{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,20]],"date-time":"2026-10-20T17:08:00Z","timestamp":1792516080298,"version":"4.5.0"},"reference-count":52,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2025,10,29]],"date-time":"2025-10-29T00:00:00Z","timestamp":1761696000000},"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>Glioblastoma (GBM) exhibits marked plasticity and intense microenvironmental crosstalk. We aimed to delineate mesenchymal programs with spatial resolution, clinical relevance, and mechanistic anchors.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Methods<\/jats:title>\n                    <jats:p>We integrated single-cell RNA-seq, bulk transcriptomes, and Visium spatial data. After rigorous QC and Harmony integration, we annotated 12 cell states using canonical markers, decoupler-based ORA, and AUCell. Tumor boundaries were defined by inferCNV\/CopyKAT; developmental potential by CytoTRACE2 and PHATE. Post-translational modification (PTM) axes were scored from curated gene sets. A cell type-aware GNN linked bulk expression to a patient-similarity graph for survival modeling and gene-level hazard attribution. Network convergence combined bulk WGCNA (TCGA\/CGGA), single-cell hdWGCNA, BayesPrism deconvolution, and external GEO validation. Ligand\u2013receptor (LR) signaling was inferred with LIANA+, embedded in a signed causal network, and mapped spatially. ARRDC3 expression was assessed in GBM tissues; U251 gain- and loss-of-function assays evaluated proliferation and migration.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>We resolved major GBM states, including two mesenchymal programs (MES1-like, MES2-like). CNV-high regions marked malignant cores, and CytoTRACE2 identified high-potency niches within MES2-like and Proliferation states along non-linear trajectories. PTM landscapes segregated by state; S-nitrosylation, glycosylation, and lactylation were enriched in mesenchymal programs. A GNN risk score stratified overall survival in TCGA (n=157) and generalized to CGGA-325 (n=85) and CGGA-693 (n=140). MES2-like abundance remained an independent adverse predictor (HR = 2.31; 95% CI, 1.04\u20135.10). MES2-high tumors upregulated EMT, TNF\u03b1\/NF-\u03baB, JAK\/STAT, hypoxia, angiogenesis, and glycolysis; S-nitrosylation associated with increased hazard. Cross-modal convergence defined a conservative MES2 core enriched for ECM remodeling, collagen modification, focal adhesion, and TGF-\u03b2 regulation. LR analysis prioritized a TAM-to-MES2 axis (e.g., GRN\u2013TNFRSF1A, ADAM9\/10\/17\u2013ITGB1, TGFB1\u2013ITGB1\/EGFR) converging on a CEBPD-centered module. Spatial mapping localized MES2 hotspots within CNV-defined territories and revealed a TNFRSF1A\u2013CEBPD\u2013ARRDC3 focus at an infiltrative rim. ARRDC3 was upregulated in GBM tissues; in U251 cells, knockdown promoted and overexpression suppressed proliferation and migration, indicating context-dependent roles.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Conclusions<\/jats:title>\n                    <jats:p>MES2-like GBM is an ECM-driven, stress-adapted state with strong prognostic impact. We nominate CEBPD and TNFRSF1A\/ITGB1 as actionable nodes and identify ARRDC3 as a spatially restricted effector with context-dependent tumor-modulatory functions warranting therapeutic exploration.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.3389\/fimmu.2025.1699134","type":"journal-article","created":{"date-parts":[[2025,10,29]],"date-time":"2025-10-29T06:58:19Z","timestamp":1761721099000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":8,"title":["Single-cell\/spatial integration reveals an MES2-like glioblastoma program orchestrated by immune communication and regulatory 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