IDH1 mutation-associated long non-coding RNA expression profile changes in glioma

Non-coding RNAs (ncRNAs) as therapeutic targets and biomarkers in oligodendroglioma

Oligodendrogliomas (ODGs) are neuroepithelial tumors that need personalized treatment plans because of their unique molecular and histological features. Non-coding RNAs form an epigenetic class of molecules that act as the first steps in gene regulation. They consist of microRNAs, long non-coding RNAs, and circular RNAs. These molecules significantly participate in ODG pathogenesis by regulating ODG initiation, progression, and treatment response. This review is designated to analyze the literature and describe the genomic profile of ODGs, the complex actions of ncRNAs in ODGs pathogenesis and treatment, and their roles as appropriate biomarkers and as one of the precision mechanisms action targets, such as antisense oligonucleotides, small interfering RNAs, gene therapy vectors, peptide nucleic acids, and small molecule inhibitors. Overall, ncRNAs considerably alter the pathological spectrum of ODGs by influencing fundamental processes in tumor biology. Applying ncRNAs in a clinical context exhibits promise for enhanced diagnosis and individualized therapeutic interventions. Nevertheless, the delivery efficacy and potential adverse "off-target" sequels retain the main obstacles undermining clinical potential. Continuous research and technological advancements in ncRNAs offer new insights and promising prospects for revolutionizing oligodendroglioma care, leading to better, personalized treatment outcomes.

Dysregulation of LINC00324 promotes poor prognosis in patients with glioma

BACKGROUND

LINC00324 is a long-stranded non-coding RNA, which is aberrantly expressed in various cancers and is associated with poor prognosis and clinical features. It involves multiple oncogenic molecular pathways affecting cell proliferation, migration, invasion, and apoptosis. However, the expression, function, and mechanism of LINC00324 in glioma have not been reported.

MATERIAL AND METHODS

We assessed the expression of LINC00324 of LINC00324 in glioma patients based on data from The Cancer Genome Atlas (TCGA) and Genotype-Tissue Expression (GTEx) to identify pathways involved in LINC00324-related glioma pathogenesis.

RESULTS

Based on our findings, we observed differential expression of LINC00324 between tumor and normal tissues in glioma patients. Our analysis of overall survival (OS) and disease-specific survival (DSS) indicated that glioma patients with high LINC00324 expression had a poorer prognosis compared to those with low LINC00324 expression. By integrating clinical data and genetic signatures from TCGA patients, we developed a nomogram to predict OS and DSS in glioma patients. Gene set enrichment analysis (GSEA) revealed that several pathways, including JAK/STAT3 signaling, epithelial-mesenchymal transition, STAT5 signaling, NF-κB activation, and apoptosis, were differentially enriched in glioma samples with high LINC00324 expression. Furthermore, we observed significant correlations between LINC00324 expression, immune infiltration levels, and expression of immune checkpoint-related genes (HAVCR2: r = 0.627, P = 1.54e-77; CD40: r = 0.604, P = 1.36e-70; ITGB2: r = 0.612, P = 6.33e-7; CX3CL1: r = -0.307, P = 9.24e-17). These findings highlight the potential significance of LINC00324 in glioma progression and suggest avenues for further research and potential therapeutic targets.

CONCLUSION

Indeed, our results confirm that the LINC00324 signature holds promise as a prognostic predictor in glioma patients. This finding opens up new possibilities for understanding the disease and may offer valuable insights for the development of targeted therapies.

