A Comprehensive Review of Genomics and Noncoding RNA in Gliomas

A Comprehensive Review of miRNAs and Their Epigenetic Effects in Glioblastoma

Glioblastoma is the most aggressive form of brain tumor originating from glial cells with a maximum life expectancy of 14.6 months. Despite the establishment of multiple promising therapies, the clinical outcome of glioblastoma patients is abysmal. Drug resistance has been identified as a major factor contributing to the failure of current multimodal therapy. Epigenetic modification, especially DNA methylation has been identified as a major regulatory mechanism behind glioblastoma progression. In addition, miRNAs, a class of non-coding RNA, have been found to play a role in the regulation as well as in the diagnosis of glioblastoma. The relationship between epigenetics, drug resistance, and glioblastoma progression has been clearly demonstrated. MGMT hypermethylation, leading to a lack of MGMT expression, is associated with a cytotoxic effect of TMZ in GBM, while resistance to TMZ frequently appears in MGMT non-methylated GBM. In this review, we will elaborate on known miRNAs linked to glioblastoma; their distinctive oncogenic or tumor suppressor roles; and how epigenetic modification of miRNAs, particularly via methylation, leads to their upregulation or downregulation in glioblastoma. Moreover, we will try to identify those miRNAs that might be potential regulators of MGMT expression and their role as predictors of tumor response to temozolomide treatment. Although we do not impact clinical data and survival, we open possible experimental approaches to treat GBM, although they should be further validated with clinically oriented studies.

circTOP2A functions as a ceRNA to promote glioma progression by upregulating RPN2

Competing endogenous RNA (ceRNA)-mediated signaling pathway dysregulation provides great insight into comprehensively understanding the molecular mechanism and combined targeted therapy for glioblastoma. circRNA is characterized by high stability, tissue/developmental stage-specific expression and abundance in brain and plays significant roles in the initiation and progression of cancer. Our previous published data have demonstrated that RPN2 was significantly upregulated in glioma and promoted tumor progression via the activation of the Wnt/β-catenin pathway. Furthermore, we proved that miR-422a regulated the Wnt/β-catenin signaling pathway by directly targeting RPN2. In this study, based on the glioblastoma microarray profiles, we identified the upstream circTOP2A, which completely bound to miR-422a and was co-expressed with the RPN2. circTOP2A was significantly overexpressed in glioma and conferred a poor prognosis. circTOP2A could regulate RPN2 expression by sponging miR-422a, verified by western blot, dual-luciferase reporter gene assay, and RNA pull-down assay. Functional assays including CCK8, transwell and FITC-annexin V were performed to explore the RPN2-mediated role of the circTOP2A effect on the glioma malignant phenotype. Additionally, TOP/FOP and immunofluorescence analysis were used to confirm that sh-circTOP2A could suppress the Wnt/β-catenin pathway partly through RPN2. Finally, a tumor xenograft model was applied to validate the biological function of circTOP2A in vivo. Taken together, our findings reveal the critical role of circTOP2A in promoting glioma proliferation and invasion via a ceRNA mechanism and provide an exploitable biomarker and therapeutic target for glioma patients.

The Role of Non-Coding RNAs in Glioma

For decades, research in cancer biology has been focused on the protein-coding fraction of the human genome. However, with the discovery of non-coding RNAs (ncRNAs), it has become known that these entities not only function in numerous fundamental life processes such as growth, differentiation, and development, but also play critical roles in a wide spectrum of human diseases, including cancer. Dysregulated ncRNA expression is found to affect cancer initiation, progression, and therapy resistance, through transcriptional, post-transcriptional, or epigenetic processes in the cell. In this review, we focus on the recent development and advances in ncRNA biology that are pertinent to their role in glioma tumorigenesis and therapy response. Gliomas are common, and are the most aggressive type of primary tumors, which account for ~30% of central nervous system (CNS) tumors. Of these, glioblastoma (GBM), which are grade IV tumors, are the most lethal brain tumors. Only 5% of GBM patients survive beyond five years upon diagnosis. Hence, a deeper understanding of the cellular non-coding transcriptome might help identify biomarkers and therapeutic agents for a better treatment of glioma. Here, we delve into the functional roles of microRNA (miRNA), long non-coding RNA (lncRNA), and circular RNA (circRNA) in glioma tumorigenesis, discuss the function of their extracellular counterparts, and highlight their potential as biomarkers and therapeutic agents in glioma.

