The use of hsa-miR-21, hsa-miR-181b and hsa-miR-106a as prognostic indicators of astrocytoma

Comparison of Oncogenes, Tumor Suppressors, and MicroRNAs Between Schizophrenia and Glioma: The Balance of Power

The risk of cancer in schizophrenia has been controversial. Confounders of the issue are cigarette smoking in schizophrenia, and antiproliferative effects of antipsychotic medications. The author has previously suggested comparison of a specific cancer like glioma to schizophrenia might help determine a more accurate relationship between cancer and schizophrenia. To accomplish this goal, the author performed three comparisons of data; the first a comparison of conventional tumor suppressors and oncogenes between schizophrenia and cancer including glioma. This comparison determined schizophrenia has both tumor-suppressive and tumor-promoting characteristics. A second, larger comparison between brain-expressed microRNAs in schizophrenia with their expression in glioma was then performed. This identified a core carcinogenic group of miRNAs in schizophrenia offset by a larger group of tumor-suppressive miRNAs. This proposed "balance of power" between oncogenes and tumor suppressors could cause neuroinflammation. This was assessed by a third comparison between schizophrenia, glioma and inflammation in asbestos-related lung cancer and mesothelioma (ALRCM). This revealed that schizophrenia shares more oncogenic similarity to ALRCM than glioma.

GlioMarker: An integrated database for knowledge exploration of diagnostic biomarkers in gliomas

Gliomas are the most frequent malignant and aggressive tumors in the central nervous system. Early and effective diagnosis of glioma using diagnostic biomarkers can prolong patients' lives and aid in the development of new personalized treatments. Therefore, a thorough and comprehensive understanding of the diagnostic biomarkers in gliomas is of great significance. To this end, we developed the integrated and web-based database GlioMarker (http://gliomarker.prophetdb.org/), the first comprehensive database for knowledge exploration of glioma diagnostic biomarkers. In GlioMarker, accurate information on 406 glioma diagnostic biomarkers from 1559 publications was manually extracted, including biomarker descriptions, clinical information, associated literature, experimental records, associated diseases, statistical indicators, etc. Importantly, we integrated many external resources to provide clinicians and researchers with the capability to further explore knowledge on these diagnostic biomarkers based on three aspects. (1) Obtain more ontology annotations of the biomarker. (2) Identify the relationship between any two or more components of diseases, drugs, genes, and variants to explore the knowledge related to precision medicine. (3) Explore the clinical application value of a specific diagnostic biomarker through online analysis of genomic and expression data from glioma cohort studies. GlioMarker provides a powerful, practical, and user-friendly web-based tool that may serve as a specialized platform for clinicians and researchers by providing rapid and comprehensive knowledge of glioma diagnostic biomarkers to subsequently facilitates high-quality research and applications.

Diagnostic, grading and prognostic role of a restricted miRNAs signature in primary and metastatic brain tumours. Discussion on their therapeutic perspectives

At present, brain tumours remain one of the "hard-to-treat" malignancies with minimal improvement in patients' survival. Recently, miRNAs have been shown to correlate with oncogenesis and metastasis and have been investigated as potential biomarkers for diagnosis, prognosis and therapy prediction in different brain malignancies. The aim of the current study was to select an accurate and affordable brain tumour detection and grading approach. In the present study, we analysed the applicability of a restricted miRNA signature that could differentiate among patients with primary as well as metastatic brain tumours. Fresh tumour tissues were collected from Bulgarian patients (n = 38), including high-grade gliomas (n = 23), low-grade gliomas (n = 10) and brain metastases (n = 5) from lung cancer. Total RNAs enriched with microRNAs were isolated and differentially expressed miRNAs were analyzed by RT-qPCR using TaqMan Advanced miRNA assay. We selected a signature of miR-21, miR-10b, miR-7, miR-491 that showed good diagnostic potential in high-grade gliomas, low-grade gliomas and brain metastases compared with normal brain tissues. Our results showed that miR-10b could reliably differentiate brain metastases from high-grade gliomas, while miR-491 could distinguish low-grade from high-grade gliomas and brain metastases from low-grade gliomas. We observed that miR-21 and miR-7 correlated with disease recurrence, survival status and the Karnofsky Performance Status. The selected signature of miR-7, miR-21, miR-10b and miR-491 could be used as a highly accurate diagnostic, grading and prognostic biomarker in differentiating various types of brain tumours. Our data suggest that the 4-miRNAs signature could be further analysed for predicting treatment response and for future miRs-based targeted therapy. The ongoing studies on miRs-based targeted therapy related to our selected miRNA signature are also reviewed.

Effect of microRNA-181b on the biological characteristics and clinical drug resistance of small-cell lung cancer by targeting angiotensin converting enzyme 2

Objective

To clarify the effect of miR‐181b on the biological function of small‐cell lung cancer (SCLC) and explore the effect of clinical resistance on SCLC.

