Single-cell molecular profiling using ex vivo functional readouts fuels precision oncology in glioblastoma

Abstract

Background Functional profiling of freshly isolated glioblastoma cells is being evaluated as a next-generation method for precision oncology. While promising, its success largely depends on the method to evaluate treatment activity which requires sufficient resolution and specificity. Methods Here, we describe the ‘precision oncology by single-cell profiling using ex vivoreadouts of functionality’ (PROSPERO) assay to evaluate the intrinsic susceptibility of highgrade brain tumor cells to respond to therapy. Different from other assays, PROSPERO extends beyond life/death screening by rapidly evaluating acute molecular drug responses at single-cell resolution. Results The PROSPERO assay was developed by correlating short-term single-cell molecular signatures using CyTOF to long-term cytotoxicity readouts in representative patientderived glioblastoma cell cultures (n=14) that were exposed to radiotherapy and the smallmolecule p53/MDM2 inhibitor AMG232. The predictive model was subsequently projected to evaluate drug activity in freshly resected GBM samples from patients (n=34). Here, PROSPERO revealed an overall limited capacity of tumor cells to respond to therapy, as reflected by the inability to induce key molecular markers upon ex vivo treatment exposure, while retaining proliferative capacity, insights that were validated in PDX models. This approach also allowed the investigation of cellular plasticity, which in PDCLs highlighted therapy-induced proneural-to-mesenchymal transitions, while in patients’ samples this was more heterogeneous. Conclusion PROSPERO provides a precise way to evaluate therapy efficacy by measuring molecular drug responses using specific biomarker changes in freshly resected brain tumor samples, in addition to providing key functional insights in cellular behavior, which may ultimately complement standard, clinical biomarker evaluations.