatinase-associated lipocalin and blood urea nitrogen and suppression of ferroptosis mediators TFRC and ACSL4. Concurrently, it enhanced phosphorylation of p70S6K and FOXO, reflecting improved survival signaling and reduced apoptosis. Together, these findings demonstrate that multiple PCD pathways contribute to early APAP-induced nephrotoxicity and nominate AKT as a central regulatory hub, which merits further exploration in translational nephrotoxicity research.