Methods

Blood samples were collected from 30 SCLC patients and 30 non‐SCLC patients in our department from 2017 to 2019 to detect the expression level of miR‐181b.The expression level of miR‐181b was detected in SCLC cells by RT‐PCR, and screening of downstream target genes by gene chip, verification with luciferase, and Western blotting. In addition, collect the general data of 30 SCLC patients and 30 non‐SCLC patients (control group), the patients were diagnosed by pathology and undergoing EC protocol in the Department of Thoracic Surgery and Oncology of our hospital to detect the expression level of mir‐181b in different periods. Furthermore, in the SCLC cell line, EC chemotherapy was administered to detect the sensitivity of drug resistance and nondrug resistance.

Results

miR‐181b in SCLC patients was lower than in normal people as well as the drug‐sensitive cell line. ACE2 was verified as a downstream target of miR‐181b by gene chip screening. First‐line chemotherapy can promote the recovery of miR‐181b, but cannot repair to normal levels. miR‐181b can enhance the drug sensitivity of SCLC drug‐resistant cells.

Conclusion

miR‐181b directly targets ACE2 to affect the biological characteristics of SCLC. The expression level of miR‐181b is highly related to the drug resistance of SCLC, which suggests that miR‐181b could be a potential biomarker candidate for treatment efficacy of SCLC.

Systematic Analysis of FASTK Gene Family Alterations in Cancer

The FASTK family of proteins have been recently reported to play a key role in the post-transcriptional regulation of mitochondrial gene expression, including mRNA stability and translation. Accumulated studies have provided evidence that the expression of some FASTK genes is altered in certain types of cancer, in agreement with the central role of mitochondria in cancer development. Here, we obtained a pan-cancer overview of the genomic and transcriptomic alterations of FASTK genes. FASTK, FASTKD1, FASTKD3 and FASTKD5 showed the highest rates of genetic alterations. FASTK and FASTKD3 alterations consisted mainly of amplifications that were seen in more than 8% of ovarian and lung cancers, respectively. FASTKD1 and FASTKD5 were the most frequently mutated FASTK genes, and the mutations were identified in 5-7% of uterine cancers, as well as in 4% of melanomas. Our results also showed that the mRNA levels of all FASTK members were strongly upregulated in esophageal, stomach, liver and lung cancers. Finally, the protein-protein interaction network for FASTK proteins uncovers the interaction of FASTK, FASTKD2, FASTKD4 and FASTKD5 with cancer signaling pathways. These results serve as a starting point for future research into the potential of the FASTK family members as diagnostic and therapeutic targets for certain types of cancer.

mRNA and miRNA Expression Analyses of the MYC/E2F/miR-17-92 Network in the Most Common Pediatric Brain Tumors

Numerous molecular factors disrupt the correctness of the cell cycle process leading to the development of cancer due to increased cell proliferation. Among known causative factors of such process is abnormal gene expression. Nowadays in the light of current knowledge such alterations are frequently considered in the context of mRNA–miRNA correlation. One of the molecular factors with potential value in tumorigenesis is the feedback loop between MYC and E2F genes in which miR-17-5p and miR-20a from the miR-17-92 cluster are involved. The current literature shows that overexpression of the members of the OncomiR-1 are involved in the development of many solid tumors. In the present work, we investigated the expression of components of the MYC/E2F/miR-17-92 network and their closely related elements including members of MYC and E2F families and miRNAs from two paralogs of miR-17-92: miR-106b-25 and miR-106a-363, in the most common brain tumors of childhood, pilocytic astrocytoma (PA), WHO grade 1; ependymoma (EP), WHO grade 2; and medulloblastoma (MB), WHO grade 4. We showed that the highest gene expression was observed in the MYC family for MYCN and in the E2F family for E2F2. Positive correlation was observed between the gene expression and tumor grade and type, with the highest expression being noted for medulloblastomas, followed by ependymomas, and the lowest for pilocytic astrocytomas. Most members of miR-17-92, miR-106a-363 and miR-106b-25 clusters were upregulated and the highest expression was noted for miR-18a and miR-18b. The rest of the miRNAs, including miR-19a, miR-92a, miR-106a, miR-93, or miR-25 also showed high values. miR-17-5p, miR-20a obtained a high level of expression in medulloblastomas and ependymomas, while close to the control in the pilocytic astrocytoma samples. miRNA expression also depended on tumor grade and histology.

The role of MiRNA-21 in gliomas: Hope for a novel therapeutic intervention?

