Unravelling the mosaic: Epigenetic diversity in glioblastoma

Glioblastoma is the most common primary malignant brain tumour. Despite decades of intensive research in the disease, its prognosis remains poor, with an average survival of only 14 months after diagnosis. The remarkable level of intra- and interpatient heterogeneity is certainly contributing to the lack of progress in tackling this tumour. Epigenetic dysregulation plays an important role in glioblastoma biology and significantly contributes to intratumour heterogeneity. However, it is becoming increasingly clear that it also contributes to intertumour heterogeneity, which historically had mainly been linked to diverse genetic events occurring in different patients. In this review, we explore how DNA methylation, chromatin remodelling, microRNA (miRNA) dysregulation, and long noncoding RNA (lncRNA) alterations contribute to intertumour heterogeneity in glioblastoma, including its implications for advanced tumour stratification, which is the essential first step for developing more effective patient-specific therapeutic approaches.

Crosstalk between SOX Genes and Long Non-Coding RNAs in Glioblastoma

Glioblastoma (GBM) continues to be the most devastating primary brain malignancy. Despite significant advancements in understanding basic GBM biology and enormous efforts in developing new therapeutic approaches, the prognosis for most GBM patients remains poor with a median survival time of 15 months. Recently, the interplay between the SOX (SRY-related HMG-box) genes and lncRNAs (long non-coding RNAs) has become the focus of GBM research. Both classes of molecules have an aberrant expression in GBM and play essential roles in tumor initiation, progression, therapy resistance, and recurrence. In GBM, SOX and lncRNAs crosstalk through numerous functional axes, some of which are part of the complex transcriptional and epigenetic regulatory mechanisms. This review provides a systematic summary of current literature data on the complex interplay between SOX genes and lncRNAs and represents an effort to underscore the effects of SOX/lncRNA crosstalk on the malignant properties of GBM cells. Furthermore, we highlight the significance of this crosstalk in searching for new biomarkers and therapeutic approaches in GBM treatment.

Long non-coding RNA-LINC00941 promotes the proliferation and invasiveness of glioma cells

Glioma is one of the most common intracranial malignant tumors worldwide, accounting for 30%-40% of primary brain tumors. Long non-coding RNAs (lncRNAs) have been implicated in cancer malignant progression. Glioma is classified into multiple subtypes, but lncRNA expression pattern in different subtypes are not fully described. Here, we reported that lncRNA-LINC00941 was highly expressed in all glioma subtypes. Overexpression of lncRNA-LINC00941 in U87 cells promoted cellular proliferation and invasiveness, and suppressed apoptosis. Our findings suggest that lncRNA-LINC00941 may function as an oncogenic factor in glioma, and targeting lncRNA-LINC00941 could be developed into a strategy for glioma management.

Integrative network analysis reveals subtype-specific long non-coding RNA regulatory mechanisms in head and neck squamous cell carcinoma

Head and neck squamous cell carcinoma (HNSC) is one of most common malignancies with high mortality worldwide. Importantly, the molecular heterogeneity of HNSC complicates the clinical diagnosis and treatment, leading to poor overall survival outcomes. To dissect the complex heterogeneity, recent studies have reported multiple molecular subtyping systems. For instance, HNSC can be subdivided to four distinct molecular subtypes: atypical, basal, classical, and mesenchymal, of which the mesenchymal subtype is characterized by upregulated epithelial-mesenchymal transition (EMT) and associated with poorer survival outcomes. Despite a wealth of studies into the complex molecular heterogeneity, the regulatory mechanism specific to this aggressive subtype remain largely unclear. Herein, we developed a network-based bioinformatics framework that integrates lncRNA and mRNA expression profiles to elucidate the subtype-specific regulatory mechanisms. Applying the framework to HNSC, we identified a clinically relevant lncRNA LNCOG as a key master regulator mediating EMT underlying the mesenchymal subtype. Five genes with strong prognostic values, namely ANXA5, ITGA5, CCBE1, P4HA2, and EPHX3, were predicted to be the putative targets of LNCOG and subsequently validated in other independent datasets. By integrative analysis of the miRNA expression profiles, we found that LNCOG may act as a ceRNA to sponge miR-148a-3p thereby upregulating ITGA5 to promote HNSC progression. Furthermore, our drug sensitivity analysis demonstrated that the five putative targets of LNCOG were also predictive of the sensitivities of multiple FDA-approved drugs. In summary, our bioinformatics framework facilitates the dissection of cancer subtype-specific lncRNA regulatory mechanisms, providing potential novel biomarkers for more optimized treatment of HNSC.

