Development Of Glioblastoma Multiforme Research Articles

CB-09 * THE CELL OF ORIGIN FOR GLIOBLASTOMA CONTRIBUTES TO THE PHENOTYPIC HETEROGENEITY OF GLIOMA STEM CELLS

Glioblastoma Multiforme (GBM) is the most frequent adult primary malignant brain tumor that remains incurable despite aggressive treatment. The cell of origin (COO) for GBM is unknown but assumed to be a glial stem or progenitor cell. GBM harbours hierarchical tumor cells called glioma stem cells (GSCs) that maintain tumor growth, drive tumor progression and cause tumor relapse due to their increased resistance to therapy. We have analyzed the significance of cellular origin for GBM development and GSC properties by comparing mouse GBMs and GSCs derived thereof induced in neural stem cells (NSCs), glial-restricted precursor cells (GPCs) or oligodendrocyte precursor cells (OPCs) by identical mutations. There were striking differences in GBM development and the phenotypes of GSCs and their response to drugs owing to the COO. Global gene expression analysis of mouse GSC lines displayed a clear separation due to COO and differential gene expression analysis identified a COO gene signature of 175 genes. Cross-species bioinformatics analyses were performed. First we analyzed the human cancer genome atlas (TCGA) GBM tissue samples and the mouse GSC expression data for a collection of TCGA GBM subtype signature genes. This showed that we could model both Proneural and Mesenchymal GBMs in mice by merely switching the COO. Next, we used the mouse COO gene signature to stratify a large number of newly established human glioma stem cell lines. This produced two groups of human GSCs; the NSC origin group and the progenitor cell (PC) origin group in which the mouse GPC- and OPC-derived genes were combined. Importantly, patient survival was significantly different between the NSC and PC COO groups with a better prognosis for the PC group patients. Thus, the cell of origin is essential for GBM biology and needs to be considered for more accurate patient stratification, target identification and drug discovery.

MiR-133b contributes to arsenic-induced apoptosis in U251 glioma cells by targeting the hERG channel.

Substantial evidence indicates that the human ether-a-go-go-related gene potassium channel (hERG, Kv11.1, KCNH2) is overexpressed in human glioblastoma multiforme (GBM) specimens and plays an essential role in the malignant proliferation of glioma cells. However, its upstream regulator in glioma cells is not fully elucidated. The present study was designed to determine whether the expression of hERG gene is regulated by miR-133b or miR-34a, thereby contributing to the anti-proliferation effect of arsenic trioxide (ATO) in U251 human glioma cells. Real-time polymerase chain reactions (qRT-PCR) and Western blot results demonstrated that hERG mRNA and protein levels were dramatically upregulated in clinical GBM specimens. Conversely, both miR-133b and miR-34a were markedly downregulated in clinical GBM specimens by qRT-PCR. The hERG gene was a direct target of miR-133b and miR-34a by bioinformatics analyses and luciferase reporter assays. Moreover, ATO, which is an emerging chemotherapy drug for glioma disease, remarkably elevated the level of miR-133b, but not miR-34a in U251 glioma cells. The level of miR-133b upstream transactivator serum response factor (SRF) was also suppressed by ATO. The transfection of anti-miR-133b oligonucleotide (AMO-133b) remarkably prevented the decrease of hERG protein by 5μM ATO treatment for 24h in U251 cells, whereas anti-miR-34a oligonucleotide (AMO-34a) did not exhibit recuperated effect. Finally, the transient overexpression by miR-133b mimics and treatment with the hERG channel-specific blocker E4031 markedly facilitated the ATO inhibition of proliferation of and induced apoptosis in U251 cells, whereas AMO-miR-133b attenuated these changes. Our study provided the evidence for the pathological role of miR-133b and miR-34a in the development of GBM and thus expanded our understanding of the hERG gene expression and ATO chemotherapeutic roles of miRNAs. Targeting miR-133b/hERG pathway may be a new strategy for chemotherapy of malignant gliomas.

