Phenotypic mapping of pathological crosstalk between glioblastoma and innate immune cells by synthetic genetic tracing

Glioblastoma is a lethal brain tumor which exhibits heterogeneity and resistance to therapy. Our understanding of tumor homeostasis is limited by a lack of genetic tools to selectively identify tumor states and fate transitions. Here, we use glioblastoma subtype signatures to construct synthetic genetic tracing cassettes and investigate tumor heterogeneity at cellular and molecular level, in vitro and in vivo. Through synthetic locus control regions, we demonstrated that proneural glioblastoma is a hardwired identity, whereas the mesenchymal glioblastoma is an adaptive and metastable cell state driven by pro-inflammatory and differentiation cues and DNA damage, but not hypoxia. Importantly, we discovered that innate immune cells divert glioblastoma cells to a proneural-to-mesenchymal transition which confers therapeutic resistance. Our synthetic genetic tracing methodology is simple, scalable and widely applicable to study homeostasis in development and diseases. In glioblastoma, the method causally links distinct (micro)environmental, genetic and pharmacological perturbations and mesenchymal commitment. Overall design: ChIPseq data set: Genome-wide chromatin landscape of MES- and PN-hGICs-MGT#1in vitro and in vivo RNAseq data set: Transcriptomic profiling of MES-hGICs-MGT#1 co-culture with human Microglia cells