gms | German Medical Science

Objective: High-dimensional technologies have provided insights into transcriptional heterogeneity and dynamic plasticity which are hallmarks of brain tumors. Although scRNA-seq recovers the diversity of transcriptional states, their spatial context within the neuronal environment has remained unexplored. Here, we integrated spatially resolved transcriptomics and metabolomics to characterize the glioma landscape of multiple molecular levels.

Methods: We integrated spatially resolved transcriptomics using the 10X Visium technology from 19 glioblastoma IDH WT and 2 IDH mutated glioma. For metabolomic profiling we performed Matrix Assisted Laser Desorption/Ionization Fourier-transform ion cyclotron resonance mass spectrometry imaging (MALDI-FTICR-MSI) from consecutive sections. For computational analysis we established an R based framework for data integration and spatial analysis (SPATA2, https://github.com/theMILOlab/SPATA2/).

Results: By integrating metabolome data, we identified a distinct transcriptional program encompassing reactive responses to hypoxia. Areas of hypoxic response were negatively correlated with proliferation (R2= -0.34, p< 0.001) and significantly enriched for gene expression signatures from the S-phase (p< 0.001). Modeling of transient spatial gradients using vector field predictions showed opposing vector directions of hypoxia response and migratory capacity, underpinning the “go-or-growth” theory, where cells either proliferate or migrate. Inferred copy-number alterations (CNA) revealed a significant increase in genomic instability, highly correlated to hypoxia response (R2= 0.78, p< 0.001). Near necrotic areas, we observed a significant accumulation of CNAs while proliferation was inhibited, and cells remained in the S-phase. We validated this hypothesis of hypoxia-driven accumulation of CNAs by chronic hypoxia cultures of primary patient-derived cell lines. A gain of chromosomal instability after long-term hypoxia was observed, suggesting that hypoxic areas in glioblastoma function as bioreactors for genomic instability.

Conclusion: Our findings elucidate the evolution of resistant subclones in glioblastoma. They provide novel insights into the dynamic regulation and interaction between host and tumor and cast a new light on hypoxic and necrotic areas which may represent the source of the heterogenous and resistant nature of glioblastomas.