Abstract 4605: STK17A is a potential therapeutic target in glioblastoma

Abstract Current targeted therapies for glioblastoma multiforme (GBM) fail to significantly improve clinical outcome. Identifying new molecular targets driving GBM tumorigenesis is imperative. Our previous study demonstrated that STK17A, a serine-threonine kinase in the death-associated protein family, is a bona fide p53 target gene. In silico analyses indicated that STK17A is highly overexpressed in GBM patients in a tumor grade-dependent manner. Furthermore, high STK17A expression correlated with poor clinical outcome and decreased survival of patients from multiple datasets. This correlation was independent of age, tumor subtype and known biomarkers such as EGFR, NF1, and IDH, suggesting STK17A may contribute to GBM development and progression. In vitro experiments confirmed increased mRNA and protein expression of STK17A in GBM cells compared to immortalized normal human astrocytes and other cancer types. ShRNA mediated STK17A knockdown in GBM cells decreased cell survival and sensitized cells to genotoxic stress. In addition, STK17A knockdown led to reduced tumor cell proliferation and clonogenicity, suggesting a tumor-promoting role for STK17A in GBM. Interestingly, STK17A depletion resulted in a cell morphological change from a spindle-like phenotype to a phenotype with a flattened, enlarged and more rounded shape that was associated with induction of actin stress fibers. This cytoskeleton remodeling was associated with impaired cell migration and invasion. In contrast STK17A overexpressing cells displayed a pronounced needle-like elongated phenotype. In addition genome-wide expression analysis of STK17A knockdown GBM cells revealed regulation of genes involved in glycolysis including PKM2, PGAM1 and HK2, suggesting that STK17A may also promote tumor growth and survival through regulating metabolism. Small molecule inhibitors that block the kinase activity of STK17A decreased cell survival of GBM cells cultured under both serum and serum-free conditions. Further investigation is required to understand the precise role of STK17A in GBM. Citation Format: Pingping Mao, Mary P. Jardine, Gilbert J. Rahme, Eric C. Yang, Janice Tam, Anita Kodali, Bijesh Biswal, Camilo E. Fadul, Arti B. Gaur, Mark A. Israel, Alexandre Pletnev, Michael Spinella. STK17A is a potential therapeutic target in glioblastoma. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 4605. doi:10.1158/1538-7445.AM2014-4605

Whole exome sequencing reveals that the majority of schwannomatosis cases remain unexplained after excluding SMARCB1 and LZTR1 germline variants.

familial and ~10 % of sporadic schwannomatosis patients [4, 10, 12]. recently, another schwannomatosis-predisposing gene within the 22q candidate region has been identified. piotrowski et al. [9] reported germline loss-of-function mutations in LZTR1 in 80 % of familial and sporadic schwannomatosis cases with combined chr22 loss and somatic NF2 mutation (MIM #615670). LZTr1 functions as an adaptor of the cullin 3-containing e3 ubiquitin ligase complex and has recently been implicated in glioblastoma multiforme development [3], indicating a broader role in tumorigenesis. We therefore sought to further explore the prevalence of LZTR1 mutations in a cohort of 23 sporadic schwannomatosis patients. eight tumor-blood DNA pairs from de novo schwannomatosis patients were subjected to whole exome schwannomatosis (MIM #162091) is characterized by the development of multiple schwannomas without vestibular nerve involvement (which is a characteristic of neurofibromatosis type 2—NF2—MIM #101000). About 10 % of patients have a family history of the disease, with the remaining 90 % presumed to be sporadic [7]. Germline mutations of NF2 are not observed [8], although schwannomas frequently harbor somatic NF2 mutations and often display chromosome 22 loss [6]. rare cases with somatic mosaicism for NF2 alterations have also been described [5]. Germline mutations in SMARCB1 (INI1), located proximal to NF2 on chromosome 22, are found in ~30–60 % of

MicroRNA-377 inhibited proliferation and invasion of human glioblastoma cells by directly targeting specificity protein 1.