Gliomas are the most common primary brain tumors in adults. They are generally very resistant to treatment and are therefore associated with negative outcomes. MicroRNAs (miRNAs) are small, non-coding RNA molecules that affect many cellular processes by regulating gene expression and, post-transcriptionally, the translation of mRNAs. MiRNA-21 has been consistently shown to be upregulated in glioma and research has shown that it is involved in a wide variety of biological pathways, promoting tumor cell survival and invasiveness. Furthermore, it has been implicated in resistance to treatment, both against chemotherapy and radiotherapy. In this review, we gathered the existent data on miRNA-21 and gliomas, in terms of its expression levels, association with grade and prognosis, the pathways it involves and its targets in glioma, and finally how it leads to treatment resistance. Furthermore, we discuss how this knowledge could be applied in clinical practice in the years to come. To our knowledge, this is the first review to assess in extent and depth the role of miRNA-21 in gliomas.

Calcium ion assisted fluorescence determination of microRNA-167 using carbon dots-labeled probe DNA and polydopamine-coated Fe3O4 nanoparticles

A selective and sensitive fluorescence biosensor is described for determination of microRNA-167 using fluorescent resonant energy transfer (FRET) strategy. The FRET system comprises carbon dots (CDs, donor) labeled with probe DNA (pDNA) and polydopamine (PDA)-coated Fe₃O₄ nanoparticles (Fe₃O₄@PDA NPs, acceptor). The CDs-pDNA can be absorbed onto the surface of Fe₃O₄@PDA NPs because of the strong π interaction between pDNA and PDA. With the enhanced adsorption ability of Fe₃O₄@PDA NPs by Ca²⁺, the fluorescence intensity of CDs at 445 nm (excitation at 360 nm) is quenched. In presence of microRNA-167, the hybridized complex of CDs-pDNA-microRNA-167 will be released from the surface of Fe₃O₄@PDA NPs due to the weak π interaction of the complex and PDA. This results in the fluorescence recovery of CDs. By application of twice-magnetic separation, the biosensor shows a wide linear range of 0.5-100 nM to microRNA-167 with a 76 pM detection limit. The method was applied to the determination of microRNA-167 in samples of total microRNA extractions from A. thaliana seedlings, and the recoveries ranged from 96.4 to 98.3%.

Prognostic value of miR-21 in gliomas: comprehensive study based on meta-analysis and TCGA dataset validation

Recent studies have highlighted the value of microRNA-21 (miR-21) as a prognostic biomarker in gliomas. However, the role of miR-21 in predicting prognosis remains controversial. We performed a comprehensive study based upon a meta-analysis and The Cancer Genome Atlas (TCGA) glioma dataset validation to clarify the prognostic significance of miR-21 in glioma patients. In this study, we searched Embase, PubMed, Web of science, CNKI, SinoMed, and Wanfang databases for records up to May 2018. Relevant data were extracted to assess the correlation between miR-21 expression and survival in glioma patients. Pooled hazard ratios (HRs) with 95% confidence intervals (CIs) were used to describe association strength. We further used multivariate Cox regression analysis to assess miR-21 expression in the TCGA glioma dataset to validate the relationship between miR-21 expression and survival. Nine studies were included in the meta-analysis. Among them, eight studies provided data on overall survival (OS) with a pooled HR of 1.91 (95% CI: 1.34, 2.73), indicating that higher expression of miR-21 was significantly associated with worse OS in glioma patients; for the other study, which provided data on progression-free survival (PFS), no statistically significant HR was reported for PFS in the glioma patients (HR = 1.23, 95% CI: 0.41, 3.72). A multivariate Cox regression analysis of the miR-21 expression in the TCGA glioma dataset revealed that overexpression of miR-21 was a potential independent prognostic biomarker of poorer OS (HR = 1.27, 95% CI: 1.01, 1.59) and poorer PFS (HR = 1.46, 95% CI: 1.17, 1.82). Our findings suggest that higher expression of miR-21 is correlated with poorer glioma prognosis.

Micro RNA Molecules as Modulators of Treatment Resistance, Immune Checkpoints Controllers and Sensitive Biomarkers in Glioblastoma Multiforme

Based on genome sequencing, it is estimated that over 90% of genes stored in human genetic material are transcribed, but only 3% of them contain the information needed for the production of body proteins. This group also includes micro RNAs representing about 1%–3% of the human genome. Recent studies confirmed the hypothesis that targeting molecules called Immune Checkpoint (IC) open new opportunities to take control over glioblastoma multiforme (GBM). Detection of markers that indicate the presence of the cancer occupies a very important place in modern oncology. This function can be performed by both the cancer cells themselves as well as their components and other substances detected in the patients’ bodies. Efforts have been made for many years to find a suitable marker useful in the diagnosis and monitoring of gliomas, including glioblastoma.

