Glioblastoma multiforme: a meta-analysis of driver genes, current diagnosis, and tumor heterogeneity
Creators: name: Avina, Katia
name: Herrera-Oropeza, Gabriel Emilio
name: Rojo, Carla Angulo
name: Lopez, Santos Alberto Gastelum
name: Varela-Echavarria, Alfredo
name: Rosales, Maribel Hernandez
Publisher: name: F1000 Research Limited
Year: 2021

description: Glioblastoma multiforme (GBM) is the most frequent and aggressive deadly primary brain tumor in adults, accounting for approximately 82% of all malignant gliomas . Although it can affect children, its incidence rises with age. GBM tumors are characterized by increased cell proliferation, aggressive invasion, active angiogenesis, and remarkable genetic heterogeneity. Histologically, tumors display a high morphological variability as they contain pleomorphic and multinucleated cells with high mitotic activity, show microvascular proliferation, undergo severe and characteristic endothelial hyperplasia, contain intravascular microthrombi, and extensive necrosis of an ischemic or pseudo-empalized nature. The multiforme denomination of GBM tumors is due to the diverse and heterogeneous microenvironments that parallel their multiple histological patterns and cytological features.<br> <br> According to their ontogeny, most GBMs are primary tumors that develop de novo in the absence of previous neoplasia. Primary GBMs are highly aggressive and invasive, tend to extend to both cerebral hemispheres, or are bilateral, and they are most commonly manifested in elderly patients. Secondary GBMs, in contrast, are located in the frontal lobe and develop mainly in younger patients suffering from anaplastic astrocytoma or low-grade astrocytoma, presenting a much better prognosis. Recent reports have determined that primary and secondary glioblastomas have distinct genetic alterations related to particular biological pathways, suggesting they require different therapeutic approaches. Hence, from the clinical perspective, discerning between primary and secondary GBM is highly relevant. Usually, primary GBMs present overexpression and gene amplification of epidermal growth factor receptor (<i>EGFR</i>) and mutations in cyclin-dependent kinase inhibitor 2A (<i>CDKN2A/p16INK4A</i>) and phosphatase tensin homolog (<i>PTEN</i>) genes. Molecular biomarkers of secondary GBM include mutations in tumor protein 53 (<i>TP53</i>) and isocitrate dehydrogenase-1 (<i>IDH1</i>) genes, which correlate strongly with O6-Methylguanine-DNA methyltransferase (<i>MGMT</i>) promoter methylation.<br> <br> Initiation and progression of GBM tumorigenesis are related to genetic and epigenetic alterations and molecular subtypes of GBM have unique transcriptional profiles. Based on expression features, GBM tumors were originally classified into four subtypes: Neural, Proneural, Classical (proliferative), and Mesenchymal, a scheme that has been recently revised using transcriptomic information. The improved classification eliminates the neural subtype and considers tumors of this molecular type as containing normal brain tissue contamination. GBM molecular subtypes are also associated with different spatial zones, heterogeneity, and aggressiveness of the tumor.<br> <br> GBMs belonging to the proneural subtype have alterations in <i>TP53, PDGFRA, PIK3CA</i>, and <i>IDH1</i> genes. The classical subtype, also known as a proliferative subtype, has been associated with high levels of cell proliferation and upregulation of <i>EGFR</i>. Mesenchymal GBMs show overexpression of mesenchymal and astrocytic markers (<i>CD44</i>, and <i>MERTK</i>) and down-regulation of neurofibromatosis type-1 (NF1) and up-regulation of chitinase 3 like 1 (<i>CHI3L1/YKL-40</i>) and <i>MET</i> are frequently observed. While the proneural subtype has been mostly reported in younger patients and is associated with a favorable prognosis, the mesenchymal and the classical subtypes are usually linked to more aggressive high-grade gliomas that appear in adult or elderly life.<br> <br> Recent advances employing Next Generation Sequencing have led to a better insight into the molecular biology of gliomas contributing potential markers for better diagnosis and new approaches to finding specific treatment strategies. GBM remains an incurable deadly disease with an abysmal prognosis that has not significantly shown improvement, causing an enormous individual and societal burden. Thus, there is a need for tumor-specific drug targets and pharmacological agents to inhibit cell migration, dispersal, and angiogenesis. <br> <br> In the last years, the clinical relevance of GBM heterogeneity has been highlighted. This particular feature makes this type of cancer one of the most challenging to treat and consists of <i>inter-tumor</i> and <i>intra-tumor</i> feature variations. Inter-tumor heterogeneity refers to GBMs from different patients with altered and differing genotypes and phenotypes related to diverse etiological and environmental factors. On the other hand, intra-tumor heterogeneity refers to the presence of multiple and different cell subpopulations within the same tumor, defining its topology and architecture. The comprehensive genomic classification of GBM paves the way for an improved understanding of GBM, which in the future may result in personalized therapy. Hence, there is an urgent need to further our knowledge of tumor heterogeneity as it will help design better therapies against GBM and tumor recurrence.<br> <br> Based on a multi-omic analysis, in this study we describe the heterogeneity of GBM at the transcriptional and genomic levels, with emphasis on driver genes currently used as genomic markers. For that purpose, from sixty clinical reports, we selected and analyzed eighteen driver genes that have shown deregulated behavior in patient samples. Using bioinformatics pipelines and the TCGA database, we examined their mRNA expression in the different GBM molecular subtypes and the presence of somatic mutations linked to possible disruption of protein function. <br> <br> This study summarizes findings describing the significant heterogeneity of GBM at the transcriptional and genomic levels, emphasizing eighteen driver genes with clinical relevance. A pattern was identified fitting the stem cell model for GBM ontogenesis, with an up-regulation profile for<i> MGMT</i> and down-regulation for <i>ATRX, H3F3A, TP53,</i> and <i>EGFR </i>in the mesenchymal subtype. We also detected overexpression of <i>EGFR, NES, VIM</i>, and <i>TP53 </i>in the classical subtype and of <i>MKi67</i> and <i>OLIG2</i> genes in the proneural subtype. Furthermore, we found a combination of the four biomarkers<i> EGFR, NES, OLIG2,</i> and <i>VIM</i> with a remarkable differential expression pattern which confers them a strong potential to determine the GBM molecular subtype. A unique distribution of somatic mutations was found for the young and adult population, particularly for genes related to DNA repair and chromatin remodeling, highlighting <i>ATRX, MGMT,</i> and <i>IDH1.</i> Our results also revealed that highly lesioned genes undergo differential regulation with particular biological pathways for young patients. This multi-omic analysis will help delineate future strategies related to the use of these molecular markers for clinical decision-making in the medical routine.