Epigenetic Role of Histone 3 Lysine Methyltransferase and Demethylase in Regulating Apoptosis Predicting the Recurrence of Atypical Meningioma

Non-coding RNAs as Genetic Biomarkers for the Diagnosis, Prognosis, Radiosensitivity, and Histopathologic Grade of Meningioma

Meningioma is considered the most common primary benign brain tumor. It originates from the arachnoid cells of the leptomeninges surrounding the brain. The mainstay treatment of meningiomas is microsurgical resection. Meningioma prognosis depends on tumor grade, location, and patient age. Recently, using non-coding RNA as a prognostic and diagnostic biomarker for many tumors became a trend. Herein, we demonstrate the importance of non-coding RNAs, including microRNAs and lncRNAs in meningioma and their potential role in meningioma's early diagnosis, prognosis, histological grade, and radiosensitivity. In this review, many microRNAs were found to be upregulated in radioresistant meningioma cells such as microRNA-221, microRNA-222, microRNA-4286, microRNA-4695-5p, microRNA-6732-5p, microRNA-6855-5p, microRNA-7977, microRNA-6765-3p, and microRNA-6787-5p. Moreover, there are many microRNAs downregulated in radioresistant meningioma cells such as microRNA-1275, microRNA-30c-1-3p, microRNA-4449, microRNA-4539, microRNA-4684-3p, microRNA-6129, and microRNA-6891-5p. Also, we highlight the possible use of non-coding RNAs as serum non-invasive biomarkers and their potential role as therapeutic targets to treat high-grade meningiomas. Recent studies show that microRNA-497, microRNA-195, microRNA-18a, microRNA-197, and microRNA-224 are downregulated in the serum of patients with meningiomas. Additionally, microRNA-106a-5p, microRNA-219-5p, microRNA-375, and microRNA-409-3p are found to be upregulated in the serum of patients with meningioma. We also found that there are many deregulated microRNAs in meningioma cells that can be used as potential biomarkers for meningioma diagnosis, prognosis, and histopathologic grade, such as microRNA-17-5p, microRNA-199a, microRNA-190a, microRNA-186-5p, microRNA155-5p, microRNA-22-3p, microRNA-24-3p, microRNA-26-5p, microRNA-27a-3p, microRNA-27b-3p, microRNA-96-5p, microRNA-146a-5p, microRNA-29c-3p, microRNA-219-5p, microRNA-335, microRNA-200a, microRNA-21, microRNA-107, microRNA-224, microRNA-195, microRNA-34a-3p, and microRNA-let-7d. Of interest, we found fewer studies discussing deregulated long non-coding RNAs (lncRNAs) in meningioma cells. LncRNAs work as competitive endogenous RNA (ceRNA) by binding to oncogenic or anti-oncogenic microRNAs. We found that lncRNA- NUP210, lncRNA-SPIRE2, lncRNA-SLC7A1, lncRNA-DMTN, lncRNA-LINC00702, and lncRNA-LINC00460 are upregulated in meningioma cells. In contrast, lncRNA-MALAT1 was found to be downregulated in meningioma cells.

Brain Invasion and Trends in Molecular Research on Meningioma

Meningiomas are the most common primary brain tumors in adults. The treatment of non-benign meningiomas remains a challenging task, and after the publication of the 2021 World Health Organization classification, the importance of molecular biological classification is emerging. In this article, we introduce the mechanisms of brain invasion in atypical meningioma and review the genetic factors involved along with epigenetic regulation. First, it is important to understand the three major steps for brain invasion of meningeal cells: 1) degradation of extracellular matrix by proteases, 2) promotion of tumor cell migration to resident cells by adhesion molecules, and 3) neovascularization and supporting cells by growth factors. Second, the genomic landscape of meningiomas should be analyzed by major categories, such as germline mutations in NF2 and somatic mutations in non-NF2 genes (TRAF7, KLF4, AKT1, SMO, and POLR2A). Finally, epigenetic alterations in meningiomas are being studied, with a focus on DNA methylation, histone modification, and RNA interference. Increasing knowledge of the molecular landscape of meningiomas has allowed the identification of prognostic and predictive markers that can guide therapeutic decision-making processes and the timing of follow-up.

