LDOC1 loss reprograms histone ubiquitination and chromatin, driving tumor plasticity and poor prognosis in NSCLC

Background Non-small cell lung cancer (NSCLC) remains a leading cause of cancer-related mortality, partly due to epigenetic dysregulation that drives tumor progression and metastasis. We previously showed that Leucine Zipper Downregulated in Cancer 1 (LDOC1) modulates the metastatic potential of NSCLC cells. Structural features of LDOC1 suggest potential interactions with nuclear histones, and its loss induces broad transcriptomic changes. RNF40, an E3 ligase responsible for H2B monoubiquitination (H2Bub1), colocalizes with LDOC1 in NSCLC cells, further implicating LDOC1 in chromatin regulation through the H2Bub1 pathway. Here, we investigated whether LDOC1 exerts epigenetic control through mechanisms involving H2Bub1. Methods Levels of H2Bub1 and its downstream mark H3K4me3 were assessed in NSCLC cell lines with or without LDOC1 knockdown. We combined transcriptomic profiling, ChIP-seq, ATAC-seq, MNase digestion assay, flow cytometry, co-immunoprecipitation, proximity ligation assays, immunohistochemistry, and functional assays (including migration, adhesion, wound healing) in A549 cells. Clinical relevance was analyzed using lung adenocarcinoma datasets from UCSC Xena. Statistical analyses included Welch’s t-test for continuous data and chi-square or Fisher’s exact tests for categorical variables, as appropriate. Results LDOC1 negatively regulates global H2Bub1 abundance by promoting proteasomal degradation of H2B and H2Bub1 via interaction with PSMA1. Although LDOC1 knockdown increased global H2Bub1 abundance, it led to a widespread loss of chromatin-associated H2Bub1 and increased chromatin compaction, partially mediated by the LDOC1–THAP12 interaction. Integrated transcriptomic and epigenomic analyses revealed that the LDOC1–H2Bub1 axis regulates key metastasis-related genes involved in cytoskeletal remodeling, adhesion, and epithelial–mesenchymal transition (EMT). Functionally, LDOC1 loss enhanced TGF-β–induced epithelial–mesenchymal plasticity and promoted a hybrid epithelial/mesenchymal (E/M) phenotype, reduced adhesion, and altered migration dynamics—features recapitulated in STAS-positive NSCLC lesions. In clinical specimens, H2Bub1 was significantly elevated in STAS regions and inversely correlated with LDOC1 expression. Importantly, high H2Bub1 levels predicted shorter progression-free survival in EGFRᵂᵀ NSCLC patients receiving chemotherapy. Analysis of TCGA LUAD data linked LDOC1 downregulation to KRAS-mutant tumors. These findings highlight the clinical relevance of the LDOC1–H2Bub1 axis as both a mechanistic driver of tumor plasticity and a candidate prognostic marker. Conclusions Our study establishes LDOC1 as a key epigenetic regulator that controls histone turnover, chromatin accessibility, and metastasis-associated transcription through modulation of H2Bub1. The LDOC1–H2Bub1 axis not only governs epithelial–mesenchymal plasticity and STAS-like behavior in NSCLC but also holds clinical value as a dual biomarker for disease aggressiveness and chemotherapy response. These findings provide a foundation for developing LDOC1- and H2Bub1-based diagnostic tools or therapeutic strategies in precision oncology.