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Identifying new biomarkers of aggressive Group 3 and SHH medulloblastoma using 3D hydrogel models, single cell RNA sequencing and 3D OrbiSIMS imaging

Linke, Franziska; Johnson, James E. C.; Kern, Stefanie; Bennett, Christopher D.; Lourdusamy, Anbarasu; Lea, Daniel; Clifford, Steven C.; Merry, Catherine L. R.; Stolnik, Snow; Alexander, Morgan R.; Peet, Andrew C.; Scurr, David J.; Griffiths, Rian L.; Grabowska, Anna M.; Kerr, Ian D.; Coyle, Beth


Franziska Linke

James E. C. Johnson

Stefanie Kern

Christopher D. Bennett

Daniel Lea

Steven C. Clifford

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Professor of Stem Glycobiology

Snow Stolnik

Andrew C. Peet

Principal Research Fellow

Professor of Cancer Microenvironment

Associate Professor

Associate Professor


The most common malignant brain tumour in children, medulloblastoma (MB), is subdivided into four clinically relevant molecular subgroups, although targeted therapy options informed by understanding of different cellular features are lacking. Here, by comparing the most aggressive subgroup (Group 3) with the intermediate (SHH) subgroup, we identify crucial differences in tumour heterogeneity, including unique metabolism-driven subpopulations in Group 3 and matrix-producing subpopulations in SHH. To analyse tumour heterogeneity, we profiled individual tumour nodules at the cellular level in 3D MB hydrogel models, which recapitulate subgroup specific phenotypes, by single cell RNA sequencing (scRNAseq) and 3D OrbiTrap Secondary Ion Mass Spectrometry (3D OrbiSIMS) imaging. In addition to identifying known metabolites characteristic of MB, we observed intra- and internodular heterogeneity and identified subgroup-specific tumour subpopulations. We showed that extracellular matrix factors and adhesion pathways defined unique SHH subpopulations, and made up a distinct shell-like structure of sulphur-containing species, comprising a combination of small leucine-rich proteoglycans (SLRPs) including the collagen organiser lumican. In contrast, the Group 3 tumour model was characterized by multiple subpopulations with greatly enhanced oxidative phosphorylation and tricarboxylic acid (TCA) cycle activity. Extensive TCA cycle metabolite measurements revealed very high levels of succinate and fumarate with malate levels almost undetectable particularly in Group 3 tumour models. In patients, high fumarate levels (NMR spectroscopy) alongside activated stress response pathways and high Nuclear Factor Erythroid 2-Related Factor 2 (NRF2; gene expression analyses) were associated with poorer survival. Based on these findings we predicted and confirmed that NRF2 inhibition increased sensitivity to vincristine in a long-term 3D drug treatment assay of Group 3MB. Thus, by combining scRNAseq and 3D OrbiSIMS in a relevant model system we were able to define MB subgroup heterogeneity at the single cell level and elucidate new druggable biomarkers for aggressive Group 3 and low-risk SHH MB.


Linke, F., Johnson, J. E. C., Kern, S., Bennett, C. D., Lourdusamy, A., Lea, D., …Coyle, B. (2023). Identifying new biomarkers of aggressive Group 3 and SHH medulloblastoma using 3D hydrogel models, single cell RNA sequencing and 3D OrbiSIMS imaging. Acta Neuropathologica Communications, 11(1), Article 6.

Journal Article Type Article
Acceptance Date Dec 19, 2022
Online Publication Date Jan 11, 2023
Publication Date Jan 11, 2023
Deposit Date Jan 24, 2023
Publicly Available Date Jan 25, 2023
Journal Acta Neuropathologica Communications
Electronic ISSN 2051-5960
Publisher Springer Verlag
Peer Reviewed Peer Reviewed
Volume 11
Issue 1
Article Number 6
Keywords Cellular and Molecular Neuroscience; Neurology (clinical); Pathology and Forensic Medicine
Public URL
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