Identification of biomarkers and construction of a microRNA-mRNA regulatory network for ependymoma using integrated bioinformatics analysis

Ependymomas (EPNs) are one of the most common types of malignant neuroepithelial tumors. In an effort to identify potential biomarkers involved in the pathogenesis of EPN, the mRNA expression profiles of the GSE25604, GSE50161, GSE66354, GSE74195 and GSE86574 datasets, in addition to the microRNA (miRNA/miR) expression profiles of GSE42657 were downloaded from the Gene Expression Omnibus (GEO) database. Differentially expressed genes (DEGs) and differentially expressed miRNAs (DEMs) between EPN and normal brain tissue samples were identified using the Limma package in R and GEO2R, respectively. Functional and pathway enrichment analyses were conducted using the Database for Annotation, Visualization and Integrated Discovery. A protein-protein interaction network was constructed using the Search Tool for Retrieval of Interacting Genes database, which was visualized using Cytoscape. The targeted genes of DEMs were predicted using miRWalk2.0 and a miRNA-mRNA regulatory network was constructed. Following analysis, a total of 948 DEGs and 129 DEMs were identified. Functional enrichment analysis revealed that 609 upregulated DEGs were significantly enriched in ‘PI3K-Akt signaling pathway’, while 339 downregulated DEGs were primarily involved in ‘cell junction’ and ‘retrograde endocannabinoid signaling’. In addition, 6 hub genes [cyclin dependent kinase 1, CD44 molecule (Indian blood group) (CD44), proliferating cell nuclear antigen (PCNA), MYC, synaptotagmin 1 (SYT1) and kinesin family member 4A] and 6 crucial miRNAs [homo sapiens (hsa)-miR-34a-5p, hsa-miR-449a, hsa-miR-106a-5p, hsa-miR-124-3p, hsa-miR-128-3p and hsa-miR-330-3p] were identified as biomarkers and potential therapeutic targets for EPN. Furthermore, a microRNA-mRNA regulatory network was constructed to highlight the interactions between DEMs and their target DEGs; this included the hsa-miR-449a-SYT1, hsa-miR-34a-5p-SYT1, hsa-miR-330-3p-CD44 and hsa-miR-124-3p-PCNA pairs, whose expression levels were confirmed using reverse transcription-quantitative polymerase chain reaction. In conclusion, the present study may provide important data for the investigation of the molecular mechanisms of EPN pathogenesis.

Gold nanoparticles-based biosensor can detect drought stress in tomato by ultrasensitive and specific determination of miRNAs

Drought stress can significantly affect the yield and quality of tomato production. However, the development of a sensitive and specific method for the determination of drought stress is somehow challenging since plant common morpho-physiological and biochemical characteristic are not generally specific to biotic and abiotic stresses. As a solution, the concentration of miRNAs in plant tissues can be a selective and specific indicator of plant stress. In this study, an optical biosensor based on gold nanoparticles is introduced to determine miRNA-1886 in tomato plant roots. Results showed that irrigation levels from 100% to 60% of field capacity increased the concentration of miRNA-1886 in a range from ca. 100 to 6800 fM (fM) causing a linear change in the biosensor response (R² = 0.97). Results also revealed that in contrast with plant conventional morpho-physiological and biochemical characteristic, miRNA-1886 concentration was not significantly affected (P < 0.01) by other stresses, i.e., salinity and temperature during the growth period. The biosensor introduced in this study is a reliable method to study stress-related functions of miRNAs in plants and their application in specific plant stress determination.

miR-181b/Oncostatin m axis inhibits prostate cancer bone metastasis via modulating osteoclast differentiation

The activation of osteoblasts is significantly correlated to prostate tumor bone metastasis and bone loss. Oncostatin M (OSM) could promote breast cancer metastasis to bone. However, its role and mechanism in prostate cancer bone metastasis remain unclear. MicroRNAs (miRNAs) could play important roles in cancers via post-transcriptionally regulating target genes via binding to specific sequences in the 3' UTR of downstream target genes. In the present study, we performed microarray profiling analyses to identify differentially-expressed miRNAs in preosteoclast before and after osteoclast differentiation that could target OSM. miR-181b-5p was downregulated during Raw264.7 cells differentiation into osteoclast. By direct targeting OSM 3' UTR, miR-181b-5p inhibited OSM messenger RNA expression and protein levels, subsequently decreasing IL-6 and AREG and increasing OPG, while OSM overexpression exerted an opposing effect. More importantly, co-culture with miR-181b-5p-overexpressing differentiated Raw264.7 cells suppressed proliferation, migration, and invasion of mouse prostate cancer RM-1 cells, while co-culture with OSM-overexpressing Raw264.7 cells led to opposing cellular effects. More importantly, the effects of miR-181b-5p on osteoclastogenic factors and RM-1 cells could be significantly reversed by OSM overexpression. In summary, miR-181b-5p/OSM axis could be a viable therapeutic target for patients with surgically removed primary tumors to reduce bone metastasis and prevent bone loss.