miR‑489 promotes apoptosis and inhibits invasiveness of glioma cells by targeting PAK5/RAF1 signaling pathways

Glioma patients receiving therapy are at a high risk of relapse and rapid progression and, thus, more effective treatments are required. The aim of the present study was to determine the suppressive role of miR-489 as an alternative therapeutic target for preventing glioma progression. The results of the present study demonstrated that patients with relatively lower levels of expression of miR-489 had more favorable clinical outcomes. Furthermore, miR-489 expression was inversely correlated with p21-activated kinase 5 (PAK5) mRNA expression levels in glioma specimens. A dual luciferase reporter assay revealed that miR-489 suppressed PAK5 expression by directly targeting the PAK5 3′-untranslated region. The effects of miR-489 on cell viability were measured using MTT and Cell Counting Kit-8 assays. The results demonstrated that ectopic expression of miR-489 mimic decreased cell viability by interfering with cyclin D1 and c-Myc signaling. Additionally, the effect of miR-489 on apoptosis was determined using Hoechst 33258 staining and flow cytometry. The results demonstrated that miR-489 decreased the activity of RAF1, reduced Bcl-2 and promoted Bax expression, resulting in increased cell apoptosis. Furthermore, the effect of miR-489 mimic on cellular motility was assessed using migration and invasion assays. miR-489 was shown to abolish the PAK5/RAF1/MMP2 pathway, resulting in decreased cell invasion ability. These results indicated that miR-489 may be involved in PAK5-mediated regulation of glioma progression, demonstrating the potential therapeutic benefits of targeting miR-489 in glioma.

Up-regulation of microRNA-497 inhibits the proliferation, migration and invasion but increases the apoptosis of multiple myeloma cells through the MAPK/ERK signaling pathway by targeting Raf-1

Multiple myeloma (MM) is a cancer that occurs in plasma cells, which fall under the category of white blood cells that are in charge of antibody production. According to previous studies, microRNA-497 (miR-497) functions as a tumor suppressor in several types of cancer, including gastric cancer and colorectal cancer. Therefore, the present study aims to investigate the effects of miR-497 on cellular function of human MM cells through the mitogen-activated protein kinase/extracellular signal-regulated kinase (MAPK/ERK) signaling pathway by targeting Raf-1. The differentially expressed genes and miRs in MM, and the relationship between the miR and gene were verified. It was found that Raf-1 was a target gene of miR-497. The data obtained from MM tissues showed increased Raf-1 level and decreased miR-497 level. MM cells were treated with mimic, inhibitor and siRNA in order to evaluate the role of miR-497, Raf-1 and MAPK/ERK in MM. The expression pattern of miR-497, Raf-1, ERK1/2, survivin, B-cell lymphoma-2 (Bcl-2) and BCL2-Associated X (Bax) as well as the extent of ERK1/2 phosphorylation were determined. Retored miR-497 and si-Raf-1 resulted in increases in the Bax expression and cell apoptosis and decreases in the expressions of Raf-1, MEK-2, survivin, Bcl-2, along with the extent of ERK1/2 phosphorylation. In addition, the biological function evaluations of MM cells revealed that miR-497 mimic or si-Raf-1 led to suppression in cell proliferation, invasion and migration. In conclusion, our results have demonstrated that miR-497 targets Raf-1 in order to inhibit the progression of MM by blocking the MAPK/ERK signaling pathway.

Pan-Cancer Analysis Reveals the Functional Importance of Protein Lysine Modification in Cancer Development

