EMPiRad: Epithelial-mesenchymal plasticity and its impact on the radiation response in breast cancer

• Applicant: Dr. Nikko Brix
• Subject Area: Nuclear Medicine, Radiotherapy, Radiobiology
• Term: since 2025
• Project identifier: Deutsche Forschungsgemeinschaft (DFG) - Project number 551613698

The EMPiRad project aims to investigate the influence of epithelial-mesenchymal (E/M) plasticity on the radiation response in breast cancer cells. Preliminary work with 14 breast cancer and two non-malignant breast epithelial cell lines revealed significant heterogeneity in both E/M phenotype and radiation resistance. At the transcriptomic level, various gene sets associated with E/M plasticity were identified as correlates of radioresistance. From this, the project derives its two central hypotheses: (1) that radioresistance depends on the specific E/M state of cancer cells, and (2) that it is modulated by differences in the expression and/or localization of radiation resistance-associated proteins (RAPs). The overarching goal of the project is to identify such RAPs – deliberately without restriction to DNA repair proteins due to preliminary findings. Using stimulators of E/M plasticity, isogenic cell systems in 5–6 different E/M cell states will be characterized through light microscopy, flow cytometry, transcriptomics, and atomic force microscopy. The cellular radiation response will be determined by measuring clonogenic survival and quantifying initial and persistent DNA damage using γH2AX measurement, qRT-PCR, and spectral karyotyping (Objective 1). Subsequently, by correlation of radioresistance and gene expression data from the isogenic models, RAP candidates will be identified to link radiation resistance of various E/M cell states to expression of potential RAPs. Molecular genetic manipulation will then be employed to selectively alter the expression of these RAP candidates, and the resulting radiation response will be examined as described above (Objective 2). For RAP validation, radiation response and RAP expression will also be investigated in organoids from breast cancer patients with different E/M phenotypes (Objective 3). Organoids will be characterized via fluorescence microscopy, flow cytometry, mass cytometry, and transcriptomic analyses at both bulk and single-cell levels. This aims to confirm the dependency of the radiation response on RAP expression in the organoids. Finally, the anticipated role of RAPs will be examined in vivo (Objective 4). The previously generated cell systems with genetically manipulated RAP expression will be locally irradiated in orthotopic xenograft experiments, measuring tumor growth and survival. The extent of DNA damage will be assessed ex vivo, and RAP expression, as the anticipated cause of radiation resistance, will be verified using flow and mass cytometry. Overall, the project aims to establish a connection between E/M plasticity and alterations in the expression of previously unknown RAPs as causes of radioresistance both in vitro and in vivo.

• DFG Programme: Research Grants