{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,31]],"date-time":"2026-10-31T19:25:18Z","timestamp":1793474718310,"version":"4.5.0"},"reference-count":45,"publisher":"Oxford University Press (OUP)","issue":"9","license":[{"start":{"date-parts":[[2025,5,2]],"date-time":"2025-05-02T00:00:00Z","timestamp":1746144000000},"content-version":"vor","delay-in-days":1,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"European Union\u2019s Horizon 2020"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2025,10,14]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Background<\/jats:title>\n                    <jats:p>Glioblastoma (GB), particularly IDH-wild type, is the most aggressive brain malignancy with a dismal prognosis. Despite advances in molecular profiling, the complexity of its tumor microenvironment and spatial organization remains poorly understood. This study aimed to create a comprehensive single-cell and spatial atlas of GB to unravel its cellular heterogeneity, spatial architecture, and clinical relevance.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Methods<\/jats:title>\n                    <jats:p>We integrated single-cell RNA sequencing data from 26 datasets, encompassing over 1.1 million cells from 240 patients, to construct GBmap, a harmonized single-cell atlas. High-resolution spatial transcriptomics was employed to map the spatial organization of GB tissues. We developed the Tumor Structure Score (TSS) to quantify tumor organization and correlated it with patient outcomes.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>We showcase the applications of GBmap for reference mapping, transfer learning, and biological discoveries. GBmap revealed extensive cellular heterogeneity, identifying rare populations such as tumor-associated neutrophils and homeostatic microglia. Spatial analysis uncovered 7 distinct tumor niches, with hypoxia-dependent niches strongly associated with poor prognosis. The TSS demonstrated that highly organized tumors, characterized by well-defined vasculature and hypoxic niches, correlated with worse survival outcomes.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Conclusions<\/jats:title>\n                    <jats:p>This study provides a comprehensive resource for understanding glioblastoma heterogeneity and spatial organization. GBmap and the TSS provide an integrative view of tumor architecture in GB, highlighting hypoxia-driven niches that may represent avenues for further investigation. Our resource can facilitate exploratory analyses and hypothesis generation to better understand disease progression.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/neuonc\/noaf113","type":"journal-article","created":{"date-parts":[[2025,4,26]],"date-time":"2025-04-26T08:15:29Z","timestamp":1745655329000},"page":"2281-2295","source":"Crossref","is-referenced-by-count":85,"title":["Charting the single-cell and spatial landscape of IDH-wild-type glioblastoma with GBmap"],"prefix":"10.1093","volume":"27","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-9689-7964","authenticated-orcid":false,"given":"Cristian","family":"Ruiz-Moreno","sequence":"first","affiliation":[{"name":"Department of Molecular Biology, Faculty of Science, Radboud University , Nijmegen,","place":["The Netherlands"]},{"name":"Prinses M\u00e1xima Centrum for Pediatric Oncology , Utrecht,","place":["The Netherlands"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sergio 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Uppsala,","place":["Sweden"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0692-6245","authenticated-orcid":false,"given":"Karin","family":"Forsberg-Nilsson","sequence":"additional","affiliation":[{"name":"Department of Immunology, Genetics and Pathology, Science for Life Laboratory; Uppsala University , Uppsala,","place":["Sweden"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mariette E G","family":"Kranendonk","sequence":"additional","affiliation":[{"name":"Prinses M\u00e1xima Centrum for Pediatric Oncology , Utrecht,","place":["The Netherlands"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Fabian J","family":"Theis","sequence":"additional","affiliation":[{"name":"Institute of Computational Biology, Helmholtz Zentrum Mu\u0308nchen, German Research Center for Environmental Health , 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