{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,7]],"date-time":"2026-09-07T06:08:12Z","timestamp":1788761292548,"version":"build-2803163510"},"reference-count":33,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2026,9,7]],"date-time":"2026-09-07T00:00:00Z","timestamp":1788739200000},"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>The tumor microenvironment (TME) of gastric adenocarcinoma is exceptionally heterogeneous, and epithelial-mesenchymal transition (EMT) is a central mechanism promoting local invasion and metastatic spread. Even so, how EMT-programmed cells are spatially arranged within tumor tissue, how they interact with neighboring immune populations, and which molecular nodes might be exploited therapeutically remain incompletely defined.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Methods<\/jats:title>\n                    <jats:p>We built a large-scale, multi-layered analytical pipeline that combined single-cell transcriptomics (approximately 250,000 cells drawn from two independent patient cohorts), Visium-based spatial transcriptomics processed through Bayesian cell2location deconvolution, niche-level SpaTopic modeling, deep-learning histology analysis (ResNet50 feature extraction paired with CellProfiler-derived morphometrics), and ensemble survival modeling spanning over one hundred algorithmic combinations. Gaussian mixture modeling was used to define EMT-high cell states, the Scissor framework was applied to link fibroblast subsets to patient mortality, and a multi-tier filtering scheme was used to nominate druggable candidate genes. The top candidate, PVR\/CD155, was interrogated experimentally by RT-qPCR, Western blotting, immunohistochemistry, and siRNA knockdown in AGS cells. We further evaluated PVR druggability by molecular docking, a 100-nanosecond molecular dynamics trajectory, and MM\/GBSA binding-energy estimation using PP-121 as a candidate ligand.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>Sub-clustering identified seven fibroblast subclusters: Fib_APOD, Fib_COL4A1, Fib_SLPI, Fib_COL1A1, Fib_CCL4, Fib_STMN1, and Fib_S100B. The SLPI-high subset preferentially localized to peritoneal metastases. Phenotype-guided Scissor mapping nominated a survival-associated fibroblast program enriched within COL4A1-expressing fibroblast states. PVR\/CD155 was prioritized as an EMT-linked candidate gene; single-cell expression profiling showed that PVR was most frequently detected in endothelial, epithelial and fibroblast compartments, with low detection in lymphoid and plasma cells. PVR\/CD155 was significantly upregulated in gastric cancer cell lines and tumor tissues. PVR\/CD155 knockdown in AGS cells decreased proliferation, migration and invasion, supporting a tumor cell-intrinsic functional role rather than establishing PVR as a stromal immune biomarker. Molecular docking and dynamics simulations identified PP-121 as a candidate PVR-binding ligand for future biochemical validation.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Conclusion<\/jats:title>\n                    <jats:p>The proposed framework connects single-cell resolution with spatial and histological data, produces validated prognostic tools and nominates PVR\/CD155 as a tumor cell-intrinsic EMT-associated target candidate for gastric cancer. Stromal or immune regulatory roles of PVR remain plausible but require direct compartment-specific and functional validation.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.3389\/fimmu.2026.1932169","type":"journal-article","created":{"date-parts":[[2026,9,7]],"date-time":"2026-09-07T05:33:20Z","timestamp":1788759200000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":0,"title":["Unraveling tumor cell heterogeneity and epithelial-mesenchymal plasticity in gastric adenocarcinoma: an integrative multi-omics framework evaluating PVR\/CD155 as a tumor cell-intrinsic EMT-associated target"],"prefix":"10.3389","volume":"17","author":[{"given":"Jianwen","family":"Li","sequence":"first","affiliation":[{"name":"Department of Oncology Surgery, The First Hospital of Lanzhou University","place":["Lanzhou, Gansu, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zitong","family":"Qin","sequence":"additional","affiliation":[{"name":"The First Clinical Medical College of Lanzhou University","place":["Lanzhou, Gansu, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ting","family":"Wang","sequence":"additional","affiliation":[{"name":"Department of Urology, The Second Hospital of Lanzhou University","place":["Lanzhou, Gansu, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Weiping","family":"Li","sequence":"additional","affiliation":[{"name":"Department of Urology, The First Hospital of Lanzhou University","place":["Lanzhou, Gansu, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jinmin","family":"Ma","sequence":"additional","affiliation":[{"name":"Medical Frontier Innovation Research Center, The First Hospital of Lanzhou University","place":["Lanzhou, Gansu, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Quanlin","family":"Guan","sequence":"additional","affiliation":[{"name":"Department