Abstract Background: Advance stages of metastatic melanoma (MM) transitions reversibly between melanocytic and mesenchymal (MES)-like cell states, enabling invasion, therapeutic resistance, and immune evasion. While transcriptional regulators of this plasticity are well described, the role of post-translational control remains underexplored. The ubiquitin E3 ligase KPC1 (RNF123) regulates NF-κB signaling through p105 processing, but its contribution to melanoma cell-state transitions is unknown. We investigated whether KPC1 regulates MES reprogramming through ubiquitin-dependent modulation of ZEB1, a central MES transcription factor. Methods: We integrated bulk RNA-seq, single-cell RNA-seq, and proteomic datasets from TCGA-SKCM, GSE115978, and PXD006003. Deconvolution (BayesPrism, CODEFACS) was used to derive melanoma-cell-specific expression profiles, and Monocle3 was applied to reconstruct pseudospatial trajectories. Functional validation included siRNA knockdown, qRT-PCR, Western blotting, cycloheximide chase, MG132 treatment, ubiquitination assays, and wound-healing migration assays. Multiplex immunofluorescence (mIF) on a clinically annotated stage III/IV melanoma FFPE tissue microarray (n = 110) assessed protein-level associations and clinical relevance. Results: Across TCGA and scRNA-seq datasets, KPC1 expression showed a strong inverse association with MES gene signatures and was lowest in melanoma cells enriched for MES pathways. Trajectory analysis demonstrated that MES progression accompanied a continuous decline in KPC1. KPC1 knockdown did not change ZEB1 mRNA but markedly increased ZEB1 protein, indicating post-transcriptional regulation. Loss of KPC1 delayed ZEB1 degradation in CHX-chase assays, reduced ZEB1 ubiquitination, enhanced CDH2 expression, suppressed CDH1, and increased cell migration. Proteasome inhibition further confirmed that ZEB1 turnover is KPC1-dependent. In melanoma patient samples, low KPC1 protein co-localized with high ZEB1 and CDH2 and predicted significantly shorter overall survival. Combined evaluation of KPC1, ZEB1, and CDH2 improved prognostic resolution beyond individual markers. Conclusions: KPC1 functions as a post-translational suppressor of MES-like reprogramming in metastatic melanoma by promoting ubiquitin-dependent degradation of ZEB1. Loss of KPC1 stabilizes ZEB1, activates MES transcriptional and phenotypic programs, and correlates with poor clinical outcomes. These findings identify KPC1 as a key regulator of melanoma cell-state plasticity and supports its potential utility as a theragnostic target. Citation Format: Yusuke Nakano, Matias Bustos, Kelly Chong, Yoshinori Hayashi, Aaron Ciechanover, Dave Hoon. KPC1 regulates mesenchymal reprogramming in metastatic melanoma through ubiquitin-dependent degradation of ZEB1 abstract. In: Proceedings of the American Association for Cancer Research Annual Meeting 2026; Part 1 (Regular Abstracts); 2026 Apr 17-22; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2026;86(7 Suppl):Abstract nr 4091.
Nakano et al. (Fri,) studied this question.