Automatic discovery of 100-miRNA signature for cancer classification using ensemble feature selection

Background

MicroRNAs (miRNAs) are noncoding RNA molecules heavily involved in human tumors, in which few of them circulating the human body. Finding a tumor-associated signature of miRNA, that is, the minimum miRNA entities to be measured for discriminating both different types of cancer and normal tissues, is of utmost importance. Feature selection techniques applied in machine learning can help however they often provide naive or biased results.

Results

An ensemble feature selection strategy for miRNA signatures is proposed. miRNAs are chosen based on consensus on feature relevance from high-accuracy classifiers of different typologies. This methodology aims to identify signatures that are considerably more robust and reliable when used in clinically relevant prediction tasks. Using the proposed method, a 100-miRNA signature is identified in a dataset of 8023 samples, extracted from TCGA. When running eight-state-of-the-art classifiers along with the 100-miRNA signature against the original 1046 features, it could be detected that global accuracy differs only by 1.4%. Importantly, this 100-miRNA signature is sufficient to distinguish between tumor and normal tissues. The approach is then compared against other feature selection methods, such as UFS, RFE, EN, LASSO, Genetic Algorithms, and EFS-CLA. The proposed approach provides better accuracy when tested on a 10-fold cross-validation with different classifiers and it is applied to several GEO datasets across different platforms with some classifiers showing more than 90% classification accuracy, which proves its cross-platform applicability.

Conclusions

The 100-miRNA signature is sufficiently stable to provide almost the same classification accuracy as the complete TCGA dataset, and it is further validated on several GEO datasets, across different types of cancer and platforms. Furthermore, a bibliographic analysis confirms that 77 out of the 100 miRNAs in the signature appear in lists of circulating miRNAs used in cancer studies, in stem-loop or mature-sequence form. The remaining 23 miRNAs offer potentially promising avenues for future research.

Electronic supplementary material

The online version of this article (10.1186/s12859-019-3050-8) contains supplementary material, which is available to authorized users.

Ratio-Based Method To Identify True Biomarkers by Normalizing Circulating ncRNA Sequencing and Quantitative PCR Data

Recent studies have indicated that circulating noncoding RNAs (ncRNAs) such as miRNAs are stable biomarkers for the diagnosis and prognosis of human diseases. However, due to low concentrations of circulating ncRNAs in blood, data normalization in plasma/serum ncRNA experiments using next-generation sequencing and quantitative real time RT-qPCR is a challenge. We found that the current normalization methods based on synthetic external spiked-in controls or published endogenous miRNA controls are inappropriate as they are not stably expressed and therefore fail to reliably detect differentially expressed ncRNAs. Using the alternative of individual ncRNAs as biomarkers, we considered a ratio-based normalization method calculated taking the ratio of any two ncRNAs in the same sample and used the resulting ratios as biomarkers. We mathematically verified the method to be independent of spiked-in and internal controls, and more robust than existing reference control based normalization methods to identify differentially expressed ncRNAs as potential biomarkers for human diseases. Thus, the ratio-based method can solve the difficult normalization problem for circuiting ncRNA data to identify reliable biomarkers to meet real clinical practice.

Significance of liquid biopsy in glioblastoma - A review

Glioblastoma (GBM) is the most common and most aggressive primary malignant brain tumor with a 16-24 -months overall survival time (OS). Effective management is hindered by intratumoral heterogeneity, a characteristic trait of GBM which results in subpopulations of cells with altered therapeutic responsiveness, different invasiveness and growth potential. Correct initial molecular profiling of the tumor, as well as following its molecular biological changes are further impeded by the intracranial location of the tumors, hence the risks of surgical interventions. Radiological examination, the sole non-invasive method of obtaining information about the tumors, also has limitations. This review article aims to summarize the currently available information about the promising applicability of liquid biopsy, extracellular vesicles (EVs), and circulating cell-free nucleic acids (cf-NAs) in GBM patients. Liquid biopsy is a quick and inexpensive way of obtaining exceptionally relevant information about tumors, and can be performed multiple times during the clinical course of the disease. Furthermore, integrating analyses of EVs and related cf-NAs in clinical practice might also help to establish diagnosis in a non-invasive manner, and complex oncotherapy could be indicated in the future without high-risk neurosurgical interventions.

Prognostic Significance of MicroRNAs in Glioma: A Systematic Review and Meta-Analysis

PURPOSE

Different microRNAs (miRs) have been demonstrated to relate with the outcome of glioma patients, while the conclusions are inconsistent. We perform a meta-analysis to clarify the relationship between different miRs and prognosis of glioma.

