Metastasis is the main cause of death for patients suffering gastric cancer. Epithelial-mesenchymal transition (EMT) and cancer stem cells (CSC) are critical attributes of metastasis, both of which are regulated tightly by DNA methylation and Wnt/β-catenin signaling. Here, we studied the functions of DNA dioxygenase TET1 in regulating Wnt signaling and in gastric cancer metastasis. Knocking-down and overexpressing TET1 in gastric cancer cells promoted and inhibited metastatic spreading to the liver in immune-deficient mice, respectively. TET1 showed inhibitory effects on metastasis-related features -EMT and CSC, which were reversed by interfering with Wnt/β-catenin signaling. RNA-sequencing identified FOXO4 as a direct transactivating target of TET1. FOXO4 directly interacted with β-catenin and recruited it in the cytoplasm, so as to inhibit β-catenin-mediated transcription of Wnt target genes, including CSC marker EpCAM. Moreover, modulation of FOXO4 could reverse the effects of TET1 manipulation on EMT and self-renewal of CSCs. The analysis with clinical samples confirmed the value of FOXO4 as an independent prognostic predictor of patients’ overall survival. Taken together, regulation of Wnt signaling by TET1/FOXO4 is essential for metastasis-associated cellular properties, and targeting TET1/FOXO4/β-catenin pathway may serve as promising therapeutics in the prevention and treatment of gastric cancer metastasis.

Background: Despite significant advances in tumor immunotherapy, hepatocellular carcinoma (HCC) remains a malignancy with a challenging prognosis. The increasing research emphasizes the crucial role of ubiquitination in tumor immunotherapy. However, the establishment of prognostic signatures based on ubiquitination-related genes (UbRGs) and their role in immunotherapy are still lacking in HCC.

Hepatocellular carcinoma (HCC) is characterized by a profoundly hypoxic microenvironment, which drives tumor aggressiveness and poor clinical outcomes. However, the precise regulatory mechanisms through which hypoxia promotes HCC progression remain incompletely understood. Here, we identified ubiquitin conjugating enzyme E2 variant 1 ( UBE2V1 ) as a novel hypoxia-responsive gene that is transcriptionally activated by hypoxia-inducible factor-1α (HIF-1α) through direct binding to a hypoxia-response element located between −208 and −201 bp in the UBE2V1 promoter. Overexpression of UBE2V1 was frequently detected in HCC tissues and correlated strongly with advanced tumor stage and unfavorable patient prognosis. Moreover, UBE2V1 facilitated the proliferation and migration of HCC cells. Further investigation revealed that up-regulated UBE2V1 competes with HIF-1α for binding to the β-domain of von Hippel–Lindau (VHL) protein and, in complex with UBE2S, catalyzes K11/K48-linked ubiquitination at VHL K196, leading to its proteasomal degradation. This disruption of VHL function attenuates HIF-1α ubiquitination and degradation, resulting in sustained HIF-1α stabilization, increased nuclear accumulation, and enhanced transcriptional activity. Consistent with these findings, genetic knockdown of UBE2V1 or pharmacological inhibition of HIF-1α markedly suppresses HCC tumorigenesis and metastasis in vivo. Altogether, our study unveils a previously unrecognized HIF-1α–UBE2V1 positive feedback loop that is self-reinforcing and critically sustains the hypoxic microenvironment to drive HCC progression, highlighting UBE2V1 as both a promising prognostic biomarker and a compelling therapeutic target for HCC.

Background: Pancreatic ductal adenocarcinoma (PDAC) is a highly lethal malignancy with a complex tumor ecosystem that contributes to its progression. Deubiquitinases (DUBs) are vital regulators in cancer. However, the overall activity of DUBs and their role in driving PDAC progression within immune microenvironment remain largely unknown. Methods: We employed an integrative multi-omics strategy combining machine learning (ML) on bulk transcriptomic data, single-cell RNA sequencing and spatial transcriptomic profiling. We applied Coxnet and Fuzzy SVM for prognostic modeling, inferCNV for malignant cell identification, SCENIC for transcription factor regulon analysis, LIANA ⁺ for inferring inter−cellular communication networks and cell2location for spatial deconvolution. USP54 expression was detected by real-time quantitative PCR, western blotting and immunohistochemistry. USP54 function was validated through in vitro and in vivo assays. Results: ML-based pathway analysis revealed post−translational modification as a major prognostic category, within which elevated DUBs activity emerged as an independent adverse prognostic factor. At the single−cell level, USP54 was upregulated along the trajectory of malignant ductal cells and correlated with an inflamed tumor microenvironment. Cell−cell communication analysis predicted signaling from monocytes/macrophages to tumor cells via the THBS1−integrin ligand−receptor pair. This immune−derived signaling potentially converged on KLF5−positive tumor cells, with KLF5 identified as a putative transcriptional activator of USP54. Spatial transcriptomics validated the co−localization of USP54 expression, elevated DUB activity, and KRAS signaling within specific tumor niches adjacent to THBS1−enriched immune regions. High USP54 expression was frequently observed in PDAC tissues and associated with poor patient survival. More importantly, in both BxPC-3 and PANC-1 cell lines, USP54 knockdown suppressed cell proliferation and metastasis, whereas its overexpression enhanced these malignant phenotypes. Subcutaneous xenograft growth and tail vein injection experiments validated these findings in vivo . Conclusions: Our comprehensive multi-omics analysis and experimental validation identify the deubiquitinase USP54 as a novel promoter of PDAC progression within a spatially organized tumor−immune microenvironment. These findings suggest USP54 as both a candidate prognostic biomarker and a potential therapeutic target for this lethal malignancy.