of Oncology Surgery, The First Hospital of Lanzhou University","place":["Lanzhou, Gansu, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1965","published-online":{"date-parts":[[2026,9,7]]},"reference":[{"key":"B1","doi-asserted-by":"publisher","DOI":"10.3322\/caac.21834","article-title":"Global cancer statistics 2022: GLOBOCAN estimates of incidence and mortality worldwide for 36 cancers in 185 countries","volume":"74","author":"Bray","year":"2024","journal-title":"CA Cancer J Clin"},{"key":"B2","doi-asserted-by":"publisher","DOI":"10.1016\/b978-0-443-15609-0.00017-9","article-title":"Gastric cancer","volume":"396","author":"Smyth","year":"2020","journal-title":"Lancet"},{"key":"B3","doi-asserted-by":"publisher","first-page":"57","DOI":"10.1186\/s13045-023-01451-3","article-title":"Gastric cancer treatment: recent progress and future perspectives","volume":"16","author":"Guan","year":"2023","journal-title":"J Hematol Oncol"},{"key":"B4","doi-asserted-by":"publisher","DOI":"10.1158\/2159-8290.cd-21-0683","article-title":"Single-cell atlas of lineage states, tumor microenvironment, and subtype-specific expression programs in gastric cancer","volume":"12","author":"Kumar","year":"2022","journal-title":"Cancer Discov"},{"key":"B5","doi-asserted-by":"publisher","DOI":"10.1038\/s41591-020-1125-8","article-title":"Single-cell dissection of intratumoral heterogeneity and lineage diversity in metastatic gastric adenocarcinoma","volume":"27","author":"Wang","year":"2021","journal-title":"Nat Med"},{"key":"B6","doi-asserted-by":"publisher","first-page":"21","DOI":"10.1016\/j.cell.2016.06.028","article-title":"EMT: 2016","volume":"166","author":"Nieto","year":"2016","journal-title":"Cell"},{"key":"B7","doi-asserted-by":"publisher","first-page":"69","DOI":"10.1038\/s41580-018-0080-4","article-title":"New insights into the mechanisms of epithelial-mesenchymal transition and implications for cancer","volume":"20","author":"Dongre","year":"2019","journal-title":"Nat Rev Mol Cell Biol"},{"key":"B8","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1016\/j.semcancer.2024.04.001","article-title":"Alternative splicing in EMT and TGF-\u03b2 signaling during cancer progression","volume":"101","author":"Zhang","year":"2024","journal-title":"Semin Cancer Biol"},{"key":"B9","doi-asserted-by":"publisher","DOI":"10.1136\/jitc-2023-008721","article-title":"POSTN(+) cancer-associated fibroblasts determine the efficacy of immunotherapy in hepatocellular carcinoma","volume":"12","author":"Wang","year":"2024","journal-title":"J Immunother Cancer"},{"key":"B10","doi-asserted-by":"publisher","DOI":"10.1038\/s41417-024-00756-w","article-title":"Enhanced epithelial-mesenchymal transition signatures are linked with adverse tumor microenvironment, angiogenesis and worse survival in gastric cancer","volume":"31","author":"Oshi","year":"2024","journal-title":"Cancer Gene Ther"},{"key":"B11","doi-asserted-by":"publisher","first-page":"233","DOI":"10.1007\/s00262-024-03820-4","article-title":"Single-cell RNA sequencing to map tumor heterogeneity in gastric carcinogenesis paving roads to individualized therapy","volume":"73","author":"Xu","year":"2024","journal-title":"Cancer Immunol Immunother"},{"key":"B12","doi-asserted-by":"publisher","DOI":"10.1038\/s41586-021-03634-9","article-title":"Exploring tissue architecture using spatial transcriptomics","volume":"596","author":"Rao","year":"2021","journal-title":"Nature"},{"key":"B13","doi-asserted-by":"publisher","DOI":"10.1038\/s41587-021-01139-4","article-title":"Cell2location maps fine-grained cell types in spatial transcriptomics","volume":"40","author":"Kleshchevnikov","year":"2022","journal-title":"Nat Biotechnol"},{"key":"B14","doi-asserted-by":"publisher","first-page":"40","DOI":"10.1038\/s41580-021-00407-0","article-title":"A guide to machine learning for biologists","volume":"23","author":"Greener","year":"2022","journal-title":"Nat Rev Mol Cell Biol"},{"key":"B15","doi-asserted-by":"publisher","first-page":"329","DOI":"10.1016\/j.cels.2019.03.003","article-title":"DoubletFinder: Doublet detection in single-cell RNA sequencing data using artificial nearest neighbors","volume":"8","author":"McGinnis","year":"2019","journal-title":"Cell Syst"},{"key":"B16","doi-asserted-by":"publisher","DOI":"10.1038\/s41592-019-0619-0","article-title":"Fast, sensitive and accurate integration of single-cell data with Harmony","volume":"16","author":"Korsunsky","year":"2019","journal-title":"Nat Methods"},{"key":"B17","doi-asserted-by":"publisher","first-page":"149","DOI":"10.1186\/s13059-023-02988-9","article-title":"scTour: a deep learning architecture for robust inference and accurate prediction of cellular dynamics","volume":"24","author":"Li","year":"2023","journal-title":"Genome Biol"},{"key":"B18","doi-asserted-by":"publisher","DOI":"10.1126\/sciadv.adp4942","article-title":"SpaTopic: A statistical learning framework for exploring tumor spatial architecture from spatially resolved transcriptomic