Targeting HOTAIRM1 Ameliorates Glioblastoma by Disrupting Mitochondrial Oxidative Phosphorylation and Serine Metabolism

Serine hydroxymethyltransferase 2 (SHMT2), which catalyzes the conversion of serine to glycine and one-carbon transfer reactions in mitochondria, is significantly upregulated in glioblastoma (GBM). However, the mechanism by which the stability of SHMT2 gene expression is maintained to drive GBM tumorigenesis has not been clarified. Herein, through microarray screening, we identified that HOXA Transcript Antisense RNA, Myeloid-Specific 1 (HOTAIRM1) modulates the SHMT2 level in various GBM cell lines. Serine catabolism and mitochondrial oxidative phosphorylation activities were decreased by HOTAIRM1 inhibition. Mechanistically, according to our mass spectrometry and eCLIP-seq results, HOTAIRM1 can bind to PTBP1 and IGF2BP2. Furthermore, HOTAIRM1 maintains the stability of SHMT2 by promoting the recognition of an m⁶A site and the interaction of PTBP1/IGF2BP2 with SHMT2 mRNA. The stability of HOTAIRM1 can also be enhanced and results in positive feedback regulation to support the progression of GBM. Thus, targeting HOTAIRM1 could be a promising metabolic therapy for GBM.

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HOTAIRM1 regulates mitochondrial activity in GBM

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The target genes of HOTAIRM1 and the interacting RBPs were screened and identified

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SHMT2 mRNA has an m⁶A site that can be recognized by IGF2BP2

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HOTAIRM1 regulates the stability of SHMT2 by binding to PTBP1 and IGF2BP2

Long non-coding RNA FAM66C regulates glioma growth via the miRNA/LATS1 signaling pathway

Glioma is one of the most common primary intracranial carcinomas and typically associated with a dismal prognosis and poor quality of life. The identification of novel oncogenes is clinically valuable for early screening and prevention. Recently, the studies have revealed that long non-coding RNAs (lncRNAs) play important roles in the development and progression of cancers including glioma. The expression of lncRNA FAM66C is reduced in glioma cell lines and clinical samples compared to non-tumor samples. Knockdown of FAM66C in U87 and U251 cells significantly promoted cell proliferation and migration, respectively. Furthermore, the correlation between FAM66C and Hippo pathway regulators YAP1 and LATS1, along with the alteration of their protein expression level indicated that FAM66C regulated cell growth through this pathway. Moreover, luciferase assay demonstrated that another two noncoding RNAs, miR15a/miR15b, directly bonded to the 3'UTR of LATS1 to facilitated its transcriptional expression and inhibited cell growth. In addition, the luciferase activity of FAM66C was block by miR15a/miR15b, and the promotion of cell growth effects caused by FAM66C deficiency was attenuated by miR15a/miR15b mimics, further proved that FAM66C functioned as a competing endogenous RNA to regulate glioma growth via the miRNA/LATS1 signaling pathway.

The Role of CASC2 and miR-21 Interplay in Glioma Malignancy and Patient Outcome

Recently long non-coding RNAs (lncRNAs) were highlighted for their regulatory role in tumor biology. The novel human lncRNA cancer susceptibility candidate 2 (CASC2) has been characterized as a potential tumor suppressor in several tumor types. However, the roles of CASC2 and its interplay with miR-21 in different malignancy grade patient gliomas remain unexplored. Here we screened 99 different malignancy grade astrocytomas for CASC2, and miR-21 gene expression by real-time quantitative polymerase chain reaction (RT-qPCR) in isocitrate dehydrogenase 1 (IDH1) and O-6-methylguanine methyltransferase (MGMT) assessed gliomas. CASC2 expression was significantly downregulated in glioblastomas (p = 0.0003). Gliomas with low CASC2 expression exhibited a high level of miR-21, which was highly associated with the higher glioma grade (p = 0.0001), IDH1 wild type gliomas (p < 0.0001), and poor patient survival (p < 0.001). Taken together, these observations suggest that CASC2 acts as a tumor suppressor and potentially as a competing endogenous RNA (ceRNA) for miR-21, plays important role in IDH1 wild type glioma pathogenesis and patients' outcomes.