Increasing evidence has indicated that microRNAs (miRNAs) are strongly implicated in the initiation and progression of glioblastoma multiforme (GBM). Here, we identified a novel tumor suppressive miRNA, miR-377, and investigated its role and therapeutic effect for GBM. MiRNA global screening was performed on GBM patient samples and adjacent nontumor brain tissues. The expression of miR-377 was detected by real-time reverse-transcription PCR. The effects of miR-377 on GBM cell proliferation, cell cycle progression, invasion, and orthotopic tumorigenicity were investigated The therapeutic effect of miR-377 mimic was explored in a subcutaneous GBM model. Western blot and luciferase reporter assay were used to identify the direct and functional target of miR-377. MiR-377 was markedly downregulated in human GBM tissues and cell lines. Overexpression of miR-377 dramatically inhibited cell growth both in culture and in orthotopic xenograft tumor models, blocked G1/S transition, and suppressed cell invasion in GBM cells. Importantly, introduction of miR-377 could strongly inhibit tumor growth in a subcutaneous GBM model. Subsequent investigation revealed that specificity protein 1 (Sp1) was a direct and functional target of miR-377 in GBM cells. Silencing of Sp1 recapitulated the antiproliferative and anti-invasive effects of miR-377, whereas restoring the Sp1 expression antagonized the tumor-suppressive function of miR-377. Finally, analysis of miR-377 and Sp1 levels in human GBM tissues revealed that miR-377 is inversely correlated with Sp1 expression. These findings reveal that miR-377/Sp1 signaling that may be required for GBM development and may consequently serve as a therapeutic target for the treatment of GBM.

MiR-331-3p regulates expression of neuropilin-2 in glioblastoma

Aberrant expression of microRNAs (miRNAs), a class of small non-coding regulatory RNAs, has been implicated in the development and progression of high-grade gliomas. However, the precise mechanistic role of many miRNAs in this disease remains unclear. Here, we investigate the functional role of miR-331-3p in glioblastoma multiforme (GBM). We found that miR-331-3p expression in GBM cell lines is significantly lower than in normal brain, and that transient overexpression of miR-331-3p inhibits GBM cell line proliferation and clonogenic growth, suggesting a possible tumor suppressor role for miR-331-3p in this system. Bioinformatics analysis identified neuropilin-2 (NRP-2) as a putative target of miR-331-3p. Using transfection studies, we validated NRP-2 mRNA as a target of miR-331-3p in GBM cell lines, and show that NRP-2 expression is regulated by miR-331-3p. RNA interference (RNAi) to inhibit NRP-2 expression in vitro decreased the growth and clonogenic growth of GBM cell lines, providing further support for an oncogenic role for NRP-2 in high-grade gliomas. We also show that miR-331-3p inhibits GBM cell migration, an effect due in part to reduced NRP-2 expression. Finally, we identified a significant inverse correlation between miR-331-3p and NRP-2 expression in The Cancer Genome Atlas GBM cohort of 491 patients. Together, our results suggest that a loss of miR-331-3p expression contributes to GBM development and progression, at least in part via upregulating NRP-2 expression and increasing cell proliferation and clonogenic growth.

Involvement of miRNAs in the Differentiation of Human Glioblastoma Multiforme Stem-Like Cells

