CGGA Databases Research Articles

ACT001 inhibits the neurosphere formation and stemness maintenance of U87-MG glioma stem cells through STAT3 signaling pathway

Objective To investigate the effect of sesquiterpene lactone derivative (ACT001) on the neurosphere formation and stemness maintenance of U87-MG glioma stem cells. Methods Bioinformatics was used to analyze the relationship between STAT3 mRNA and different grades of human glioma as well as the overall survival in 1 477 glioma patients in CGGA, TCGA, and GEO (GSE4290, GSE16011) databases. Magnetic activated cell sorting method was used to obtain CD133-positive U87-MG cells. The effect of ACT001 on the survival viability of U87-MG GSCs was detected via Cell Counting Kit-8 (CCK-8). The effect of ACT001 on the ability of neurosphere formation was observed by single-cell neurosphere formation assay. Immunofluorescence staining was used to measure the effect of ACT001 on stem cells markers (CD133、CD44 and Nestin) in neurospheres of U87-MG GSCs. The expressions of STAT3, p-STAT3, CD44 and CD133 were detected using western blot after treatment of ACT001. Results Bioinformatics analysis showed that as the grades of glioma increased, the expression of STAT3 mRNA also increased (all P 0.05), while the protein expression of p-STAT3 was decreased through assessment by Western blot (all P<0.01). Conclusion ACT001 could suppress the neurosphere formation ability and reduce the stemness maintenance in U87-MG glioma stem cells by inhibiting STAT3 signaling pathway. Key words: Glioma; Neoplastic stem cells; Sesquiterpene lactone derivative; STAT3 signaling pathway

Identification of 3 subpopulations of tumor-infiltrating immune cells for malignant transformation of low-grade glioma

BackgroundTumor-infiltrating immune cells (TIICs) are highly relevant to clinical outcome of glioma. However, previous studies cannot account for the diverse functions that make up the immune response in malignant transformation (MT) from low-grade glioma (LGG) to high-grade glioma (HGG).MethodsTranscriptome level, genomic profiles and its relationship with clinical practice were obtained from TCGA and CGGA database. The “Cell type Identification By Estimating Relative Subsets Of RNA Transcripts (CIBERSORT)” algorithm was used to estimate the fraction of 22 immune cell types. We divided the TCGA and CGGA set into an experiment set (n = 174) and a validation set (n = 74) by random number table method. Univariate and multivariate analyses were performed to evaluate the 22 TIICs’ value for MT in LGG. ROC curve was plotted to calculate area under curve (AUC) and cut-off value.ResultsHeterogeneity between TIICs exists in both intra- and inter-groups. Several TIICs are notably associated with tumor grade, molecular subtypes and survival. T follicular helper (TFH) cells, activated NK Cells and M0 macrophages were screened out to be independent predictors for MT in LGG and formed an immune risk score (IRS) (AUC = 0.732, p < 0.001, 95% CI 0.657–0.808 cut-off value = 0.191). In addition, the IRS model was validated by validation group, Immunohistochemistry (IHC) and functional enrichment analyses.ConclusionsThe proposed IRS model provides promising novel signatures for predicting MT from LGG to HGG and may bring a better design of glioma immunotherapy studies in years to come.

