GBM-Space

A holistic multi-modal atlas of glioblastoma

Glioblastoma is an incurable brain tumour with extensive heterogeneity and plasticity of cancer cells. Despite extensive research, many fundamental aspects of glioblastoma biology remain unknown. As part of the Wellcome LEAP 'Delta Tissue' programme, we chart the most comprehensive cell and tissue atlas of glioblastoma. Towards developing new treatments, we mapped the cellular trajectories of glioblastoma cancer cells and their interactions with the tumour microenvironment in unprecedented detail.

In our initial efforts, we applied high-throughput single cell and spatial multiomic profiling to bridge the genetic, cellular and tissue architecture of these tumours. The resulting GBM-Space atlas uniquely combines:

Multi-region sampling each tumour
Paired single cell and spatial multiomics of each tumour site
state-of-the-art computational integrations of these datasets

The initial single cell and spatial transcriptomics datasets can be interactively navigated and downloaded on this portal.

Publications

A spatiotemporal cancer cell trajectory underlies glioblastoma heterogeneity (submitted)

De Jong G, Memi F, Gracia T, Lazareva O et al.

Decoding Plasticity Regulators and Transition Trajectories in Glioblastoma with Single-cell Multiomics (submitted)

Saraswat M, Rueda-Gensini L, Heinzelmann E, Gracia T, Memi F et al.

Datasets

Single nuclei Transcriptomics data on CELLxGENE

1,025,329 nuclei from 12 glioblastoma tumours across 4-15 sampling sites. The resulting data shows 28 malignant cell states and 71 cell types from the tumour microenvironment, totalling 99 annotated clusters.

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Integrated single cell and spatial data on Webatlas

Integration of 1 million single nuclei transcriptomes with 0.3 million spatial transcriptomes over 97 Visium sections. The resulting data shows gene expression, cell state abundances, and histopathological annotations for each spatial tissue location.

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