Glioblastoma multiforme (GBM)-initiating cells (GICs) represent a tumor subpopulation with neural stem cell-like properties that is responsible for the development, progression and therapeutic resistance of human GBM. We have recently shown that blockade of NFκB pathway promotes terminal differentiation and senescence of GICs both in vitro and in vivo, indicating that induction of differentiation may be a potential therapeutic strategy for GBM. MicroRNAs have been implicated in the pathogenesis of GBM, but a high-throughput analysis of their role in GIC differentiation has not been reported. We have established human GIC cell lines that can be efficiently differentiated into cells expressing astrocytic and neuronal lineage markers. Using this in vitro system, a microarray-based high-throughput analysis to determine global expression changes of microRNAs during differentiation of GICs was performed. A number of changes in the levels of microRNAs were detected in differentiating GICs, including over-expression of hsa-miR-21, hsa-miR-29a, hsa-miR-29b, hsa-miR-221 and hsa-miR-222, and down-regulation of hsa-miR-93 and hsa-miR-106a. Functional studies showed that miR-21 over-expression in GICs induced comparable cell differentiation features and targeted SPRY1 mRNA, which encodes for a negative regulator of neural stem-cell differentiation. In addition, miR-221 and miR-222 inhibition in differentiated cells restored the expression of stem cell markers while reducing differentiation markers. Finally, miR-29a and miR-29b targeted MCL1 mRNA in GICs and increased apoptosis. Our study uncovers the microRNA dynamic expression changes occurring during differentiation of GICs, and identifies miR-21 and miR-221/222 as key regulators of this process.

Dynamic Quantitative Intravital Imaging of Glioblastoma Progression Reveals a Lack of Correlation between Tumor Growth and Blood Vessel Density

The spatiotemporal and longitudinal monitoring of cellular processes occurring in tumors is critical for oncological research. We focused on glioblastoma multiforme (GBM), an untreatable highly vascularized brain tumor whose progression is thought to critically depend on the oxygen and metabolites supplied by blood vessels. We optimized protocols for orthotopic GBM grafting in mice that were able to recapitulate the biophysical constraints normally governing tumor progression and were suitable for intravital multiphoton microscopy. We repeatedly imaged tumor cells and blood vessels during GBM development. We established methods for quantitative correlative analyses of dynamic imaging data over wide fields in order to cover the entire tumor. We searched whether correlations existed between blood vessel density, tumor cell density and proliferation in control tumors. Extensive vascular remodeling and the formation of new vessels accompanied U87 tumor cell growth, but no strong correlation was found between local cell density and the extent of local blood vessel density irrespective of the tumor area or time points. The technique moreover proves useful for comparative analysis of mice subjected either to Bevacizumab anti-angiogenic treatment that targets VEGF or to AMD3100, an antagonist of CXCR4 receptor. Bevacizumab treatment massively reduced tumoral vessel densities but only transiently reduced U87 tumor growth rate. Again, there was no correlation between local blood vessel density and local cell density. Moreover, Bev applied only prior to tumor implantation inhibited tumor growth to the same extent as post-grafting treatment. AMD3100 achieved a potent inhibition of tumor growth without significant reduction in blood vessel density. These results indicate that in the brain, in this model, tumor growth can be sustained without an increase in blood vessel density and suggest that GBM growth is rather governed by stromal properties.

Umbilical Cord Blood-Derived Mesenchymal Stem Cells Inhibit, But Adipose Tissue-Derived Mesenchymal Stem Cells Promote, Glioblastoma Multiforme Proliferation

Mesenchymal stem cells (MSCs) possess self-renewal and multipotential differentiation abilities, and they are thought to be one of the most reliable stem cell sources for a variety of cell therapies. Recently, cell therapy using MSCs has been studied as a novel therapeutic approach for cancers that show refractory progress and poor prognosis. MSCs from different tissues have different properties. However, the effect of different MSC properties on their application in anticancer therapies has not been thoroughly investigated. In this study, to characterize the anticancer therapeutic application of MSCs from different sources, we established two different kinds of human MSCs: umbilical cord blood-derived MSCs (UCB-MSCs) and adipose-tissue-derived MSCs (AT-MSCs). We used these MSCs in a coculture assay with primary glioblastoma multiforme (GBM) cells to analyze how MSCs from different sources can inhibit GBM growth. We found that UCB-MSCs inhibited GBM growth and caused apoptosis, but AT-MSCs promoted GBM growth. Terminal deoxynucleotidyl transferase-mediated biotinylated UTP nick-end labeling assay clearly demonstrated that UCB-MSCs promoted apoptosis of GBM via tumor necrosis factor-related apoptosis-inducing ligand (TRAIL). TRAIL was expressed more highly by UCB-MSCs than by AT-MSCs. Higher mRNA expression levels of angiogenic factors (vascular endothelial growth factor, angiopoietin 1, platelet-derived growth factor, and insulin-like growth factor) and stromal-derived factor-1 (SDF-1/CXCL12) were observed in AT-MSCs, and highly vascularized tumors were developed when AT-MSCs and GBM were cotransplanted. Importantly, CXCL12 inhibited TRAIL activation of the apoptotic pathway in GBM, suggesting that AT-MSCs may support GBM development in vivo by at least two distinct mechanisms-promoting angiogenesis and inhibiting apoptosis. The opposite effects of AT-MSCs and UCB-MSCs on GBM clearly demonstrate that differences must be considered when choosing a stem cell source for safety in clinical application.