In silico characterization of competing endogenous RNA network in glioblastoma multiforme with a systems biology approach

Glioblastoma multiforme (GBM) is the most frequent malignant type of primary brain cancers and is a malignancy with poor prognosis. Thus, it is necessary to find novel therapeutic modalities based on molecular events occur at different stages of tumor progression. We used expression profiles of GBM tissues that contained long non-coding RNA (lncRNA), microRNA (miRNA) and mRNA signatures to make putative ceRNA networks. Our strategy led to identification of 1080 DEmRNAs, including 777 downregulated DEmRNAs (such as GJB6 and SLC12A5) and 303 upregulated DEmRNAs (such as TOP2A and RRM2), 19 DElncRNAs, including 16 downregulated DElncRNAs (such as MIR7-3HG and MIR124-2HG) and 3 upregulated DElncRNAs (such as CRNDE and XIST) and 49 DEmiRNAs, including 10 downregulated DEmiRNAs (such as hsa-miR-10b-5p and hsa-miR-1290) and 39 upregulated DEmiRNAs (such as hsa-miR-219a-2-3p and hsa-miR-338-5p). We also identified DGCR5, MIAT, hsa-miR-129-5p, XIST, hsa-miR-128-3p, PART1, hsa-miR-10b-5p, LY86-AS1, CRNDE, and DLX6-AS1 as 10 hub genes in the ceRNA network. The current study provides novel insight into molecular events during GBM pathogenesis. The identified molecules can be used as therapeutic targets for GBM.

LncRNA SOX2-OT regulates miR-192-5p/RAB2A axis and ERK pathway to promote glioblastoma cell growth

Glioblastoma (GBM) is the most frequent tumor in the central nervous system. Long non-coding RNAs (lncRNAs) have been widely accepted as essential participators in cancer progression. Nonetheless, the specific role and mechanism of lncRNA SRY-box transcription factor 2 overlapping transcript (SOX2-OT) in GBM have not been studied. We evaluated expression levels of SOX2-OT, miR-192-5p and Ras-related protein Rab-2A (RAB2A) in GBM cells via qRT-PCR. To investigate the roles of SOX2-OT in GBM cells, CCK-8, JC-1, EdU, and western blot assays were performed. The connection among SOX2-OT, miR-192-5p and RAB2A in GBM cells was explored through pull down, luciferase reporter, and RIP assays. Western blot and qRT-PCR were employed to analyze the activity of extracellular-signal-regulated kinase (ERK) signaling pathway. SOX2-OT expression was higher in GBM cell lines than in normal cells. SOX2-OT knockdown repressed proliferation and promoted apoptosis of GBM cells. Mechanism assays revealed that SOX2-OT could sponge miR-192-5p. Moreover, RAB2A was certified to be the target gene of miR-192-5p. Overexpression of RAB2A reversed the repressive function of SOX2-OT knockdown on GBM cell growth. Furthermore, SOX2-OT activated ERK signaling pathway in GBM cells. SOX2-OT regulated miR-192-5p/RAB2A axis and ERK pathway to promote GBM cell growth.

Identification of dysregulated competing endogenous RNA networks in glioblastoma: A way toward improved therapeutic opportunities

Glioblastoma is recognized as one of the leading causes of death worldwide. Although there have been considerable advancements in understanding the causative molecular mechanisms of this malignancy, effective therapeutic strategies are still in limited use. It has been revealed that non-coding RNAs (ncRNAs) play critical roles in glioblastoma development, while interactions between the regulatory molecules such as long ncRNAs (lncRNAs), microRNAs (miRNAs), transcribed pseudogenes, and circular RNAs (circRNAs) remain to be fully deciphered. Over the recent years, researchers have discovered a new category of RNA molecules called competing endogenous RNA (ceRNA). This kind of RNA can contribute to molecular interactions in the form of ceRNA networks (ceRNETs). Multiple lines of evidence have demonstrated that dysregulation of various ceRNA networks is involved in glioblastoma development. Therefore, gaining insights into these dysregulations might offer potential for the early diagnosis of glioblastoma patients and identification of efficient therapeutic targets. In this review, we provide an overview of recent discoveries on ceRNA networks and the involvement of dysregulated networks in posing limitations to temozolomide therapy. We also describe signaling pathways relevant to the progression of glioblastoma.

LncRNA HOXA-AS3 promotes the malignancy of glioblastoma through regulating miR-455-5p/USP3 axis

Our objective was to determine the molecular mechanisms by which lncRNA HOXA‐AS3 regulates the biological behaviour of glioblastoma multiforme (GBM). We used an lncRNA microarray assay to identify GBM‐related lncRNA expression profiles. Qrt‐PCR was used to survey the levels of expression of long non‐coding RNA (lncRNA) HOXA‐AS3 and the target gene. Dual‐luciferase reporter assays were used to investigate the interaction of lncRNA HOXA‐AS3, the target gene and miRNA. Western blot analysis was used to examine the expression of USP3 and epithelial‐mesenchymal transition (EMT) genes. The MTT assay, transwell assay and wound healing assay were used to analyse the effects of lncRNA HOXA‐AS3 on GBM cell viability, mobility and invasiveness, respectively. Our results showed that lncRNA HOXA‐AS3 was significantly up‐regulated in GBM cells and could promote GBM cell proliferation, invasion and migration in vitro and in vivo. HOXA‐AS was found to be associated with poor survival prognosis in glioma patients. The dual‐luciferase reporter assay also revealed that lncRNA HOXA‐AS3 acts as a mir‐455‐5p sponge by up‐regulating USP3 expression to promote GBM progression. Western blot analysis showed that lncRNA HOXA‐AS3 could up‐regulate EMT‐related gene expression in GBM. Experiments showed mir‐455‐5p could rescue the effect of lncRNA HOXA‐AS3 on cell proliferation and invasion. The newly identified HOXA‐AS3/mir‐455‐5p/USP3 pathway offers important clues to understanding the key mechanisms underlying the action of lncRNA HOXA‐AS3 in glioblastoma.