{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,18]],"date-time":"2026-03-18T08:00:55Z","timestamp":1773820855375,"version":"3.50.1"},"reference-count":57,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2026,3,18]],"date-time":"2026-03-18T00:00:00Z","timestamp":1773792000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["frontiersin.org"],"crossmark-restriction":true},"short-container-title":["Front. Immunol."],"abstract":"<jats:sec>\n                    <jats:title>Background<\/jats:title>\n                    <jats:p>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.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Methods<\/jats:title>\n                    <jats:p>\n                      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\n                      <jats:sup>+<\/jats:sup>\n                      for inferring inter\u2212cellular 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\n                      <jats:italic>in vitro<\/jats:italic>\n                      and\n                      <jats:italic>in vivo<\/jats:italic>\n                      assays.\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>\n                      ML-based pathway analysis revealed post\u2212translational modification as a major prognostic category, within which elevated DUBs activity emerged as an independent adverse prognostic factor. At the single\u2212cell level, USP54 was upregulated along the trajectory of malignant ductal cells and correlated with an inflamed tumor microenvironment. Cell\u2212cell communication analysis predicted signaling from monocytes\/macrophages to tumor cells via the THBS1\u2212integrin ligand\u2212receptor pair. This immune\u2212derived signaling potentially converged on KLF5\u2212positive tumor cells, with KLF5 identified as a putative transcriptional activator of USP54. Spatial transcriptomics validated the co\u2212localization of USP54 expression, elevated DUB activity, and KRAS signaling within specific tumor niches adjacent to THBS1\u2212enriched 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\n                      <jats:italic>in vivo<\/jats:italic>\n                      .\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Conclusions<\/jats:title>\n                    <jats:p>Our comprehensive multi-omics analysis and experimental validation identify the deubiquitinase USP54 as a novel promoter of PDAC progression within a spatially organized tumor\u2212immune microenvironment. These findings suggest USP54 as both a candidate prognostic biomarker and a potential therapeutic target for this lethal malignancy.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.3389\/fimmu.2026.1791707","type":"journal-article","created":{"date-parts":[[2026,3,18]],"date-time":"2026-03-18T06:59:18Z","timestamp":1773817158000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":0,"title":["Multi-omics and experimental validation identify USP54 as a prognostic deubiquitinase promoting pancreatic ductal adenocarcinoma progression within the immune microenvironment"],"prefix":"10.3389","volume":"17","author":[{"given":"Zibo","family":"Yuan","sequence":"first","affiliation":[{"name":"The Qingdao Medical College of Qingdao University","place":["Qingdao, China"]},{"name":"Zhejiang Key Laboratory of Tumor Molecular Diagnosis and Individualized Medicine, Zhejiang Provincial People\u2019s Hospital (Affiliated People\u2019s 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