The Tumor Microenvironment Strongly Impacts Master Transcriptional Regulators and Gene Expression Class of Glioblastoma

Abstract

The Cancer Genome Atlas (TCGA) project has generated gene expression data that divides glioblastoma (GBM) into four transcriptional classes: proneural, neural, classical, and mesenchymal. Because transcriptional class is only partially explained by underlying genomic alterations, we hypothesize that the tumor microenvironment may also have an impact. In this study, we focused on necrosis and angiogenesis because their presence is both prognostically and biologically significant. These features were quantified in digitized histological images of TCGA GBM frozen section slides that were immediately adjacent to samples used for molecular analysis. Correlating these features with transcriptional data, we found that the mesenchymal transcriptional class was significantly enriched with GBM samples that contained a high degree of necrosis. Furthermore, among 2422 genes that correlated with the degree of necrosis in GBMs, transcription factors known to drive the mesenchymal expression class were most closely related, including C/EBP-β, C/EBP-δ, STAT3, FOSL2, bHLHE40, and RUNX1. Non-mesenchymal GBMs in the TCGA data set were found to become more transcriptionally similar to the mesenchymal class with increasing levels of necrosis. In addition, high expression levels of the master mesenchymal factors C/EBP-β, C/EBP-δ, and STAT3 were associated with a poor prognosis. Strong, specific expression of C/EBP-β and C/EBP-δ by hypoxic, perinecrotic cells in GBM likely account for their tight association with necrosis and may be related to their poor prognosis.

Whole Slide Imaging for Analytical Anatomic Pathology and Telepathology: Practical Applications Today, Promises, and Perils

“…66,67 Earlier studies from our department established the role of Ki-67 quantitation in glial neoplasms. 68,69 Recently, using multimodal, multiscale approaches and machine-based classification, researchers have devised ways to mine scanned histologic data on glioblastoma in The Cancer Genome Atlas Project and other sources; the resulting quantitative morphometric analysis findings have been further integrated with molecular data to provide in silico cancer research [70][71][72][73][74][75][76][77][78][79][80] and with radiologic data to provide clinicopathoradiologic correlation. 81 Insights from this work also include findings on the importance of tumor-infiltrating lymphocytes in glioblastoma, 72 and in silico approaches from these studies have uncovered novel findings regarding the regulation of asymmetric cell division in glioblastoma by such mediators as the human Brat ortholog TRIM3.…”

miR-218 opposes a critical RTK-HIF pathway in mesenchymal glioblastoma

“…Moreover, an independent study revealed that GBM samples with high levels of necrosis are significantly enriched for the mesenchymal transcriptional gene signature (4). In particular, hypoxic GBM cells surrounding necrotic zones express high levels of the mesenchymal transcription factors C/EBP-β and C/EBP-δ, indicating a clear association between hypoxia, necrosis, and a mesenchymal GBM cellular identity (4).…”

“…This cellular architecture is a common feature of glioblastoma multiforme (GBM), highly malignant brain tumors with a median patient survival of only 12-14 mo (2). Pseudopalisading GBM cells at the periphery of necrotic areas exhibit nuclear hypoxia-inducible factor 1α (HIF1α) protein accumulation and express hypoxia-regulated genes that control angiogenesis, extracellular matrix degradation, and invasive behavior (3,4). Recent genomic sequencing and transcriptome analyses stratified GBM into distinct subtypes, including mesenchymal and proneural (5,6).…”

Augmented expression of RUNX1 deregulates the global gene expression of U87 glioblastoma multiforme cells and inhibits tumor growth in mice

“…3,6 Recent studies demonstrated that the mesenchymal signature of GBM is largely driven by six transcription factors (TFs) including STAT3, CEBP, BHLHB2, FOSL2, ZNF238, and RUNX1. 7,8 These factors control the expression of over 70% of genes comprising the MGES of highgrade gliomas. 7 STAT3 and CEBP were established as the initiators and master regulators of this process and when silenced led to elimination of the mesenchymal signature and decreased tumor aggressiveness.…”

“…[23][24][25][26][27] Nevertheless, despite being heavily studied, little is known regarding the role of RUNX1 in malignancies of the central nervous system, specifically GBM. 8,26,[28][29][30] In this study, we utilized the U87 GBM cell line to evaluate the independent role of RUNX1 in GBM development and progression. Enhanced expression of RUNX1 in U87 cells led to diminished tumor growth in a mice xenograft model.…”