Single-Cell Multiomics Reveals That OTUD7B Is a Central Driver of Epithelial Remodelling and the Immunosuppressive Microenvironment in Pancreatic Ductal Adenocarcinoma

Abstract

Pancreatic ductal adenocarcinoma (PAAD) is characterized by extreme malignancy and profound resistance to therapy, largely driven by a fibrotic and immunosuppressive tumour microenvironment (TME). The deubiquitinase OTU domain-containing protein 7B (OTUD7B) has been implicated in inflammatory and oncogenic signalling, but its role in PAAD and its TME remains unclear. This study integrated single-cell RNA-seq datasets from the GEO and bulk RNA-seq data from the TCGA to delineate the cellular ecosystem of PAAD, and employed cell–cell communication analysis, high-dimensional weighted gene coexpression network analysis (hdWGCNA), and nonnegative matrix factorization (NMF) to identify OTUD7B-associated modules and epithelial subpopulations, while assessing the survival and clinicopathologic correlations of OTUD7B in the TCGA-PAAD cohort. Quantitative proteomics of OTUD7B-knockout PAAD cells was performed and combined with GO/KEGG and GSEA to explore downstream pathways, and immune infiltration was inferred by deconvolution algorithms and validated by multiplex immunofluorescence staining of OTUD7B, CD4, and FOXP3. Single-cell RNA-seq revealed the expansion of epithelial cells, fibroblasts, and macrophages with dense ligand–receptor networks, alongside the depletion of effector T and NK cells, indicating a shift toward an immunosuppressive TME. hdWGCNA identified epithelial–ECM modules in which OTUD7B served as a hub gene, and NMF revealed an OTUD7B-high epithelial subset enriched in glycosylation-related metabolic programs and positioned at an early stage of the malignant trajectory. OTUD7B was significantly upregulated in PAAD and was associated with higher grade, lymph node metastasis, and advanced stage, and predicted poorer overall survival. Proteomic profiling of OTUD7B-deficient cells revealed broad remodelling of mitochondrial oxidative phosphorylation, ROS metabolism, and redox homeostasis. OTUD7B expression was positively correlated with M2 macrophage infiltration, immunomodulatory gene expression, and CD4⁺FOXP3⁺ regulatory T-cell accumulation, and tissue staining further confirmed the positive association between OTUD7B expression and Treg-rich regions. Collectively, OTUD7B acts as a key integrative node that links epithelial remodelling, mitochondrial metabolic reprogramming, and TME immunosuppression in PAAD, serving as an adverse prognostic biomarker and a potential therapeutic target to remodel tumour metabolism and enhance antitumor immunity.