METHODS

Related studies were retrieved from PubMed, Embase, and Cochrane Library. Pooled hazard ratios (HRs) of different miRs expression for survival and 95% confidence intervals (CIs) were calculated using random-effects model.

RESULTS

A total of 15 miRs with 4708 glioma patients were ultimately included. Increased expression of miR-15b (HR, 1.584; 95% CI, 1.199-2.092), 21 (HR, 1.591; 95% CI, 1.278-1.981), 148a (HR, 1.122; 95% CI, 1.023-1.231), 196 (HR, 1.877; 95% CI, 1.033-3.411), 210 (HR, 1.251; 95% CI, 1.010-1.550), and 221 (HR, 1.269; 95% CI, 1.054-1.527) or decreased expression of miR-106a (HR, 0.809; 95% CI, 0.655-0.998) and 124 (HR, 0.833; 95% CI, 0.729-0.952) was correlated with poor outcome of glioma patients.

CONCLUSIONS

miR-15b, 21, 148a, 196, 210, 221, 106a, and 124 are valuable biomarkers for the prognosis of glioma which might be used in clinical settings.

MicroRNAs, Hypoxia and the Stem-Like State as Contributors to Cancer Aggressiveness

MicroRNAs (miRNAs) are small non-coding RNA molecules that play key regulatory roles in cancer acting as both oncogenes and tumor suppressors. Due to their potential roles in improving cancer prognostic, predictive, diagnostic and therapeutic approaches, they have become an area of intense research focus in recent years. Several studies have demonstrated an altered expression of several miRNAs under hypoxic condition and even shown that the hypoxic microenvironment drives the selection of a more aggressive cancer cell population through cellular adaptations referred as the cancer stem-like cell. These minor fractions of cells are characterized by their self-renewal abilities and their ability to maintain the tumor mass, suggesting their crucial roles in cancer development. This review aims to highlight the interconnected role between miRNAs, hypoxia and the stem-like state in contributing to the cancer aggressiveness as opposed to their independent contributions, and it is based in four aggressive tumors, namely glioblastoma, cervical, prostate, and breast cancers.

Prognostic role of microRNA-155 expression in gliomas: A meta-analysis

Recent studies have reported that microRNA-155 (miR-155) is linked to the clinical outcomes of many tumors. However, its role in prognosis of gliomas remains unclear. This meta-analysis aims to evaluate the prognostic value of miR-155 in the survival of patients with gliomas. Hazard ratios (HRs) with 95% confidence intervals (CIs) for overall survival (OS) were pooled with random effects or fixed effects models on the basis of heterogeneity. Subgroup analysis and sensitivity analysis were performed to elucidate the possible confounding factors and investigate the source of heterogeneity. In addition, we assessed publication bias using the Begg's funnel plots, Egger's test, and Begg's test. Only non-laboratory studies were considered for our analysis. 9 studies from 6 articles containing 1259 glioma patients were included. The pooled HR of elevated miR-155 for OS in patients with gliomas was 1.40 (95%CI [1.19-1.63], P < 0.001) (I-squared = 52.4%, P = 0.032) suggesting that miR-155 might be a promising biomarker for the prognosis of gliomas in future clinical applications.

miR-454-3p Is an Exosomal Biomarker and Functions as a Tumor Suppressor in Glioma

Glioma is the most common type of primary malignant brain tumor in adults. Our previous work discovered that plasma miR-454-3p may have some advantages in glioma prognosis, but the clinical significance and the regulatory mechanism of miR-454-3p in glioma have not been systematically investigated, especially regarding the relationship between circulating and tissue miR-454-3p. The expression level of miR-454-3p in glioma serum and tissues was analyzed through quantitative real-time PCR (qRT-PCR). Cell-Counting Kit 8 (CCK-8), wound healing, transwell invasion, apoptosis, and immunofluorescence assays were used to assess the role of miR-454-3p in glioma cancer cells. ATG12 was selected as the target gene of miR-454-3p by bioinformatic analysis. The relationship between ATG12 and miR-454-3p was further validated by luciferase reporter assays and Western blot analysis. miR-454-3p was significantly downregulated in tumor tissues, while it was remarkably upregulated in exosomes from the same patients with glioma. The area under curve (AUC) of exosomal miR-454-3p for glioma diagnosis was 0.8663. The exosomal miR-454-3p was prominently lower in the postoperative serums than that in the preoperative serums. High miR-454-3p expression in exosomes or low miR-454-3p expression in tissue was associated with poor prognosis. Restored expression of miR-454-3p suppressed cell proliferation, migration, invasion, and autophagy in glioma. ATG12 was validated as a direct target of miR-454-3p. The overexpression of ATG12 could partially reverse the effects induced by miR-454-3p suppression. Our data indicate that miR-454-3p may serve as an exosomal biomarker and may be developed into a novel treatment for glioma.

