Comparative epigenetic analysis of tumour initiating cells and syngeneic EPSC-derived neural stem cells in glioblastoma

Claire Vinel,Catherine L R Merry,Sven Nelander,Anaëlle Dumas ,James Boot ,Thomas O Millner ,Juho Vuononvirta,Gabriel Rosser,Myrianni Constantinou,Juliette Thompson ,Tedani El Assan,T Alwyn Jones ,Nicola Pomella,Vardhman K Rakyan ,Federica M Marelli‐Berg ,Yung‐Yao Lin ,Suchita Nadkarni,Xinyu Zhang,Sebastian Brandner,Natasha Aley,Jeremy Rees,Denise Sheer,Loredana Guglielmi,Pentao Liu,Silvia Marino

doi:10.1038/s41467-021-26297-6

Abstract

Epigenetic mechanisms which play an essential role in normal developmental processes, such as self-renewal and fate specification of neural stem cells (NSC) are also responsible for some of the changes in the glioblastoma (GBM) genome. Here we develop a strategy to compare the epigenetic and transcriptional make-up of primary GBM cells (GIC) with patient-matched expanded potential stem cell (EPSC)-derived NSC (iNSC). Using a comparative analysis of the transcriptome of syngeneic GIC/iNSC pairs, we identify a glycosaminoglycan (GAG)-mediated mechanism of recruitment of regulatory T cells (Tregs) in GBM. Integrated analysis of the transcriptome and DNA methylome of GBM cells identifies druggable target genes and patient-specific prediction of drug response in primary GIC cultures, which is validated in 3D and in vivo models. Taken together, we provide a proof of principle that this experimental pipeline has the potential to identify patient-specific disease mechanisms and druggable targets in GBM.

Highlights

Epigenetic mechanisms which play an essential role in normal developmental processes, such as self-renewal and fate specification of neural stem cells (NSC) are responsible for some of the changes in the glioblastoma (GBM) genome
We show that the number of differentially methylated regions (DMRs) detected between the expanded potential stem cell (EPSC) lines and two reference embryonic stem cells” (ESC) lines[27,28] is similar to the number observed with published iPSC lines generated using different strategies (HipSci Initiative and28,29) (Fig. S2e)
Deregulated transcriptional programmes and epigenetic mechanisms have been convincingly shown to play a role, together with genetic lesions, in the neoplastic transformation of these cells into GIC and in conferring essential tumour maintenance properties to the latter6. iNSC derived from iPSC have been extensively characterized and shown to share marker expression and functional properties with endogenous NSC61,62

Summary

Introduction

Epigenetic mechanisms which play an essential role in normal developmental processes, such as self-renewal and fate specification of neural stem cells (NSC) are responsible for some of the changes in the glioblastoma (GBM) genome. The isolation, enrichment, and propagation of GIC in vitro either as adherent cultures or neurospheres is a powerful tool for screening and functional validation of targets These primary patient-derived cell lines retain the ability to generate tumours reflecting the heterogeneity of the parental tumour as shown in barcoding experiments followed by characterization of clonal expansion[13]. They recapitulate to some degree the cellular states and plasticity found in GBM14 and core regulatory circuits identified in these cells are maintained in matched primary tumours[15]. Epigenetic remodelling which locks GIC into an undifferentiated state upon prolonged culturing[9,16] and the lack of interactions between these cells and various other cell types existing in vivo are known limitations of this experimental system

Methods

Results

Conclusion