Is neurocysticercosis a risk factor for glioblastoma multiforme or a mere coincidence: A case report with review of literature

Simultaneous occurrence of Neurocysticercosis (NC) along with Glioblastoma Multiforme (GBM) is a very rare presentation. We herein describe a case report of treated case of NC 2 years back who presented with secondary GBM. The brief report highlights that there may be some associated factors which may lead to development of secondary GBM in preexisting helminthic infection.

Discovering gene–environment interactions in Glioblastoma through a comprehensive data integration bioinformatics method

Glioblastoma multiforme (GBM) is the most common and aggressive type of human brain tumor. Although considerable efforts to delineate the underlying pathophysiological pathways have been made during the last decades, only very limited progress on treatment have been achieved because molecular pathways that drive the aggressive nature of GBM are largely unknown. Recent studies have emphasized the importance of environmental factors and the role of gene–environment interactions (GEI) in the development of GBM. Factors such as small sample sizes and study costs have limited the conduct of GEI studies in brain tumors however. Additionally, advances in high-throughput microarrays have produced a wealth of information concerning molecular biology of glioma. In particular, microarrays have been used to obtain genetic and epigenetic changes between normal non-tumor tissue and glioma tissue. Due to the relative rarity of gliomas, microarray data for these tumors is often the product of small studies, and thus pooling this data becomes desirable. To address the challenge of small sample sizes and GEI study difficulties, we introduce a comprehensive bioinformatics method using genetic variations (copy number variations and small-scale variations) and environmental data integration that links with Glioblastoma (GEG) to identify: (1) genes that interact with chemicals and have genetic variants linked to the development of GBM, (2) important pathways that may be influenced by environmental exposures (or endogenous chemicals), and (3) genes with variants in GBM that have been understudied in relation to GBM development. The first step in our GEG method identified genes responsive to environmental exposures using the Environmental Genome Project, Comparative Toxicology, and Seattle SNPs databases. These environmentally responsive genes were then compared to a curated list of genes containing copy number variation and/or mutations in GBM. This comparison produced a list of genes responsive to the environment and important to GBM that was then further analyzed using gene networking tools such as RSpider, Cytoscape, and DAVID. Using this GEG bioinformatics method we were able to identify 173 genes with the potential to be involved in GEI that may be important to the development of GBM. Sixty five of these environmentally responsive genes have not been reported as important to GBM development, despite several of them having substantial potential for response to chemicals and subsequent disease related actions. The main biological functions of these 173 genes include signaling by Nerve Growth Factor, DNA Repair, Integrin Cell Surface Interactions, Biological Oxidations, Apoptosis, Synaptic Transmission, Cell Cycle Checkpoints, and Arachidonic Acid Metabolism. Importantly, some of these functions have been implicated in the development of several cancers, including glioma. In summary, our GEG bioinformatics approach revealed potential gene–environment interactions, and generated new data for hypothesis generation, in GBM.

