Identification of key modules and hub genes in glioblastoma multiforme based on co-expression network analysis

GARNL3 identified as a crucial target for overcoming temozolomide resistance in EGFRvIII-positive glioblastoma

OBJECT

Amplification of the epidermal growth factor receptor (EGFR) and its active mutant type III (EGFRvIII), frequently occurr in glioblastoma (GBM), contributing to chemotherapy and radiation resistance in GBM. Elucidating the underlying molecular mechanism of temozolomide (TMZ) resistance in EGFRvIII GBM could offer valuable insights for cancer treatment.

METHODS

To elucidate the molecular mechanisms underlying EGFRvIII-mediated resistance to TMZ in GBM, we conducted a comprehensive analysis using Gene Expression Omnibus and The cancer genome atlas (TCGA) databases. Initially, we identified common significantly differentially expressed genes (DEGs) and prioritized those correlating significantly with patient prognosis as potential downstream targets of EGFRvIII and candidates for drug resistance. Additionally, we analyzed transcription factor expression changes and their correlation with candidate genes to elucidate transcriptional regulatory mechanisms. Using estimate method and databases such as Tumor IMmune Estimation Resource (TIMER) and CellMarker, we assessed immune cell infiltration in TMZ-resistant GBM and its relationship with candidate gene expression. In this study, we examined the expression differences of candidate genes in GBM cell lines following EGFRvIII intervention and in TMZ-resistant GBM cell lines. This preliminary investigation aimed to verify the regulatory impact of EGFRvIII on candidate targets and its potential involvement in TMZ resistance in GBM.

RESULTS

Notably, GTPase Activating Rap/RanGAP Domain Like 3 (GARNL3) emerged as a key DEG associated with TMZ resistance and poor prognosis, with reduced expression correlating with altered immune cell profiles. Transcription factor analysis suggested Epiregulin (EREG) as a putative upstream regulator of GARNL3, linking it to EGFRvIII-mediated TMZ resistance. In vitro experiments confirmed EGFRvIII-mediated downregulation of GARNL3 and decreased TMZ sensitivity in GBM cell lines, further supported by reduced GARNL3 levels in TMZ-resistant GBM cells.

CONCLUSION

GARNL3 downregulation in EGFRvIII-positive and TMZ-resistant GBM implicates its role in TMZ resistance, suggesting modulation of EREG/GARNL3 signaling as a potential therapeutic strategy.

FOXM1-mediated NUF2 expression confers temozolomide resistance to human glioma cells by regulating autophagy via the PI3K/AKT/mTOR signaling pathway

Glioma is the most common malignant tumor in the central nervous system and has a high mortality rate. Temozolomide (TMZ) is a widely used chemotherapeutic drug for glioma. NDC80 kinetochore complex (NUF2) is suggested to play a regulatory role in different cancers, but its specific function and mechanism in glioblastoma TMZ resistance remain unknown. NUF2, assessed by reverse transcription quantitative polymerase chain reaction (RT-qPCR), was highly expressed in glioma cell lines. TMZ was used to treat cells to establish a TMZ-resistant cell line. The potential functions of NUF2 in glioma were assessed using cell counting kit-8 (CCK-8) assays, colony formation assays, 5-Ethynyl-2'-deoxyuridine (EdU) assays, flow cytometry, Western blotting, and a tumor xenograft model. The results showed that NUF2 knockdown attenuated malignant phenotypes of TMZ-resistant cells and prevented tumor growth. Mechanistically, as luciferase reporter assays and chromatin immunoprecipitation (ChIP) as showed, Fox transcription factor M1 (FOXM1) had binding sites on the NUF2 promoter. Rescue assays demonstrated that FOXM1 upregulation counteracted the inhibitory effects of NUF2 depletion on the malignancies of TMZ-resistant cells. This study demonstrates that FOXM1-activated NUF2 promotes TMZ to human glioma cells by regulating proliferation, apoptosis, and autophagy.

