Cullin 3 ubiquitin ligase regulates redox defense and metabolic programs in proximal tubule cells
Abstract Background Chronic kidney disease (CKD) is characterized by proximal tubule (PT) stress, oxidative injury, and metabolic dysfunction. Human kidney single-nucleus RNA-sequencing (snRNA-seq) identified enrichment of ubiquitin-dependent protein catabolic processes in injured PT cells, suggesting activation of the ubiquitin-proteasome system during tubular stress. Because Cullin 3 (CUL3), scaffold of ubiquitin ligases, regulates oxidative stress signaling through the KEAP1-NRF2 axis, we investigated its role in PT injury and stress adaptation. Methods Human CKD snRNA-seq data and kidney immunostaining were used to define PT cell states, CUL3-associated pathways, and CUL3 localization. Injury-associated CUL3 regulation was examined in wildtype mice after ischemia-reperfusion injury (IRI). Inducible PT-specific knockout mice (Slc34a1-CreER; Cul3flox/flox) were analyzed at baseline and after injury by histology, immunostaining, proteomics, and injury assessment. In addition, proteomic analysis of a whole-tubule epithelial knockout model (Pax8-rtTA/LC1; Cul3flox/flox) was performed. In immortalized human PT cells, CUL3 was suppressed or activated using CRISPR interference and CRISPR activation, followed by bulk RNA sequencing. Results CUL3 transcript and protein expression was enriched in stressed PT states in human CKD. In mice, CUL3 protein abundance increased after injury, supporting injury-associated induction in vivo. PT-specific CUL3 deletion increased antioxidant NQO1 expression without causing overt baseline injury. Proteomic analysis of isolated CUL3-deficient PT cells revealed induction of antioxidant, detoxification, proteostasis, and lipid metabolic programs, together with suppression of mitochondrial oxidative metabolism. Similar changes were observed in whole-tubule Cul3 knockout model. In gene-edited human PT cells, CUL3 suppression recapitulated stress-associated and metabolic remodeling programs, whereas CUL3 activation induced reciprocal transcriptional changes. Despite induction of antioxidant pathways, PT-specific CUL3 deletion did not alter disease severity after IRI or aristolochic acid nephropathy. Conclusion CUL3 is an injury-induced regulator of PT metabolic and stress-associated states and modulates antioxidant defense and mitochondrial metabolism in PT cells.