data","volume":"10","author":"Zhang","year":"2024","journal-title":"Sci Adv"},{"key":"B19","doi-asserted-by":"publisher","DOI":"10.1038\/s41592-019-0667-5","article-title":"NicheNet: modeling intercellular communication by linking ligands to target genes","volume":"17","author":"Browaeys","year":"2020","journal-title":"Nat Methods"},{"key":"B20","doi-asserted-by":"publisher","first-page":"433","DOI":"10.1186\/s12859-021-04344-9","article-title":"CellProfiler 4: improvements in speed, utility and usability","volume":"22","author":"Stirling","year":"2021","journal-title":"BMC Bioinf"},{"key":"B21","doi-asserted-by":"publisher","DOI":"10.1016\/j.csbj.2024.06.035","article-title":"Mime: A flexible machine-learning framework to construct and visualize models for clinical characteristics prediction and feature selection","volume":"23","author":"Liu","year":"2024","journal-title":"Comput Struct Biotechnol J"},{"key":"B22","doi-asserted-by":"publisher","DOI":"10.1021\/acs.jcim.1c00203","article-title":"AutoDock Vina 1.2.0: New docking methods, expanded force field, and Python bindings","volume":"61","author":"Eberhardt","year":"2021","journal-title":"J Chem Inf Model"},{"key":"B23","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pcbi.1004586","article-title":"AutoDockFR: Advances in protein-ligand docking with explicitly specified binding site flexibility","volume":"11","author":"Ravindranath","year":"2015","journal-title":"PloS Comput Biol"},{"key":"B24","doi-asserted-by":"publisher","DOI":"10.1002\/jcc.20035","article-title":"Development and testing of a general amber force field","volume":"25","author":"Wang","year":"2004","journal-title":"J Comput Chem"},{"key":"B25","doi-asserted-by":"publisher","first-page":"104101","DOI":"10.1063\/1.2464095","article-title":"Langevin stabilization of molecular-dynamics simulations of polymers by means of quasisymplectic algorithms","volume":"126","author":"Larini","year":"2007","journal-title":"J Chem Phys"},{"key":"B26","doi-asserted-by":"publisher","DOI":"10.1021\/ct3010485","article-title":"Improved generalized Born solvent model parameters for protein simulations","volume":"9","author":"Nguyen","year":"2013","journal-title":"J Chem Theory Comput"},{"key":"B27","doi-asserted-by":"publisher","DOI":"10.1002\/ijc.23746","article-title":"Overexpression of a secretory leukocyte protease inhibitor in human gastric cancer","volume":"123","author":"Cheng","year":"2008","journal-title":"Int J Cancer"},{"key":"B28","doi-asserted-by":"publisher","DOI":"10.7717\/peerj.9400","article-title":"Targeting secretory leukocyte protease inhibitor (SLPI) inhibits colorectal cancer cell growth, migration and invasion via downregulation of AKT","volume":"8","author":"Wei","year":"2020","journal-title":"PeerJ"},{"key":"B29","doi-asserted-by":"publisher","first-page":"22","DOI":"10.1016\/j.cytogfr.2021.01.005","article-title":"Secretory leukocyte protease inhibitor (SLPI) in mucosal tissues: Protects against inflammation, but promotes cancer","volume":"59","author":"Nugteren","year":"2021","journal-title":"Cytokine Growth Factor Rev"},{"key":"B30","doi-asserted-by":"publisher","DOI":"10.1080\/2162402x.2020.1832761","article-title":"Expression of the immune modulator secretory leukocyte protease inhibitor (SLPI) in colorectal cancer liver metastases and matched primary tumors is associated with a poorer prognosis","volume":"9","author":"Nugteren","year":"2020","journal-title":"Oncoimmunology"},{"key":"B31","doi-asserted-by":"publisher","first-page":"351","DOI":"10.1186\/s12957-022-02813-w","article-title":"Prognostic and clinicopathological significance of CD155 expression in cancer patients: a meta-analysis","volume":"20","author":"Zhang","year":"2022","journal-title":"World J Surg Oncol"},{"key":"B32","doi-asserted-by":"publisher","DOI":"10.1016\/j.ccell.2014.10.018","article-title":"The immunoreceptor TIGIT regulates antitumor and antiviral CD8(+) T cell effector function","volume":"26","author":"Johnston","year":"2014","journal-title":"Cancer Cell"},{"key":"B33","doi-asserted-by":"publisher","first-page":"512","DOI":"10.1016\/j.immuni.2022.02.005","article-title":"Mechanistic convergence of the TIGIT and PD-1 inhibitory pathways necessitates co-blockade to optimize anti-tumor CD8(+) T cell responses","volume":"55","author":"Banta","year":"2022","journal-title":"Immunity"}],"container-title":["Frontiers in Immunology"],"original-title":[],"link":[{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fimmu.2026.1932169\/full","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,9,7]],"date-time":"2026-09-07T05:33:23Z","timestamp":1788759203000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fimmu.2026.1932169\/full"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,9,7]]},"references-count":33,"alternative-id":["10.3389\/fimmu.2026.1932169"],"URL":"https:\/\/doi.org\/10.3389\/fimmu.2026.1932169","relation":{},"ISSN":["1664-3224"],"issn-type":[{"value":"1664-3224","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,9,7]]},"article-number":"1932169"}}