Integrated Transcriptome Profiling Identifies Prognostic Hub Genes as Therapeutic Targets of Glioblastoma: Evidenced by Bioinformatics Analysis

Glioblastoma (GBM) is the most devastating and frequent type of primary brain tumor with high morbidity and mortality. Despite the use of surgical resection followed by radio- and chemotherapy as standard therapy, the progression of GBM remains dismal with a median overall survival of <15 months. GBM embodies a populace of cancer stem cells (GSCs) that is associated with tumor initiation, invasion, therapeutic resistance, and post-treatment reoccurrence. However, understanding the potential mechanisms of stemness and their candidate biomarkers remains limited. Hence in this investigation, we aimed to illuminate potential candidate hub genes and key pathways associated with the pathogenesis of GSC in the development of GBM. The integrated analysis discovered differentially expressed genes (DEGs) between the brain cancer tissues (GBM and GSC) and normal brain tissues. Multiple approaches, including gene ontology (GO) analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis, were employed to functionally annotate the DEGs and visualize them through the R program. The significant hub genes were identified through the protein-protein interaction network, Venn diagram analysis, and survival analysis. We observed that the upregulated DEGs were prominently involved in the ECM-receptor interaction pathway. The downregulated genes were mainly associated with the axon guidance pathway. Five significant hub genes (CTNNB1, ITGB1, TNC, EGFR, and SHOX2) were screened out through multiple analyses. GO and KEGG analyses of hub genes uncovered that these genes were primarily enriched in disease-associated pathways such as the inhibition of apoptosis and the DNA damage repair mechanism, activation of the cell cycle, EMT (epithelial-mesenchymal transition), hormone AR (androgen receptor), hormone ER (estrogen receptor), PI3K/AKT (phosphatidylinositol 3-kinase and AKT), RTK (receptor tyrosine kinase), and TSC/mTOR (tuberous sclerosis complex and mammalian target of rapamycin). Consequently, the epigenetic regulatory network disclosed that hub genes played a vital role in the progression of GBM. Finally, candidate drugs were predicted that can be used as possible drugs to treat GBM patients. Overall, our investigation offered five hub genes (CTNNB1, ITGB1, TNC, EGFR, and SHOX2) that could be used as precise diagnostic and prognostic candidate biomarkers of GBM and might be used as personalized therapeutic targets to obstruct gliomagenesis.

Glioblastoma gene network reconstruction and ontology analysis by online bioinformatics tools

Glioblastoma is the most aggressive type of brain tumors resistant to a number of antitumor drugs. The problem of therapy and drug treatment course is complicated by extremely high heterogeneity in the benign cell populations, the random arrangement of tumor cells, and polymorphism of their nuclei. The pathogenesis of gliomas needs to be studied using modern cellular technologies, genome- and transcriptome-wide technologies of high-throughput sequencing, analysis of gene expression on microarrays, and methods of modern bioinformatics to find new therapy targets. Functional annotation of genes related to the disease could be retrieved based on genetic databases and cross-validated by integrating complementary experimental data. Gene network reconstruction for a set of genes (proteins) proved to be effective approach to study mechanisms underlying disease progression. We used online bioinformatics tools for annotation of gene list for glioma, reconstruction of gene network and comparative analysis of gene ontology categories. The available tools and the databases for glioblastoma gene analysis are discussed together with the recent progress in this field.

Inhibiting microcephaly genes as alternative to microtubule targeting agents to treat brain tumors

Medulloblastoma (MB) and gliomas are the most frequent high-grade brain tumors (HGBT) in children and adulthood, respectively. The general treatment for these tumors consists in surgery, followed by radiotherapy and chemotherapy. Despite the improvement in patient survival, these therapies are only partially effective, and many patients still die. In the last decades, microtubules have emerged as interesting molecular targets for HGBT, as various microtubule targeting agents (MTAs) have been developed and tested pre-clinically and clinically with encouraging results. Nevertheless, these treatments produce relevant side effects since they target microtubules in normal as well as in cancerous cells. A possible strategy to overcome this toxicity could be to target proteins that control microtubule dynamics but are required by HGBT cells much more than in normal cell types. The genes mutated in primary hereditary microcephaly (MCPH) are ubiquitously expressed in proliferating cells, but under normal conditions are selectively required during brain development, in neural progenitors. There is evidence that MB and glioma cells share molecular profiles with progenitors of cerebellar granules and of cortical radial glia cells, in which MCPH gene functions are fundamental. Moreover, several studies indicate that MCPH genes are required for HGBT expansion. Among the 25 known MCPH genes, we focus this review on KNL1, ASPM, CENPE, CITK and KIF14, which have been found to control microtubule stability during cell division. We summarize the current knowledge about the molecular basis of their interaction with microtubules. Moreover, we will discuss data that suggest these genes are promising candidates as HGBT-specific targets.