ID #1107 Integrated bulk and single cell profiling of diffuse paediatric-type high-grade glioma tumours and models
Alan Mackay, Yura Grabovska, Laura Bevington, Anna Burford, Drenusha Sejdiu, Sara Temelso, Rita Pereira, Haider Tari, Diana Carvalho, Molina Das, Shauna Crampsie, Valeria Molinari, Rebecca Rogers, Ketty Kessler, Lynn Bjerke, Jiin Song, Emma Lamden, Iza Jasyck, Joselin de Faye, Leslie Bridges, Zita Reisz, Safa Al-Sarraj, Navneet Singh, Simon Stapleton, Cristina Bleil, Samantha Hettige, Bassel Zebian, Julia Cockle, Fernando Carceller, Matthew Clarke, Chris JonesAbstract
Background
Within the WHO2021 CNS Tumour Classification, oncohistone H3-mutations define around half of paediatric-type diffuse high-grade glioma, however the remaining tumours (H3-WT-PDHGG) are less well described.
Methods
Published and unpublished DNA sequencing from n = 762 H3-WT-PDHGG cases were integrated with n = 1292 cases with methylation array profiling, along with bulk (n = 294) and single-cell (n = 32) RNAseq data. We additionally prospectively generated 43 patient-derived models both in vitro and in vivo that were molecularly credentialled in parallel.
Results
Within H3-WT high-grade glioma, a total of 13 MNP12.8-defined subgroups were found to have a peak incidence <21years, spanning infant hemispheric glioma to the novel TYA-enriched HGG_B/MAPK. Clustering of methylation data by tSNE/UMAP highlighted two highly distinct superclusters, with multiple subgroups within each. Supercluster I was defined by radiation-induced secondary and/or hypermutant tumours, incorporating HGG-E (n = 43), cerebellar-enriched tumours (n = 40), and the paediatric RTK1 group (n = 363), further split into A, B and C subgroups. There were profound molecular differences between RTK1A and B/C subgroups, with 1A harbouring few CNAs and many more SNVs (SETD2, NF1), even in the absence of a hypermutator phenotype (also enriched compared to RTK1B/C), as well as a significantly longer overall survival. Distinct from these subgroups was Supercluster_II, which included pedHGG-RTK2A/B (n = 144), but also pedHGGA/B (n = 103) and pedHGG-MYCN (n = 150) subgroups, in addition to the predominantly H3-WT DMG-EGFR (n = 96). Although seemingly disparate, a common feature of these tumours was a highly infiltrative phenotype, either involving multiple cerebral lobes (gliomatosis cerebri) or thalami (bithalamic glioma). Analogous to pedHGG-RTK1, RTK2A harboured few CNAs and more CNVs (BCOR, PIK3CA), and a longer survival compared with 2B. Integrating subgroup-specific differential methylation and gene expression identified subgroup-specific epigenetic regulation of numerous developmentally-restricted transcription factors associated with their distinct neurodevelopmental origins; combining deconvolution approaches to bulk analyses with integrated scRNAseq allowed for identification of subgroup-specific immune cell annotation.
Conclusion
H3-WT-PDHGG segregate into two major classes with common clinical features, but each with multiple subgroups harbouring key molecular and phenotypic differences. A novel panel of patient-derived models which reflect these subgroups will aid in mechanistic and preclinical studies to develop biologically-rational treatments.