Bioinformatics Strategies to Identify Shared Molecular Biomarkers That Link Ischemic Stroke and Moyamoya Disease with Glioblastoma

Expanding data suggest that glioblastoma is accountable for the growing prevalence of various forms of stroke formation, such as ischemic stroke and moyamoya disease. However, the underlying deterministic details are still unspecified. Bioinformatics approaches are designed to investigate the relationships between two pathogens as well as fill this study void. Glioblastoma is a form of cancer that typically occurs in the brain or spinal cord and is highly destructive. A stroke occurs when a brain region starts to lose blood circulation and prevents functioning. Moyamoya disorder is a recurrent and recurring arterial disorder of the brain. To begin, adequate gene expression datasets on glioblastoma, ischemic stroke, and moyamoya disease were gathered from various repositories. Then, the association between glioblastoma, ischemic stroke, and moyamoya was established using the existing pipelines. The framework was developed as a generalized workflow to allow for the aggregation of transcriptomic gene expression across specific tissue; Gene Ontology (GO) and biological pathway, as well as the validation of such data, are carried out using enrichment studies such as protein-protein interaction and gold benchmark databases. The results contribute to a more profound knowledge of the disease mechanisms and unveil the projected correlations among the diseases.

miR‑497/MIR497HG inhibits glioma cell proliferation by targeting CCNE1 and the miR‑588/TUSC1 axis

Emerging evidence has shown that microRNA (miR)-497 serves pivotal roles in tumorigenesis, cancer progression, metastasis and chemotherapy resistance in several types of cancer. In the present study, the expression and biological functions of miR-497 host gene (MIR497HG) were investigated in glioma tissue. The expression levels of miR-497 and MIR497HG were measured in glioma, adjacent non-cancerous and normal brain tissue and their association with the prognosis of patients with glioma were analyzed. The biological roles of miR-497 and MIR497HG were investigated in glioma cell lines. In addition, bioinformatics analysis, luciferase reporter assay and functional experiments were performed to identify and validate the downstream targets of miR-497 or MIR497HG. The expression levels of miR-497 and MIR497HG were downregulated in glioma tissue and cell lines compared with those in adjacent non-cancerous and normal brain tissue and normal human cortical neuron cell line. Patients with low miR-497 or MIR497HG expression levels exhibited a poor prognostic outcome. In addition, forced overexpression of miR-497 or MIR497HG significantly inhibited the proliferation and cell cycle progression of glioma cell lines. Furthermore, the results indicated that miR-497 and MIR497HG exerted their biological functions by direct targeting of cyclin E1 and miR-588/tumor suppressor candidate 1. In summary, the data indicated that miR-497 and MIR497HG served as tumor suppressors and may be used as potential therapeutic targets and prognostic biomarkers in glioma.

Identification of three new microsatellites and their effects on body measurement traits in pigs using time of flight-mass spectrometry (TOF-MS)

The body status of livestock affects their physiological function and productive performances. Microsatellites, one of the most used DNA markers, have been found to be associated with pig productive traits. However, their identifications and effects on body measurement traits of the Chinese Qinghai Bamei pig still uncovered. According to our previous sequencing data, in this study, three novel microsatellites were found in this breed. Using time of flight-mass spectrometry (TOF-MS) method, these microsatellites were further identified in a large Bamei pig population. TOF-MS spectra showed that there are three microsatellites loci, named P1, P2 and P3. These microsatellites were linkage equilibrium based on the values of D' and r² tests. Association results demonstrated that P1 locus was associated with the body length, body height and chest width and the beneficial genotype was 150-/150-bp (p < 0.05); and P2 locus was associated with the body height (p < 0.05), and the 145-/145-bp, 145-/147-bp and 145-/149-bp were claimed as favorable genotypes and 145-bp allele was considered as the favorable allele. These findings suggested that P1 and P2 microsatellites might be considered as the candidate genetic markers to select pigs with superior body sizes, especially in local breed.

