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.
Preprint available https://www.biorxiv.org/content/10.1101/2025.05.13.653495v1Decoding 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.
Preprint available https://www.biorxiv.org/content/10.1101/2025.05.13.653733v1Datasets
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.
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.
Single-nuclei ATAC data
Xenium data
Coming soon
Our Team
Omer Bayraktar
Principal Investigator
Wellcome Sanger Institute
Tannia Gracia
Data Production Lead
Wellcome Sanger Institute
Fani Memi
Spatial Transcriptomics Specialist
Wellcome Sanger Institute
Grant de Jong
Omics Data Analysis and Integration
Wellcome Sanger Institute
Oliver Gould
Technical Specialist
Wellcome Sanger Institute
Sabine Eckert
Multiomics Data Generation
Wellcome Sanger Institute
Qianqian Zhang
Omics Computational Analysis
University of Cambridge
Hayden Powell
Multiomics Data Generation
Wellcome Sanger Institute
Shreya Rai
Spatial Transcriptomics Data Generation
Wellcome Sanger Institute
Zoi Katsirea
Sample QC and Data Organisation
Wellcome Sanger Institute
João Barros-Silva
Immunohistochemical Profiling
Francis Crick Institute
Manas Dave
LCM Data Generation
Wellcome Sanger Institute
Stanislaw Makarchuk
Image Annotation System Integration
Wellcome Sanger Institute
Olga Lazareva
Omics Computational Analysis
DKFZ
Manu Saraswat
Omics Computational Analysis
DKFZ
Laura Rueda
Omics Computational Analysis
DKFZ
David Rowitch
Co-Principal Investigator
University of Cambridge
Richard Mair
Consultant Neurosurgeon
Cancer Research UK - Cambridge Institute
Oliver Stegle
Co-Principal Investigator
DKFZ
Moritz Mall
Co-Principal Investigator
DKFZ
Sam Behjati
Co-Principal Investigator
Wellcome Sanger Institute
James Briscoe
Co-Principal Investigator
Francis Crick Institute
Acknowledgements
Wellcome Sanger Institute, University of Cambridge, Cambridge University Hospital Trust, Francis Crick Institute, DKFZ, Patients.