Targeting Glioblastoma Stem Cells: Cell Surface Markers

Glioblastoma multiforme (GBM) is the most common primary brain tumor and among the most lethal cancers. There is increasing evidence that cancer stem cells within GBMs, which are often referred to as glioblastoma stem cells (GSCs), play a critical role in tumor initiation and maintenance. Identification of novel markers for GSCs will lead to better targeting of GSCs which could have tremendous impact on treatment of GBMs. Cell surface markers are particularly suitable as therapeutic targets. Although several promising cell surface markers have successfully been used for enrichment of GSCs, their functional roles in maintenance of GSC properties as well as in GBM formation and development remain to be characterized. In this review, we primarily summarize recent advances in identification of GSC markers, with a particular focus on cell surface markers.

Targeting Glioblastoma Stem Cells: Cell Surface Markers

Glioblastoma multiforme (GBM) is the most common primary brain tumor and among the most lethal cancers. There is increasing evidence that cancer stem cells within GBMs, which are often referred to as glioblastoma stem cells (GSCs), play a critical role in tumor initiation and maintenance. Identification of novel markers for GSCs will lead to better targeting of GSCs which could have tremendous impact on treatment of GBMs. Cell surface markers are particularly suitable as therapeutic targets. Although several promising cell surface markers have successfully been used for enrichment of GSCs, their functional roles in maintenance of GSC properties as well as in GBM formation and development remain to be characterized. In this review, we primarily summarize recent advances in identification of GSC markers, with a particular focus on cell surface markers.

Resistance to EGF receptor inhibitors in glioblastoma mediated by phosphorylation of the PTEN tumor suppressor at tyrosine 240

Glioblastoma multiforme (GBM) is the most aggressive of the astrocytic malignancies and the most common intracranial tumor in adults. Although the epidermal growth factor receptor (EGFR) is overexpressed and/or mutated in at least 50% of GBM cases and is required for tumor maintenance in animal models, EGFR inhibitors have thus far failed to deliver significant responses in GBM patients. One inherent resistance mechanism in GBM is the coactivation of multiple receptor tyrosine kinases, which generates redundancy in activation of phosphoinositide-3'-kinase (PI3K) signaling. Here we demonstrate that the phosphatase and tensin homolog deleted on chromosome 10 (PTEN) tumor suppressor is frequently phosphorylated at a conserved tyrosine residue, Y240, in GBM clinical samples. Phosphorylation of Y240 is associated with shortened overall survival and resistance to EGFR inhibitor therapy in GBM patients and plays an active role in mediating resistance to EGFR inhibition in vitro. Y240 phosphorylation can be mediated by both fibroblast growth factor receptors and SRC family kinases (SFKs) but does not affect the ability of PTEN to antagonize PI3K signaling. These findings show that, in addition to genetic loss and mutation of PTEN, its modulation by tyrosine phosphorylation has important implications for the development and treatment of GBM.

Metformin inhibits leptin-induced growth and migration of glioblastoma cells.

Metformin, a derivative of biguanide, is a first-line therapy for type 2 diabetes mellitus. Since the drug has been shown to significantly reduce the risk of various cancers and cancer mortality in diabetic patients, it is being considered as a potential anticancer therapeutic or preventive agent. In cellular models, metformin inhibits the growth of many types of cancer cells; however, its effects on glioblastoma multi-forme (GBM) are not well characterized. Here, we analyzed the effects of metformin on the growth and migration of LN18 and LN229 GBM cells cultured under basal conditions or exposed to leptin, a cytokine that has recently been implicated in GBM development. We found that 2-16 mM metformin reduced basal and leptin-stimulated growth of GBM cells in a dose-dependent manner. Furthermore, the drug significantly inhibited the migration of GBM cells. The action of metformin was mediated through the upregulation of its main signaling molecule, the adenosine monophosphate-activated protein kinase (AMPK), as well as through the downregulation of the signal transducer and activator of transcription 3 (STAT3) and the Akt/PKB serine/threonine protein kinase. In leptin-treated cells, the drug reversed the effects of the cytokine on the AMPK and STAT3 pathways, but modulated Akt activity in a cell-dependent manner. Our results suggest that metformin or similar AMPK-targeting agents with optimized blood-brain-barrier penetrability could be developed as potential treatments of GBM and could be used in conjunction with other target drugs such as leptin receptor antagonists.