Study of Linc00574 Regulatory Effect on the TCTE3 Expression in Sperm Motility

We investigated the relationship of t-complex-associated-testis-expressed 3 (TCTE3) and linc00574 expression levels with sperm motility and morphology in patients with asthenozoospermia (AZ) and terato-asthenozoospermia (TAZ). The study population consisted of 31 AZ patients, 31 TAZ patients, and 32 normozoospermia (NZ) as controls. Quantitative real-time PCR was conducted to evaluate the expression levels of TCTE3 and linc00574. Bioinformatics investigations were performed using databases to find molecular pathway. TCTE3 expression was reduced significantly in AZ and TAZ patients (P < 0.05). Linc00574 expression level increased only in the AZ patients (P < 0.05). The subsequent analyses showed a significantly positive correlation between TCTE3 and linc00574 expression levels (P < 0.05). In addition, a significantly positive relationship was observed between TCTE3 expression level and sperm motility and morphology (P < 0.05). The present study suggests that TCTE3 expression is regulated by linc00574 through a negative self-regulating mechanism and therefore may affect the flagella structure and function.

Long Intergenic Non-Protein Coding RNA 1089 Suppresses Cell Proliferation and Metastasis in Gastric Cancer by Regulating miRNA-27a-3p/Epithelial-Mesenchymal Transition (EMT) Axis

Aim

To explore the expression and biological function of long intergenic non-protein coding RNA 1089 (LINC01089) in gastric cancer (GC) progression and its underlying mechanism.

Methods

LINC01089 and microRNA-27a-3p (miR-27a-3p) expressions were detected with the quantitative real-time polymerase chain reaction (RT-qPCR). Cell proliferation, migration and invasion were evaluated by Cell Counting Kit-8 (CCK-8) and Transwell assay. Epithelial-mesenchymal transition (EMT)-related proteins were also measured by Western blot. The relationship between LINC01089 and miR-27a-3p was revealed by a bioinformatics analysis and dual-luciferase reporter assay.

Results

LINC01089 was significantly down-regulated in GC tissues, as well as GC cell lines. GC patients with lower LINC01089 expression were more likely to have poor outcomes. Overexpression of LINC01089 significantly suppressed GC cells growth, migration and invasion and forbade the EMT process. LINC01089 was directly targeted at miR-27a-3p. The transfection of miR-27a-3p mimics reversed the inhibitory effects on proliferative and metastatic abilities of GC cells with LINC01089 overexpression.

Conclusion

LINC01089 inhibits cell proliferation and metastasis in GC by targeting miR-27a-3p/EMT axis, which should be considered as a promising therapeutic target.

Brain immunology and immunotherapy in brain tumours

Gliomas, the most common malignant primary brain tumours, remain universally lethal. Yet, seminal discoveries in the past 5 years have clarified the anatomy, genetics and function of the immune system within the central nervous system (CNS) and altered the paradigm for successful immunotherapy. The impact of standard therapies on the response to immunotherapy is now better understood, as well. This new knowledge has implications for a broad range of tumours that develop within the CNS. Nevertheless, the requirements for successful therapy remain effective delivery and target specificity, while the dramatic heterogeneity of malignant gliomas at the genetic and immunological levels remains a profound challenge.

Artificial microenvironment of in vitro glioblastoma cell cultures changes profile of miRNAs related to tumor drug resistance

Purpose: The in vitro environment can influence not only the molecular background of glioblastoma drug-resistance and treatment efficiency, but also the mechanisms and pathways of cell death. Both crucial molecular pathways and the deregulation of miRNAs are thought to participate in tumor therapy-resistance. The aim of our study is to examine the potential influence of ex vivo conditions on the expression of miRNAs engaged in the machinery of tumor-drug resistance, since in vitro models are commonly used for testing new therapeutics.

Methods: Glioblastoma-derived cells, cultured under three different sets of conditions, were used as experimental models in vitro. The expression of 84 miRNAs relevant to brain tumorigenesis was evaluated by multi-miRNA profiling for initial tumors and their corresponding cultures. Finally, the expression of selected miRNAs related to temozolomide-resistance (miR-125b, miR-130a, miR-21, miR-221, miR-222, miR-31, miR-149, miR-210, miR-181a) was assessed by real-time PCR for each tumor and neoplastic cells in cultures.

