Comparative single-cell RNA-sequencing profiling of BMP4-treated primary glioma cultures reveals therapeutic markers

• Published in: Neuro-oncology (Charlottesville, Va.) Va.), 2022-12, Vol.24 (12), p.2133-2145
• Main Authors: Verploegh, Iris S C, Conidi, Andrea, Brouwer, Rutger W W, Balcioglu, Hayri E, Karras, Panagiotis, Makhzami, Samira, Korporaal, Anne, Marine, Jean-Christophe, Lamfers, Martine, Van IJcken, Wilfred F J, Leenstra, Sieger, Huylebroeck, Danny
• Format: Article
• Language: English
• Subjects: Biomarkers - metabolism; Bone Morphogenetic Protein 4 - genetics; Bone Morphogenetic Protein 4 - metabolism; Bone Morphogenetic Protein 4 - pharmacology; Brain Neoplasms - drug therapy; Brain Neoplasms - genetics; Brain Neoplasms - metabolism; Cell Differentiation; Cell Proliferation; Gene Expression Profiling; Glioblastoma - drug therapy; Glioblastoma - genetics; Glioblastoma - metabolism; Glioma - pathology; Humans; Neoplastic Stem Cells - metabolism; RNA - metabolism
• ISSN: 1522-8517; 1523-5866
• DOI: 10.1093/neuonc/noac143

Glioblastoma (GBM) is the most aggressive primary brain tumor. Its cellular composition is very heterogeneous, with cells exhibiting stem-cell characteristics (GSCs) that co-determine therapy resistance and tumor recurrence. Bone Morphogenetic Protein (BMP)-4 promotes astroglial and suppresses oligodendrocyte differentiation in GSCs, processes associated with superior patient prognosis. We characterized variability in cell viability of patient-derived GBM cultures in response to BMP4 and, based on single-cell transcriptome profiling, propose predictive positive and early-response markers for sensitivity to BMP4. Cell viability was assessed in 17 BMP4-treated patient-derived GBM cultures. In two cultures, one highly-sensitive to BMP4 (high therapeutic efficacy) and one with low-sensitivity, response to treatment with BMP4 was characterized. We applied single-cell RNA-sequencing, analyzed the relative abundance of cell clusters, searched for and identified the aforementioned two marker types, and validated these results in all 17 cultures. High variation in cell viability was observed after treatment with BMP4. In three cultures with highest sensitivity for BMP4, a substantial new cell subpopulation formed. These cells displayed decreased cell proliferation and increased apoptosis. Neuronal differentiation was reduced most in cultures with little sensitivity for BMP4. OLIG1/2 levels were found predictive for high sensitivity to BMP4. Activation of ribosomal translation (RPL27A, RPS27) was up-regulated within one day in cultures that were very sensitive to BMP4. The changes in composition of patient-derived GBM cultures obtained after treatment with BMP4 correlate with treatment efficacy. OLIG1/2 expression can predict this efficacy, and upregulation of RPL27A and RPS27 are useful early-response markers.