Integrated Metabolomics and Transcriptomics Analysis of Monolayer and Neurospheres from Established Glioblastoma Cell Lines.

Joana Peixoto,Lisa Schlicker,Jorge Lima,Paula Soares,Alina M Winkelkotte,Almut Schulze,Christel Herold-Mende,Werner Schmitz,Susanne Walz,Sudha Janaki-Raman

doi:10.3390/cancers13061327

Abstract

Simple SummaryGlioblastomas are very aggressive tumours without efficient treatment, where cancer stem-like cells are thought to be responsible for relapse. This pilot study investigated the metabolic discrepancies between monolayer and neurosphere cultures of two glioblastoma cell lines using transcriptomics and metabolomics. We show that the two culture systems display substantial differences regarding their metabolome and transcriptome. Specifically, we found that metabolic reactions connected to arginine biosynthesis are crucial to support the different metabolic needs of neurospheres from the two cell lines. By identifying metabolic vulnerabilities in different glioblastoma subpopulations, new therapeutic strategies may be emerging that can be explored to treat this disease. Moreover, this data set may be of great value as a resource for the scientific community.Altered metabolic processes contribute to carcinogenesis by modulating proliferation, survival and differentiation. Tumours are composed of different cell populations, with cancer stem-like cells being one of the most prominent examples. This specific pool of cells is thought to be responsible for cancer growth and recurrence and plays a particularly relevant role in glioblastoma (GBM), the most lethal form of primary brain tumours. Here, we have analysed the transcriptome and metabolome of an established GBM cell line (U87) and a patient-derived GBM stem-like cell line (NCH644) exposed to neurosphere or monolayer culture conditions. By integrating transcriptome and metabolome data, we identified key metabolic pathways and gene signatures that are associated with stem-like and differentiated states in GBM cells, and demonstrated that neurospheres and monolayer cells differ substantially in their metabolism and gene regulation. Furthermore, arginine biosynthesis was identified as the most significantly regulated pathway in neurospheres, although individual nodes of this pathway were distinctly regulated in the two cellular systems. Neurosphere conditions, as opposed to monolayer conditions, cause a transcriptomic and metabolic rewiring that may be crucial for the regulation of stem-like features, where arginine biosynthesis may be a key metabolic pathway. Additionally, TCGA data from GBM patients showed significant regulation of specific components of the arginine biosynthesis pathway, providing further evidence for the importance of this metabolic pathway in GBM.

Highlights

The cancer stem cell concept is based on the scientific discovery that tumours, like normal tissues, are composed of subpopulations of cells that can both self-renew and differentiate into several different cell populations
To identify changes in gene expression in GBM cells exposed to different culture conditions that promote either a stem-like or differentiated phenotype, U87 and NCH644 cells were exposed to neurosphere (NS) and monolayer (ML) culture conditions (Figure 1a) and total RNA was prepared
Using two different culture conditions in two GBM cell lines, U87 and NCH644, we have shown here that the induction of a stem-like phenotype induces the remodelling of specific metabolic pathways, and that the metabolic portrait of glioblastoma stem-like cells (GSCs) is fundamentally different from that of cells in a more differentiated state

Summary

Introduction

The cancer stem cell concept is based on the scientific discovery that tumours, like normal tissues, are composed of subpopulations of cells that can both self-renew and differentiate into several different cell populations. In glioblastoma (GBM) models, both in vitro and in vivo studies have identified the existence of glioblastoma stem-like cells (GSCs) expressing stem cell-related markers, which are able to initiate and recapitulate tumour heterogeneity when injected orthotopically into mice [1,2]. In this context, GSCs are defined as tumour cells with unlimited self-renewal potential, multipotent differentiation capacity and high tumourigenic ability [1]. The high degree of intratumoural heterogeneity, along with the infiltrative, migratory and plastic nature of GBM cells, as well as the high recurrence rate of this disease, represent the major contributors for the poor prognosis of GBM patients

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