Results: Our results demonstrate significant discrepancies in the expression of several miRNAs between tumor cells in vivo and in vitro, with miR-130a, miR-221, miR-31, miR-21, miR-222, miR-210 being the most marked. Also differences were observed between particular models in vitro. The results of computational analysis revealed the interplay between examined miRNAs and their targets involved in processes of glioblastoma chemosensitivity, including the genes relevant to temozolomide response (MGMT, PTEN, MDM2, TP53, BBC3A).

Conclusion: The artificial environment may influence the selective proliferation of cell populations carrying specific patterns of miRNAs and/or the phenotype of neoplastic cells (eg differentiation) by the action of molecular events including miRNAs. These phenomena may influence the tumor-responsiveness to particular drugs, disturbing the evaluation of their efficacy in vitro, with unpredictable results caused by the interdependency of molecular pathways.

Distribution of cancer stem cells in two human brain gliomas

There is compelling evidence that brain tumors, particularly glioblastoma multiforme (GBM), harbor a small population of cancer stem cells (CSCs). These CSCs have the ability to undergo self-renewal, initiate tumors in vivo, and are resistant to chemotherapy and radiation therapy. The present study determined the spatial distribution of CSCs within the donated brains of two deceased patients affected by glioblastoma multiforme. The following six grossly visible functional regions were identified: Necrotic tumor, viable solid tumor, infiltrating tumor edge, peritumoral normal brain, normal brain close to the tumor and normal brain distant from the tumor. Each region was snap-frozen, sectioned and immunostained for the CSC biomarkers prominin-1 (CD133) and sex-determining region Y-box 2 (SOX2). The percentages of CD133⁺ and SOX2⁺ cells within each region were determined. Different percentages of CD133⁺ and SOX2⁺ cells were identified in different regions. Significantly higher percentages of CD133⁺ and SOX2⁺ cells were indicated at the infiltrating tumor edge when compared with other areas. In summary, the spatial distributions of CSCs in these two brains with glioblastoma multiforme were similar, with the highest concentration being at the infiltrating tumor edge. This suggests that the edge of the tumor is the moving front for tumor progression and invasion, and should be targeted for therapeutic intervention.

The miR-200 family: multiple effects on gliomas

Gliomas are the most common type of primary brain tumors. MicroRNAs (miRNAs) are small noncoding RNAs that can epigenetically regulate target gene expression. The microRNA 200 family includes miR-200a, 200b, 200c, 141 and 429. Numerous studies have indicated that members of the miR-200 family play an important role in glioma development and metastasis. In this review, we summarize the data from various studies and highlight the effects of miR-200 on glioma metastasis, therapeutic response and prognosis.

Association between long non-coding RNAs expression and pathogenesis and progression of gliomas

The incidence rate of gliomas is the highest among primary brain tumors. Although the understanding of the molecular pathology of glioma has improved during the previous two decades, effective therapies are not yet available to treat these tumors. Previous studies have indicated that long non-coding RNAs (lncRNAs) have a close association with glioma, suggesting that lncRNAs may be potential targets for the development of novel treatments for glioma. The present review summarized the latest studies on the dysregulation of lncRNAs in glioma, and discussed their potential use in the diagnosis, prognosis and therapies of glioma. The emergence of lncRNAs has revealed an additional facet to glioma oncogenesis. An improved understanding of their functions is important to advance lncRNA-based diagnosis, prognosis and therapeutic interventions of glioma.

Long noncoding RNAs (lncRNAs) in triple negative breast cancer

Long noncoding RNAs (lncRNAs) are dysregulated in many cancer types, which are believed to play crucial roles in regulating several hallmarks of cancer biology. Triple Negative Breast Cancer (TNBC) is a very aggressive subtype of normal breast cancer, which has features of negativity for ER, PR, and HER2. Great efforts have been made to identify an association between lncRNAs expression profiles and TNBC, and to understand the functional role and molecular mechanism on aberrant-expressed lncRNAs. In this review, we summarized the existed knowledge on the systematics, biology, and function of lncRNAs. The advances from the most recent studies of lncRNAs in the predicament of breast cancer, TNBC, are highlighted, especially the functions of specifically selected lncRNAs. We also discussed the potential value of these lncRNAs in TNBC, providing clues for the diagnosis and treatments of TNBC.