RNA Interference Nanotherapeutics for Treatment of Glioblastoma Multiforme

Nucleic acid therapeutics for RNA interference (RNAi) are gaining attention in the treatment and management of several kinds of the so-called "undruggable" tumors via targeting specific molecular pathways or oncogenes. Synthetic ribonucleic acid (RNAs) oligonucleotides like siRNA, miRNA, shRNA, and lncRNA have shown potential as novel therapeutics. However, the delivery of such oligonucleotides is significantly hampered by their physiochemical (such as hydrophilicity, negative charge, and instability) and biopharmaceutical features (in vivo serum stability, fast renal clearance, interaction with extracellular proteins, and hindrance in cellular internalization) that markedly reduce their biological activity. Recently, several nanocarriers have evolved as suitable non-viral vectors for oligonucleotide delivery, which are known to either complex or conjugate with these oligonucleotides efficiently and also overcome the extracellular and intracellular barriers, thereby allowing access to the tumoral micro-environment for the better and desired outcome in glioblastoma multiforme (GBM). This Review focuses on the up-to-date advancements in the field of RNAi nanotherapeutics utilized for GBM treatment.

LncRNA-135528 inhibits tumor progression by up-regulating CXCL10 through the JAK/STAT pathway

Spontaneous tumor regression can be observed in many tumors, however, studies related to the altered expression of lncRNA in spontaneous glioma regression are limited, and the potential contributions of lncRNAs to spontaneous glioma regression remain unknown. To investigate the biological roles of lncRNA-135528 in spontaneous glioma regression. The cDNA fragment of lncRNA-135528 was obtained by rapid-amplification of cDNA ends (RACE) technology and cloned into the plvx-mcmv-zsgreen-puro vector. Additionally, we stably silenced or overexpressed lncRNA-135528 in G422 cells by transfecting with siRNA against lncRNA-135528 or lncRNA-135528 overexpression plasmid. Then, we examined lncRNA-135528 overexpressing and lncRNA-135528 silencing on glioma cells and its effects on CXCL10 and JAK/STAT pathways. The main findings indicated that lncRNA-135528 promoted glioma cell apoptosis, inhibited cell proliferation and arrested cell cycle progression; the up-regulation of lncRNA135528 led to significantly increased CXCL10 levels and the differential expression of mRNA associated with JAK/STAT pathway in glioma cells. lncRNA-135528 can inhibit tumor progression by up-regulating CXCL10 through the JAK/STAT pathway.

Non-Coding RNAs in Glioma

Glioma is the most aggressive brain tumor of the central nervous system. The ability of glioma cells to migrate, rapidly diffuse and invade normal adjacent tissue, their sustained proliferation, and heterogeneity contribute to an overall survival of approximately 15 months for most patients with high grade glioma. Numerous studies indicate that non-coding RNA species have critical functions across biological processes that regulate glioma initiation and progression. Recently, new data emerged, which shows that the cross-regulation between long non-coding RNAs and small non-coding RNAs contribute to phenotypic diversity of glioblastoma subclasses. In this paper, we review data of long non-coding RNA expression, which was evaluated in human glioma tissue samples during a five-year period. Thus, this review summarizes the following: (I) the role of non-coding RNAs in glioblastoma pathogenesis, (II) the potential application of non-coding RNA species in glioma-grading, (III) crosstalk between lncRNAs and miRNAs (IV) future perspectives of non-coding RNAs as biomarkers for glioma.

Long Non-Coding RNAs in Gliomas: From Molecular Pathology to Diagnostic Biomarkers and Therapeutic Targets

Gliomas are the most common malignancies of the central nervous system. Because of tumor localization and the biological behavior of tumor cells, gliomas are characterized by very poor prognosis. Despite significant efforts that have gone into glioma research in recent years, the therapeutic efficacy of available treatment options is still limited, and only a few clinically usable diagnostic biomarkers are available. More and more studies suggest non-coding RNAs to be promising diagnostic biomarkers and therapeutic targets in many cancers, including gliomas. One of the largest groups of these molecules is long non-coding RNAs (lncRNAs). LncRNAs show promising potential because of their unique tissue expression patterns and regulatory functions in cancer cells. Understanding the role of lncRNAs in gliomas may lead to discovery of the novel molecular mechanisms behind glioma biological features. It may also enable development of new solutions to overcome the greatest obstacles in therapy of glioma patients. In this review, we summarize the current knowledge about lncRNAs and their involvement in the molecular pathology of gliomas. A conclusion follows that these RNAs show great potential to serve as powerful diagnostic, prognostic, and predictive biomarkers as well as therapeutic targets.