Potential risk factors for incident glioblastoma multiforme: the Honolulu Heart Program and Honolulu-Asia Aging Study.

Glioblastoma multiforme (GBM) is the most common adult primary malignant brain tumor. Ninety percent of adult GBM patients die within 24 months after diagnosis. The etiology of GBM is unknown. The Honolulu Heart Program (HHP) and Honolulu-Asia Aging Study (HAAS) are prospective, cohort studies of cardiovascular and neurodegenerative disease based on 8,006 Japanese-American men followed since 1965. The Japan Hawaii Cancer Study provides data on incident cancer cases in the HHP/HAAS cohort. We used data from these studies to obtain epidemiologic information about GBM. GBM cases were identified by searching the 1965-1998 databases using International Classification of Diseases (ICD-9) codes. Nine histologically confirmed GBM cases, 58-80 years old, were identified. The incidence rate was 6.2/100,000 person-years. Records of each case were reviewed. Selected variables from the first three examinations (1965-1968; 1968-1970; 1971-1974) were used to identify potential candidate GBM risk factors. A multivariate Cox proportional hazards model showed sugar intake and occupational exposure to carbon tetrachloride were independently and significantly associated with development of GBM.

Predicting glioblastoma prognosis networks using weighted gene co-expression network analysis on TCGA data

BackgroundUsing gene co-expression analysis, researchers were able to predict clusters of genes with consistent functions that are relevant to cancer development and prognosis. We applied a weighted gene co-expression network (WGCN) analysis algorithm on glioblastoma multiforme (GBM) data obtained from the TCGA project and predicted a set of gene co-expression networks which are related to GBM prognosis.MethodsWe modified the Quasi-Clique Merger algorithm (QCM algorithm) into edge-covering Quasi-Clique Merger algorithm (eQCM) for mining weighted sub-network in WGCN. Each sub-network is considered a set of features to separate patients into two groups using K-means algorithm. Survival times of the two groups are compared using log-rank test and Kaplan-Meier curves. Simulations using random sets of genes are carried out to determine the thresholds for log-rank test p-values for network selection. Sub-networks with p-values less than their corresponding thresholds were further merged into clusters based on overlap ratios (>50%). The functions for each cluster are analyzed using gene ontology enrichment analysis.ResultsUsing the eQCM algorithm, we identified 8,124 sub-networks in the WGCN, out of which 170 sub-networks show p-values less than their corresponding thresholds. They were then merged into 16 clusters.ConclusionsWe identified 16 gene clusters associated with GBM prognosis using the eQCM algorithm. Our results not only confirmed previous findings including the importance of cell cycle and immune response in GBM, but also suggested important epigenetic events in GBM development and prognosis.

Eosinophils in glioblastoma biology.

Glioblastoma multiforme (GBM) is the most common primary brain tumor in adults. The development of this malignant glial lesion involves a multi-faceted process that results in a loss of genetic or epigenetic gene control, un-regulated cell growth, and immune tolerance. Of interest, atopic diseases are characterized by a lack of immune tolerance and are inversely associated with glioma risk. One cell type that is an established effector cell in the pathobiology of atopic disease is the eosinophil. In response to various stimuli, the eosinophil is able to produce cytotoxic granules, neuromediators, and pro-inflammatory cytokines as well as pro-fibrotic and angiogenic factors involved in pathogen clearance and tissue remodeling and repair. These various biological properties reveal that the eosinophil is a key immunoregulatory cell capable of influencing the activity of both innate and adaptive immune responses. Of central importance to this report is the observation that eosinophil migration to the brain occurs in response to traumatic brain injury and following certain immunotherapeutic treatments for GBM. Although eosinophils have been identified in various central nervous system pathologies, and are known to operate in wound/repair and tumorstatic models, the potential roles of eosinophils in GBM development and the tumor immunological response are only beginning to be recognized and are therefore the subject of the present review.

