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In this study, we investigated in what respect a scaffold-based (Matrigel\u2122) 3D culture technique can ameliorate the limitations of 2D cultures. NGS-based bulk and single-cell sequencing of matched pairs of 2D and 3D models showed an altered transcription of key immune regulatory genes in around 36% of 3D models, indicating the reoccurrence of an immune suppressive phenotype. Changes included the presentation of different HLA surface molecules as well as cellular stressors. We also investigated the 3D tumor organoids in a co-culture setting with tumor-infiltrating lymphocytes (TILs). Of note, lymphocyte-mediated cell killing appeared less effective in clearing 3D models than their 2D counterparts. IFN-\u03b3 release, as well as live cell staining and proliferation analysis, pointed toward an elevated resistance of 3D models. In conclusion, we found that the scaffold-based (Matrigel\u2122) 3D culture technique affects the transcriptional profile in a subset of GBM models. Thus, these models allow for depicting clinically relevant aspects of tumor-immune interaction, with the potential to explore immunotherapeutic approaches in an easily accessible in vitro system.<\/jats:p>","DOI":"10.3390\/cells12141856","type":"journal-article","created":{"date-parts":[[2023,7,14]],"date-time":"2023-07-14T08:35:47Z","timestamp":1689323747000},"page":"1856","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":21,"title":["Scaffold-Based (Matrigel\u2122) 3D Culture Technique of Glioblastoma Recovers a Patient-like Immunosuppressive Phenotype"],"prefix":"10.3390","volume":"12","author":[{"given":"Frank K.","family":"Braun","sequence":"first","affiliation":[{"name":"Department of Neuropathology, Regensburg University Hospital, 93053 Regensburg, 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Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Saida","family":"Zoubaa","sequence":"additional","affiliation":[{"name":"Department of Neuropathology, Regensburg University Hospital, 93053 Regensburg, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Martin","family":"Proescholdt","sequence":"additional","affiliation":[{"name":"Department of Neurosurgery, Regensburg University Hospital, 93053 Regensburg, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6910-8843","authenticated-orcid":false,"given":"Nils O.","family":"Schmidt","sequence":"additional","affiliation":[{"name":"Department of Neurosurgery, Regensburg University Hospital, 93053 Regensburg, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3894-5053","authenticated-orcid":false,"given":"Peter","family":"Hau","sequence":"additional","affiliation":[{"name":"Department of Neurology and Wilhelm Sander-NeuroOncology Unit, Regensburg University Hospital, 93053 Regensburg, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Philipp","family":"Beckhove","sequence":"additional","affiliation":[{"name":"Division of Interventional Immunology, Leibniz Institute for Immunotherapy, 93053 Regensburg, Germany"},{"name":"Department of Internal Medicine III, University Hospital Regensburg, 93053 Regensburg, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Beate","family":"Winner","sequence":"additional","affiliation":[{"name":"Department of Stem Cell Biology, Friedrich-Alexander-Universit\u00e4t (FAU) Erlangen-N\u00fcrnberg, 91054 Erlangen, Germany"},{"name":"IZKF Junior Research Group 3 and BMBF Research Group Neuroscience, Interdisciplinary Center for Clinical Research, Friedrich-Alexander-Universit\u00e4t (FAU) Erlangen-N\u00fcrnberg, 91054 Erlangen, 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