Grade II/III Glioma Microenvironment Mining and Its Prognostic Merit

The tumor microenvironment greatly influences tumor formation, invasion, and progression. The ESTIMATE (Estimation of STromal and Immune cells in MAlignant Tumor tissues) algorithm quantifies stromal and immune components in a tumor, reflecting the tumor microenvironment. This study aimed to explore key prognostic genes in a grade II/III glioma microenvironment. We obtained stromal/immune scores for the Cancer Genome Atlas (TCGA) grade II/III glioma cohort from the online ESTIMATE portal. The associations of stromal/immune scores with clinicopathologic characteristics and overall survival of patients with grade II/III glioma were assessed by the Mann-Whitney U test and the Kaplan-Meier method, respectively. Functional enrichment analysis and protein-protein interaction network assessments were employed to analyze differentially expressed genes (DEGs). The top 7 genes with 5 or more edges in the protein-protein interaction network were selected. For validation, CGGA grade II/III glioma data were analyzed. The results showed that elevated stromal/immune/ESTIMATE score was significantly associated with poor survival of patients with TCGA grade II/III glioma. Functional enrichment analysis showed that DEGs were associated with immune cell regulation, extracellular matrix, cytokine activation, and receptor binding. The selected DEGs (interleukin-10, beta-2 microglobulin, C-C motif chemokine ligand 5, cluster of differentiation 74, human leukocyte antigen-DRA, lymphocyte cytosolic protein 2, and myxovirus resistance protein 1) showed prognostic values in patients with grade II/III glioma of the TCGA and CGGA database. Stromal/immune/ESTIMATE scores have prognostic values in patients with grade II/III glioma. The selected DEGs, including interleukin-10, beta-2 microglobulin, C-C motif chemokine ligand 5, cluster of differentiation 74, human leukocyte antigen-DRA, lymphocyte cytosolic protein 2, and myxovirus resistance protein 1, associated with tumor immunity and microenvironment, have prognostic values in grade II/III glioma. Further investigation of these genes could provide novel insights into the tumor microenvironment of glioma.

Napabucasin, a novel STAT3 inhibitor suppresses proliferation, invasion and stemness of glioblastoma cells

BackgroundGlioblastoma (GBM) cells with stem cell-like properties are called glioma stem cells (GSCs). GSCs display highly treatment resistance and are responsible for tumor recurrence. Napabucasin (BBI608), a novel small molecule inhibitor of STAT3, has been identified to eliminate stemness-like tumor cells in some cancers. However, the influence of Napabucasin on GBM cells, especially on GSCs, is currently unclear. In this study, we explored the influence and underlying mechanisms of Napabucasin on GBM cells.MethodsSTAT3 expression and its correlation with the glioma grade and patient survival were analyzed using CGGA and TCGA glioma databases. The influence of Napabucasin on proliferation, stemness, the cell cycle, apoptosis, and invasion of human GBM cell lines U87MG and LN229 was tested by CCK8, EdU incorporation, colony formation, Transwell invasion, and three-dimensional spheroid assays as well as flow cytometry, qPCR, and western blot analysis. The ability of Napabucasin to inhibit cell proliferation of U87MG tumor xenografts in mice was assessed using a live animal bioluminescence imaging system and immunohistochemistry.ResultsNapabucasin suppressed the proliferation, colony formation, and invasion of U87MG and LN229 cells. Furthermore, Napabucasin induced cell cycle arrest and apoptosis. More importantly, Napabucasin treatment obviously inhibited expression of stemness-associated genes including STAT3 and suppressed the spheroid formation of glioma cells in vitro. Napabucasin also disrupted the NF-κB signaling pathway via downregulation of RelA (p65). Finally, glioma growth was effectively impaired by Napabucasin in nude mice bearing intracranial glioma xenografts.ConclusionsNapabucasin treatment may be a novel approach for the treatment of GBM, particularly GSCs.

Epithelial membrane protein 1 promotes glioblastoma progression through the PI3K/AKT/mTOR signaling pathway

Glioblastoma multiforme (GBM) is the most malignant intracranial tumor. Although the affected patients are usually treated with surgery combined with radiotherapy and chemotherapy, the median survival time for GBM patients is still approximately 12–14 months. Identifying the key molecular mechanisms and targets of GBM development may therefore lead to the development of improved therapies for GBM patients. In the present study, the clinical significance and potential function of epithelial membrane protein 1 (EMP1) in malignant gliomas were investigated. Increased EMP1 expression was associated with increasing tumor grade (P<0.001) and worse prognosis in patients (P<0.001) based on TCGA, Rembrandt and CGGA databases for human gliomas. In vitro, gene silencing of EMP1 in U87MG and P3 GBM (primary glioma) cells significantly inhibited tumor proliferation and invasion. In addition, it was revealed that activation of the PI3K/AKT/mTOR signaling pathway is the driving force of EMP1-promoted glioma progression. Finally, it was demonstrated, using an intracranial GBM animal model, that EMP1 knockdown significantly inhibits tumor growth in vivo and increases overall survival in tumor-bearing animals. Our research provides new insights into the molecular mechanisms underlying EMP1 knockdown-mediated inhibition of GBM cell invasion and raises the possibility that targeting of EMP1 may represent a promising strategy for the treatment of GBM.