Genetic landscape of long noncoding RNA (lncRNAs) in glioblastoma: identification of complex lncRNA regulatory networks and clinically relevant lncRNAs in glioblastoma

The major part of the genome that was previously called junk DNA has been shown to be dynamically transcribed to produce non-coding RNAs. Among them, the long non-coding RNAs (lncRNA) play diverse roles in the cellular context and are therefore involved in various diseases like cancer. LncRNA transcript profiling of glioblastoma (n = 19) and control brain samples (n = 9) identified 2,774 and 5,016 lncRNAs to be upregulated and downregulated in GBMs respectively. Correlation analysis of differentially regulated lncRNAs with mRNA and lncRNA identified several lncRNAs that may potentially regulate many tumor relevant mRNAs and lncRNAs both at nearby locations (cis) and far locations (trans). Integration of our data set with TCGA GBM RNA-Seq data (n = 172) revealed many lncRNAs as a host as well as decoy for many tumor regulated miRNAs. The expression pattern of seven lncRNAs- HOXD-AS2, RP4-792G4.2, CRNDE, ANRIL, RP11-389G6.3, RP11-325122.2 and AC123886.2 was validated by TCGA RNA-Seq data and RT-qPCR. Silencing ANRIL, a GBM upregulated lncRNA, inhibited glioma cell proliferation and colony growth. Cox regression analysis identified several prognostic lncRNAs. An lncRNA risk score derived from five lnRNAs-RP6-99M1.2, SOX21-AS1, CTD-2127H9.1, RP11-375B1.3 and RP3-449M8.9 predicted survival independent of all other markers. Multivariate cox regression analysis involving G-CIMP, IDH1 mutation, MGMT promoter methylation identified lncRNA risk score to be an independent poor predictor of GBM survival. The lncRNA risk score also stratified GBM patients into low and high risk with significant survival difference. Thus our study demonstrates the importance of lncRNA in GBM pathology and underscores the potential possibility of targeting lncRNA for GBM therapy.

Long non-coding RNAs: potential molecular biomarkers for gliomas diagnosis and prognosis

The current grade classification system of gliomas is based on the histopathological features of these tumors and has great significance in defining groups of patients for clinical assessment. However, this classification system is also associated with a number of limitations, and as such, additional clinical assessment criteria are required. Long non-coding RNAs (lncRNAs) play a critical role in cellular functions and are currently regarded as potential biomarkers for glioma diagnosis and prognosis. Therefore, the molecular classification of glioma based on lncRNA expression may provide additional information to assist in the systematic identification of glioma. In the present paper, we review the emerging evidence indicating that specific lncRNAs may have the potential for use as key novel biomarkers and thus provide a powerful tool for the systematic diagnosis of glioma.

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.

An Insight into the Increasing Role of LncRNAs in the Pathogenesis of Gliomas

Long non-coding RNAs (LncRNAs) are essential epigenetic regulators with critical roles in tumor initiation and malignant progression. However, the roles and mechanisms of aberrantly expressed lncRNAs in the pathogenesis of gliomas are not fully understood. With the development of deep sequencing analyses, an extensive amount of functional non-coding RNAs has been discovered in glioma tissues and cell lines. Additionally, the contributions of several lncRNAs, such as Hox transcript antisense intergenic RNA, H19 and Colorectal neoplasia differentially expressed, previously reported to be involved in other pathogenesis and processes to the oncogenesis of glioblastoma are currently addressed. Thus, lncRNAs detected in tumor tissues could serve as candidate diagnostic biomarkers and therapeutic targets for gliomas. To understand the potential function of lncRNAs in gliomas, in this review, we briefly describe the profile of lncRNAs in human glioma research and therapy. Then, we discuss the individual lncRNA that has been under intensive investigation in glioma research, and the focus is its mechanism and clinical implication.