Large-scale tumor genome sequencing projects have revealed a complex landscape of genomic mutations in multiple cancer types. A major goal of these projects is to characterize somatic mutations and discover cancer drivers, thereby providing important clues to uncover diagnostic or therapeutic targets for clinical treatment. However, distinguishing only a few somatic mutations from the majority of passenger mutations is still a major challenge facing the biological community. Fortunately, combining other functional features with mutations to predict cancer driver genes is an effective approach to solve the above problem. Protein lysine modifications are an important functional feature that regulates the development of cancer. Therefore, in this work, we have systematically analyzed somatic mutations on seven protein lysine modifications and identified several important drivers that are responsible for tumorigenesis. From published literature, we first collected more than 100,000 lysine modification sites for analysis. Another 1 million non-synonymous single nucleotide variants (SNVs) were then downloaded from TCGA and mapped to our collected lysine modification sites. To identify driver proteins that significantly altered lysine modifications, we further developed a hierarchical Bayesian model and applied the Markov Chain Monte Carlo (MCMC) method for testing. Strikingly, the coding sequences of 473 proteins were found to carry a higher mutation rate in lysine modification sites compared to other background regions. Hypergeometric tests also revealed that these gene products were enriched in known cancer drivers. Functional analysis suggested that mutations within the lysine modification regions possessed higher evolutionary conservation and deleteriousness. Furthermore, pathway enrichment showed that mutations on lysine modification sites mainly affected cancer related processes, such as cell cycle and RNA transport. Moreover, clinical studies also suggested that the driver proteins were significantly associated with patient survival, implying an opportunity to use lysine modifications as molecular markers in cancer diagnosis or treatment. By searching within protein-protein interaction networks using a random walk with restart (RWR) algorithm, we further identified a series of potential treatment agents and therapeutic targets for cancer related to lysine modifications. Collectively, this study reveals the functional importance of lysine modifications in cancer development and may benefit the discovery of novel mechanisms for cancer treatment.

MiR-34a-3p alters proliferation and apoptosis of meningioma cells in vitro and is directly targeting SMAD4, FRAT1 and BCL2

Micro (mi)RNAs are short, noncoding RNAs and deregulation of miRNAs and their targets are implicated in tumor generation and progression in many cancers. Meningiomas are mostly benign, slow growing tumors of the central nervous system with a small percentage showing a malignant phenotype.

Following in silico prediction of potential targets of miR-34a-3p, SMAD4, FRAT1, and BCL2 have been confirmed as targets by dual luciferase assays with co-expression of miR-34a-3p and reporter gene constructs containing the respective 3'UTRs. Disruption of the miR-34a-3p binding sites in the 3'UTRs resulted in loss of responsiveness to miR-34a-3p overexpression. In meningioma cells, overexpression of miR-34a-3p resulted in decreased protein levels of SMAD4, FRAT1 and BCL2, while inhibition of miR-34a-3p led to increased levels of these proteins as confirmed by Western blotting. Furthermore, deregulation of miR-34a-3p altered cell proliferation and apoptosis of meningioma cells in vitro.

We show that SMAD4, FRAT1 and BCL2 are direct targets of miR-34a-3p and that deregulation of miR-34a-3p alters proliferation and apoptosis of meningioma cells in vitro. As part of their respective signaling pathways, which are known to play a role in meningioma genesis and progression, deregulation of SMAD4, FRAT1 and BCL2 might contribute to the aberrant activation of these signaling pathways leading to increased proliferation and inhibition of apoptosis in meningiomas.

The anti-apoptotic protein survivin can improve the prognostication of meningioma patients

BACKGROUND

The 2016 WHO histopathological grading includes a substantial within-variation in recurrence risk, and is thus insufficient to predict prognosis after initial surgery of patients suffering from meningiomas. The aim of this study was to compare the prognostic value of the histopathological grading and the conventional biomarker MIB-1 with expression of the anti-apoptotic protein survivin to see if this biomarker could complement recurrence prediction.

METHODS

Using immunohistochemistry, the expression of MIB-1 and survivin were determined as labeling indices (LIs) in tissue micro arrays from 160 human meningiomas. The accuracy of prognostication was assessed with receiver operator characteristics analyses and standard survival analyses.

RESULTS

The expression of survivin was significantly associated with both histopathological grade (P = 0.022) and recurrence status (P = 0.035). A survivin LI of 1% was identified as the optimal cutoff value to predict recurrence (P = 0.003), and was proven as more reliable than the histopathological grading (P = 0.497) and MIB-1 expression (P = 0.091). This result was further strengthened in multivariate analyses where survivin expression was revealed as an independent predictor of recurrence-free survival, while the histopathological grading and MIB-1 expression did not reach significance (P ≥ 0.156).

CONCLUSIONS

These findings suggest that incorporation of survivin in the clinical practice might be useful as complement for the histopathological grading and should further be evaluated in independent prospective studies.