A Novel Methylation Signature Predicts Radiotherapy Sensitivity in Glioma

Background: Glioblastoma (GBM) is the most common and malignant cancer in the central nervous system, and radiotherapy is wildly applied in GBM treatment. However, the sensitivity of radiotherapy varies in different patients. In order to solve this clinical dilemma, a radiosensitivity prediction signature was constructed based on genomic methylation. Methods: In this study, a total of 1044 primary GBM samples with clinical and methylation microarray data were involved. LASSO-COX, GSVA, Kaplan-Meier survive curve and COX regression were performed in construction and verification of predictive models. R language was used as the main tool for statistical analysis and graphical work. Findings: Through the integration analysis of methylation and survival data in primary GBM, a novel prognostic and radio-sensitivity prediction signature was constructed. Interpretation: This signature was stable in prognosis prediction in TCGA and CGGA databases. The possible mechanism was also explored, this signature was closely related to DNA repair functions. Importantly, this signature could predict whether GBM patients could benefit from radiotherapy. In conclusion, our study built a radiosensitivity prediction signature for GBM patients based on five methylated probes with great potential for clinical application. Funding: National Natural Science Foundation of China (No. 81672479). Declaration of Interest: The authors declare no potential conflicts of interest. Ethical Approval: This study was approved by Beijing Tiantan Hospital institutional review board (IRB).

ISG20 promotes local tumor immunity and contributes to poor survival in human glioma

ABSTRACTRecent evidence has confirmed that a mutation of the isocitrate dehydrogenase (IDH) gene occurs early in gliomagenesis and contributes to suppressed immunity. The present study aimed to determine the candidate genes associated with IDH mutation status that could serve as biomarkers of immune suppression for improved prognosis prediction. Clinical information and RNA-seq gene expression data were collected for 932 glioma samples from the CGGA and TCGA databases, and differentially expressed genes in both lower-grade glioma (LGG) and glioblastoma (GBM) samples were identified according to IDH mutation status. Only one gene, interferon-stimulated exonuclease gene 20 (ISG20), with reduced expression in IDH mutant tumors, demonstrated significant prognostic value. ISG20 expression level significantly increased with increasing tumor grade, and its high expression was associated with a poor clinical outcome. Moreover, increased ISG20 expression was associated with increased infiltration of monocyte-derived macrophages and neutrophils, and suppressed adaptive immune response. ISG20 expression was also positively correlated with PD-1, PD-L1, and CTLA4 expression, along with the levels of several chemokines. We conclude that ISG20 is a useful biomarker to identify IDH-mediated immune processes in glioma and may serve as a potential therapeutic target.

Genotype prediction of ATRX mutation in lower-grade gliomas using an MRI radiomics signature.

To predict ATRX mutation status in patients with lower-grade gliomas using radiomic analysis. Cancer Genome Atlas (TCGA) patients with lower-grade gliomas were randomly allocated into training (n = 63) and validation (n = 32) sets. An independent external-validation set (n = 91) was built based on the Chinese Genome Atlas (CGGA) database. After feature extraction, an ATRX-related signature was constructed. Subsequently, the radiomic signature was combined with a support vector machine to predict ATRX mutation status in training, validation and external-validation sets. Predictive performance was assessed by receiver operating characteristic curve analysis. Correlations between the selected features were also evaluated. Nine radiomic features were screened as an ATRX-associated radiomic signature of lower-grade gliomas based on the LASSO regression model. All nine radiomic features were texture-associated (e.g. sum average and variance). The predictive efficiencies measured by the area under the curve were 94.0 %, 92.5 % and 72.5 % in the training, validation and external-validation sets, respectively. The overall correlations between the nine radiomic features were low in both TCGA and CGGA databases. Using radiomic analysis, we achieved efficient prediction of ATRX genotype in lower-grade gliomas, and our model was effective in two independent databases. • ATRX in lower-grade gliomas could be predicted using radiomic analysis. • The LASSO regression algorithm and SVM performed well in radiomic analysis. • Nine radiomic features were screened as an ATRX-predictive radiomic signature. • The machine-learning model for ATRX-prediction was validated by an independent database.