A Comprehensive Review of Genomics and Noncoding RNA in Gliomas

Glioblastoma (GBM) is the most malignant primary adult brain tumor. In spite of our greater understanding of the biology of GBMs, clinical outcome of GBM patients remains poor, as their median survival with best available treatment is 12 to 18 months. Recent efforts of The Cancer Genome Atlas (TCGA) have subgrouped patients into 4 molecular/transcriptional subgroups: proneural, neural, classical, and mesenchymal. Continuing efforts are underway to provide a comprehensive map of the heterogeneous makeup of GBM to include noncoding transcripts, genetic mutations, and their associations to clinical outcome. In this review, we introduce key molecular events (genetic and epigenetic) that have been deemed most relevant as per studies such as TCGA, with a specific focus on noncoding RNAs such as microRNAs (miRNA) and long noncoding RNAs (lncRNA). One of our main objectives is to illustrate how miRNAs and lncRNAs play a pivotal role in brain tumor biology to define tumor heterogeneity at molecular and cellular levels. Ultimately, we elaborate how radiogenomics-based predictive models can describe miRNA/lncRNA-driven networks to better define heterogeneity of GBM with clinical relevance.

Silencing of Long Non-Coding RNA MALAT1 Promotes Apoptosis of Glioma Cells

The metastasis-associated lung adenocarcinoma transcription 1 (MALAT1) is a highly conserved long non-coding RNA (lncRNA) gene. However, little is known about the pathological role of lncRNA MALAT1 in glioma. In the present study, we explored the expression level of lncRNA MALAT1 in primary glioma tissues as well as in U87 and U251 glioma cell lines. Using qRT-PCR, we found that the expression of lncRNA MALAT1 was significantly increased in glioma tissues compared with that of paracancerous tissues. Meanwhile, the expression of MALAT1 was highly expressed in U98 and U251 cells. In order to explore the function of MALAT1, the expression of MALAT1 was greatly reduced in U87 and U251 cells transfected with siRNA specifically targeting MALAT1. Consequently, cell viability of U87 and U251 cells were drastically decreased after the knockdown of MALAT1. Concomitantly, the apoptosis rate of the two cell lines was dramatically increased. Furthermore, the expression levels of some tumor markers were reduced after the knockdown of MALAT1, such as CCND1 and MYC. In summary, the current study indicated a promoting role of MALAT1 in the development of glioma cell.

Uncovering the roles of long noncoding RNAs in neural development and glioma progression

In the past decade, thousands of long noncoding RNAs (lncRNAs) have been identified, and emerging data indicate that lncRNAs can have important biological functions and roles in human diseases including cancer. Many lncRNAs appear to be expressed specifically in the brain, and the roles of lncRNAs in neural stem cells (NSCs) and brain development are now beginning to be discovered. Here we review recent advances in understanding the diversity of lncRNA structure and functions in NSCs and brain development. NSCs in the adult mouse ventricular-subventricular zone (V-SVZ) generate new neurons throughout life, and we discuss how key elements of this adult neurogenic system have facilitated the discovery and functional characterization of known and novel lncRNAs. A review of lncRNAs described in other NSC systems reveals a variety of molecular mechanisms, including binding and recruitment of transcription factors, epigenetic modifiers, and RNA-splicing factors. Finally, we review emerging evidence indicating that specific lncRNAs can be key drivers of glial tumors, and discuss next steps towards an in vivo understanding of lncRNA function in development and disease.