A 4-miRNA signature to predict survival in glioblastomas

Glioblastomas are among the most lethal cancers; however, recent advances in survival have increased the need for better prognostic markers. microRNAs (miRNAs) hold great prognostic potential being deregulated in glioblastomas and highly stable in stored tissue specimens. Moreover, miRNAs control multiple genes representing an additional level of gene regulation possibly more prognostically powerful than a single gene. The aim of the study was to identify a novel miRNA signature with the ability to separate patients into prognostic subgroups. Samples from 40 glioblastoma patients were included retrospectively; patients were comparable on all clinical aspects except overall survival enabling patients to be categorized as short-term or long-term survivors based on median survival. A miRNome screening was employed, and a prognostic profile was developed using leave-one-out cross-validation. We found that expression patterns of miRNAs; particularly the four miRNAs: hsa-miR-107_st, hsa-miR-548x_st, hsa-miR-3125_st and hsa-miR-331-3p_st could determine short- and long-term survival with a predicted accuracy of 78%. Heatmap dendrograms dichotomized glioblastomas into prognostic subgroups with a significant association to survival in univariate (HR 8.50; 95% CI 3.06–23.62; p<0.001) and multivariate analysis (HR 9.84; 95% CI 2.93–33.06; p<0.001). Similar tendency was seen in The Cancer Genome Atlas (TCGA) using a 2-miRNA signature of miR-107 and miR-331 (miR sum score), which were the only miRNAs available in TCGA. In TCGA, patients with O6-methylguanine-DNA-methyltransferase (MGMT) unmethylated tumors and low miR sum score had the shortest survival. Adjusting for age and MGMT status, low miR sum score was associated with a poorer prognosis (HR 0.66; 95% CI 0.45–0.97; p = 0.033). A Kyoto Encyclopedia of Genes and Genomes analysis predicted the identified miRNAs to regulate genes involved in cell cycle regulation and survival. In conclusion, the biology of miRNAs is complex, but the identified 4-miRNA expression pattern could comprise promising biomarkers in glioblastoma stratifying patients into short- and long-term survivors.

Selectivity enhancements in gel-based DNA-nanoparticle assays by membrane-induced isotachophoresis: thermodynamics versus kinetics

Selectivity against mutant nontargets with a few mismatches remains challenging in nucleic acid sensing. Sensitivity enhancement by analyte concentration does not improve selectivity because it affects targets and nontargets equally. Hydrodynamic or electrical shear enhanced selectivity is often accompanied by substantial losses in target signals, thereby leading to poor limits of detection. We introduce a platform based on depletion isotachophoresis in agarose gel generated by an ion-selective membrane that allows both selectivity and sensitivity enhancement with a two-step assay involving concentration polarization at an ion-selective membrane. By concentrating both the targets and probe-functionalized nanoparticles by ion enrichment at the membrane, the effective thermodynamic dissociation constant is lowered from 40 nM to below 500 pM, and the detection limit is 10 pM as reported previously. A dynamically optimized ion depletion front is then generated from the membrane with a high electrical shear force to selectively and irreversibly dehybridize nontargets. The optimized selectivity against a two-mismatch nontarget (in a 35-base pairing sequence) is shown to be better than the thermodynamic equilibrium selectivity by more than a hundred-fold, such that there is no detectable signal from the two-mismatch nontarget. We offer empirical evidence that irreversible cooperative dehybridization plays an important role in this kinetic selectivity enhancement and that mismatch location controls the optimum selectivity even when there is little change in the corresponding thermodynamic dissociation constant.

Prognostic value of miRNA-181a/b in colorectal cancer: a meta-analysis

AIMS

miR-181a and miR-181b have been investigated as prognostic biomarkers of colorectal cancer (CRC). However, there is controversy about the role of miR-181a and miR-181b in predicting CRC prognosis. Therefore, we performed this meta-analysis to evaluate prognostic values of miR-181a and miR-181b in CRC patients.

MATERIALS & METHODS

Studies were systemically searched from publications and analyzed, and 999 CRC cases in nine studies were examined in this meta-analysis.

RESULTS

Hazard ratio for overall survival of high miR-181a and miR-181b expression in CRC was 1.65. More prominent predictive effects were observed in black people, miR-181b group and small-sample-size group.

CONCLUSION

High levels of miR-181a and miR-181b predict poor overall survival in CRC patients. miR-181a and miR-181b are promising biomarkers for CRC prognosis.