RNA-binding Protein UNR Promotes Glioma Cell Migration and Regulates the Expression of Ribosomal Protein L9.

Objective To investigate the role of RNA binding protein─upstream-of-N-Ras (UNR) in the development of glioma and its molecular mechanism.Methods First, bioinformatics analysis of CGGA database was performed to detect UNR expression level and prognosis of patients with glioma. Western blot and real-time PCR were used to detect UNR expression level in glioma cell lines and tissues. Next, UNR siRNAs were transfected in glioma cells, and MTS assay and scratch wound-healing assay were used to detect changes in cell proliferation and migration. Then, the candidate UNR target mRNAs were identified by analyzing the sequencing data of UNR iCLIP-seq, RNA sequencing and ribosome profiling databases of human melanoma. RNA immunoprecipitation and biotin pull-down assays were used to identify the UNR target mRNAs in glioma cells. Finally, western blot was used to detect the effect of UNR knockdown on ribosomal protein L9 (RPL9) and RPL9 protein expression level in glioma cell lines. RPL9 siRNA was transfected in A172 and T98G and the expression of vimentin in the cells was detected with western blot.Results Bioinformatics analysis showed that UNR mRNA expression level was significantly higher in high-grade glioma [Grade 2 (n=126), Grade 3 (n=51), Grade 4 (n=128), P<0.001]. UNR high expression levels were associated with poor prognosis (P=0.0177). UNR had high expression level in glioma cell lines and patient samples compared with normal cell lines and normal brain samples (P<0.01). Knockdown of UNR inhibited glioma cells migration (P<0.05), but did not inhibit glioma cells growth in three glioma cell lines. UNR binded the 3' untranslated region (UTR) of PTEN and RPL9 mRNAs. RPL9 protein was significantly highly expressed in most glioma cell lines (n=9) and knockdown of UNR resulted in a downregulation of RPL9 protein expression. Epithelial-mesenchymal transition (EMT)-related marker─vimentin was positively regulated by RPL9.Conclusions UNR could bind to the 3'UTR of PTEN and RPL9 in glioma cell lines, therefore promoting glioma cell migration and regulating the expression of RPL9. Here, we establish a link between UNR and RPL9 protein, which will provide new ideas for the further study of glioma.

CBX7 negatively regulates migration and invasion in glioma via Wnt/β-catenin pathway inactivation.

CBX7, a member of the Polycomb-group proteins, plays a significant role in normal and cancerous tissues and has been defined as a tumor suppressor in thyroid, breast and pancreatic cancers. However, its function in glioma remains undefined. CBX7 expression is decreased in glioma, especially in higher grade cases, according to data in the CGGA, GSE16001 and TCGA databases. Further experimental evidence has shown that exogenous CBX7 overexpression induced apoptosis and inhibited cell proliferation, colony formation and migration of glioma cells. In this study, we show that the invasive ability of glioma cells was decreased following CBX7 overexpression and CBX7 overexpression was associated with Wnt/β-catenin pathway inhibition, which also decreased downstream expression of ZEB1, a core epithelial-to-mesenchymal transition factor. This reduction in Wnt signaling is controlled by DKK1, a specific Wnt/β-catenin inhibitor. CBX7 enhances DKK1 expression by binding the DKK1 promoter, as shown in Luciferase reporter assays. Our data confirm that CBX7 inhibits EMT and invasion in glioma, which is manifested by influencing the expression of MMP2, MMP9, E-cadherin, N-cadherin and Vimentin in LN229, T98G cells and primary glioma cells (PGC). Furthermore, as a tumor suppressor, CBX7 expression is pivotal to reduce tumor invasion and evaluate prognosis.