Highlights from Recent Cancer Literature

Highlights from Recent Cancer Literature

The evolving picture of the glioblastoma genome.

Survival rates for patients with glioblastoma multiforme (GBM), the most common malignant brain tumor, remain dismal despite decades of basic and clinical research. New treatment strategies are desperately needed. Consequently, the high-throughput genomic technologies developed to facilitate examination of cancer genomes have recently been focused on GBM, with goals of identifying novel molecular targets and developing a clinically-relevant biological classification of this deadly cancer. These genomic analyses have provided an unprecedented view of the complex genetic landscape of GBM, confirming the central role of both well-established and previously-unsuspected genes in the development of these tumors [1,2]. In addition, despite the plethora of genes found to be altered in GBMs, these data have allowed a semblance of order to be applied to these tumors through the identification of a small number of core pathways critical to GBM pathogenesis and the elucidation of discrete molecular subgroups of GBM [3]. The list of biologically-relevant GBM genes remains incomplete, however, due in large part to the logistical challenge of establishing the functional significance of the numerous genes found to be infrequently altered (between 1 and 5%) in these cancers. The detection of focal regions of recurrent copy number gain or loss (amplifications or homozygous deletions) can be a useful tool for the identification of candidate cancer genes. Using such a high-resolution genomic approach, Duncan et al. have identified two genes as potentially relevant to the emerging picture of the GBM genome, ERRFI1 (located at chr1p36) and TACC3 (located at chr4p16) [4]. Genomic alterations in these two regions have been reported in a number of human cancers, but the specific target genes of these copy number alterations are not known. The Digital Karotyping and SNP array data provided by Duncan et al. have provided initial evidence for two reasonable candidates. Importantly, given the significant challenge of distinguishing between altered genes which are drivers (i.e. genes that contribute to tumorigenesis) and those that are merely passengers (i.e. genes that accumulate alterations during tumor development but are not biologically relevant), preliminary studies of the potential functional significance of the candidate genes have been conducted. Recurrent focal deletions at 1p36, previously reported in numerous cancers including GBM, were found by Duncan et al. in their cohort of GBMs and validated using data from The Cancer Genome Atlas (TCGA) project. Two distinct minimal deleted regions were identified, with the most commonly-deleted region containing a single gene, ERRFI1. ERRFI1 expression was also found to be downregulated in ~34% of GBM samples analyzed, and functional studies of a cell line with a homozygous deletion of ERRFI1 revealed impaired wound-healing and a lower rate of trans-well migration after transfection with a vector containing ERRFI1, suggesting ERRFI1 as a potential tumor suppressor gene in GBMs. Similarly, focal gains at 4p16, most commonly involving TACC3, and overexpression of TACC3 were found in tumor samples, raising the possibility of TACC3 as a potential GBM oncogene. Both of these genes are biologically-plausible as GBM-related candidates. ERRFI1 acts as a negative regulator of EGFR and the ERbB family, while dysregulation of TACC (transforming acidic coiled coil) genes, components of the centrosome, has been implicated in cancer development. Significant work remains, however, in order to confirm the relevance of these genes for the pathogenesis of GBM and identify them as potential targets of molecular therapeutics. In particular, additional functional data firmly establishing the genes as “drivers” and demonstrating their specific biological role in GBM development are required. In addition, clarification of how these genomic data fit in with the evolving picture of the molecular classification of GBM will be illuminating: for example, are alterations of ERRFI1 specifically identified in the subgroup of GBMs with downstream evidence of EGFR activation that lack EGFR amplification or mutation [3]? Further research building on the foundation of this intriguing genomic data will surely add to our evolving picture of the glioblastoma genome. Hopefully it will also contribute to the improved care of our patients with these deadly cancers.