{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,28]],"date-time":"2026-07-28T13:03:49Z","timestamp":1785243829433,"version":"3.55.0"},"reference-count":34,"publisher":"MDPI AG","issue":"4","license":[{"start":{"date-parts":[[2026,7,28]],"date-time":"2026-07-28T00:00:00Z","timestamp":1785196800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Methods Protoc.","MPs"],"abstract":"<jats:p>Tumor cell invasion is a critical step in local tumor progression, recurrence, and metastasis. Conventional two-dimensional migration assays and many existing three-dimensional invasion models often assess cell migration, invasion into the extracellular matrix and matrix degradation as separate endpoints, although these processes are tightly coupled in vivo. Therefore, robust and reproducible in vitro models are needed to investigate tumor cell invasion under defined extracellular matrix conditions. We developed an agarose-based three-dimensional invasion assay, termed the Freiburg 3D invasion assay, for the simultaneous analysis of tumor cell migration, invasion, and extracellular matrix degradation. The system consists of a 2.8% agarose matrix containing defined microcavities connected by a common loading channel. Tumor cells are seeded into these microcavities, where they form compact cell aggregates. The cavities are subsequently filled with collagen type I or extracellular matrix gel. After polymerization, the matrix-containing agarose strips are transferred into parking pockets, cultured for several days, and monitored by microscopy. Invasion distance, single-cell migration, and ECM-cleared area are quantified from serial microscopic images using image analysis software. The system distinguished weakly invasive MCF7 breast cancer cells from highly invasive MDA-MB-231 cells. In addition, treatment with a protease inhibitor and irradiation reduced tumor cell invasion and extracellular matrix remodeling, demonstrating the suitability of the assay for pharmacological and radiation-response studies. The Freiburg 3D invasion assay provides a practical and reproducible three-dimensional in vitro model for analyzing tumor cell invasion and protease-associated extracellular matrix degradation.<\/jats:p>","DOI":"10.3390\/mps9040112","type":"journal-article","created":{"date-parts":[[2026,7,28]],"date-time":"2026-07-28T11:45:26Z","timestamp":1785239126000},"page":"112","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Agarose-Based 3D Invasion Assay for Simultaneous Quantification of Tumor Cell Invasion and Extracellular Matrix Degradation"],"prefix":"10.3390","volume":"9","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-0163-8677","authenticated-orcid":false,"given":"Andreas R.","family":"Thomsen","sequence":"first","affiliation":[{"name":"Department of Radiation Oncology, University of Freiburg, 79106 Freiburg, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4273-147X","authenticated-orcid":false,"given":"Pascaline","family":"Kouam-Daniel","sequence":"additional","affiliation":[{"name":"Institute for Molecular Oncology, Radio-Biology and Experimental Radiotherapy, Marien Hospital Herne, University Clinic of Ruhr-University Bochum, 44265 Herne, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Bettina","family":"Priesch-Grzeszkowiak","sequence":"additional","affiliation":[{"name":"Institute for Molecular Oncology, Radio-Biology and Experimental Radiotherapy, Marien Hospital Herne, University Clinic of Ruhr-University Bochum, 44265 Herne, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Anja","family":"Grillenberger","sequence":"additional","affiliation":[{"name":"Institute for Molecular Oncology, Radio-Biology and Experimental Radiotherapy, Marien Hospital Herne, University Clinic of Ruhr-University Bochum, 44265 Herne, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sandra","family":"Kumbruch","sequence":"additional","affiliation":[{"name":"Institute for Molecular Oncology, Radio-Biology and Experimental Radiotherapy, Marien Hospital Herne, University Clinic of Ruhr-University Bochum, 44265 Herne, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7575-4152","authenticated-orcid":false,"given":"Ali H.","family":"Acikelli","sequence":"additional","affiliation":[{"name":"Department of Haematology and Oncology, Institute of Molecular Oncology and Experimental Therapeutics, Marien Hospital Herne, University Clinic of Ruhr-University Bochum, 44265 Herne, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Helmut","family":"B\u00fchler","sequence":"additional","affiliation":[{"name":"Institute for Molecular Oncology, Radio-Biology and Experimental Radiotherapy, Marien Hospital Herne, University Clinic of Ruhr-University Bochum, 44265 Herne, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1733-6064","authenticated-orcid":false,"given":"Christian","family":"Baues","sequence":"additional","affiliation":[{"name":"Institute for Molecular Oncology, Radio-Biology and Experimental Radiotherapy, Marien Hospital Herne, University Clinic of Ruhr-University Bochum, 44265 Herne, Germany"},{"name":"Department of Radiotherapy and Radio-Oncology, Marien Hospital Herne, University Clinic of Ruhr-University Bochum, 44265 Herne, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2026,7,28]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"737","DOI":"10.1038\/nrc2229","article-title":"Illuminating the metastatic process","volume":"7","author":"Sahai","year":"2007","journal-title":"Nat. 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