MicroRNA Regulation of Glycolytic Metabolism in Glioblastoma

Glioblastoma (GBM) is the most aggressive and common malignant brain tumour in adults. A well-known hallmark of GMB and many other tumours is aerobic glycolysis. MicroRNAs (miRNAs) are a class of short nonprotein coding sequences that exert posttranscriptional controls on gene expression and represent critical regulators of aerobic glycolysis in GBM. In GBM, miRNAs regulate the expression of glycolytic genes directly and via the regulation of metabolism-associated tumour suppressors and oncogenic signalling pathways. This review aims to establish links between miRNAs expression levels, the expression of GBM glycolytic regulatory genes, and the malignant progression and prognosis of GBM. In this review, the involvement of 25 miRNAs in the regulation of glycolytic metabolism of GBM is discussed. Seven of these miRNAs have been shown to regulate glycolytic metabolism in other tumour types. Further eight miRNAs, which are differentially expressed in GBM, have also been reported to regulate glycolytic metabolism in other cancer types. Thus, these miRNAs could serve as potential glycolytic regulators in GBM but will require functional validation. As such, the characterisation of these molecular and metabolic signatures in GBM can facilitate a better understanding of the molecular pathogenesis of this disease.

Prognostic role of miR-17-92 family in human cancers: evaluation of multiple prognostic outcomes

Recent evidence indicates that miR-17–92 family might be an essential prognostic biomarker for human cancers. However, results are still inconsistent. We therefore performed a meta-analysis to evaluate the predictive role of miR-17–92 family in human cancer prognosis. We searched literatures published before March 31th, 2017 inPubMed, Cochrane and Embase databases. Twenty six studies were included in our analyses. The overall hazard ratios (HRs) showed that high expression level of miR-17-92 family was a predictor of poor overall survival (OS): adjusted HRs = 1.71, 95% confidence intervals (CIs): 1.39–2.11, p < 0.00001, and poor disease-free survival (DFS): adjusted HRs = 2.29, 95% CIs: 1.41–3.72, p = 0.0008. However, no association between miR-17-92 family expression and cancer progress-free survival (PFS) was found (p > 0.05). Subgroup analyses showed that high expression of miR-17-92 family was associated with poor OS (adjusted HRs = 1.89, 95% CIs: 1.43–2.49, p < 0.00001) and DFS (adjusted HRs = 2.83, 95% CIs: 1.59–5.04, p = 0.0003) among the Asian, and no association was found for the Caucasian (p > 0.05). Besides, the HRs of miR-17-92 family high expression in tissue and serum samples was 1.68 (1.35–2.09) and 2.20 (1.08–4.46) for OS, and 1.73 (0.80–3.74) and 3.37 (2.25–5.02) for DFS. It also found that high expression of miR-17-92 family predicted a poor OS in breast cancer, esophageal squamous cell carcinoma, lymphoma and other cancers. Findings suggest that miR-17-92 family can be an effective predictor for prognosis prediction in cancer patients.

Differential expression of miR16 in glioblastoma and glioblastoma stem cells: their correlation with proliferation, differentiation, metastasis and prognosis

The function of miR16 in multiforme glioblastoma multiforme (GBM) and its stem cells (GSCs) remains elusive. To this end, we investigated the patterns of miR16 expression in these cells and their correlation with malignant behaviors and clinical outcomes. The levels of miR16 and its targeted genes in tumor tissue of GBM and GBM SGH44, U87, U251 cells as well as their stem cell counterparts were measured by qRT–PCR or western blot or immunohistochemistry. Luciferase reporter assay was used to confirm the binding of miR16 to 3′-UTR of its target genes. The effects of miR16 on malignant behaviors were investigated, including tumor cell viability, soft-agar colony formation, GSCs Matrigel colony forming and migration and invasion as well as nude mice xenograft model. Differentially expression patterns of miR16 in glioblastoma cells and GSCs cells were found in this study. Changes of miR16 targeted genes, Bcl2 (B cell lymphoma 2), CDK6 (Cyclin-dependent kinase 6), CCND1 (cyclin D1), CCNE1 (cyclin E1) and SOX5 were confirmed in glioblastoma cell lines and tissue specimens. In vitro and in vivo studies showed that tumor cell proliferation was inhibited by miR16 mimic, but enhanced by miR16 inhibitor. The expression level of miR16 positively correlates with GSCs differentiation, but negatively with the abilities of migration, motility, invasion and colony formation in glioblastoma cells. The inhibitory effects of miR16 on its target genes were also found in nude mice xenograft model. Our findings revealed that the miR16 functions as a tumor suppressor in GSCs and its association with prognosis in GBM.

MiR-181b modulates EGFR-dependent VCAM-1 expression and monocyte adhesion in glioblastoma

Tumor-associated macrophages (TAMs) originate as circulating monocytes, and are recruited to gliomas, where they facilitate tumor growth and migration. Understanding the interaction between TAM and cancer cells may identify therapeutic targets for glioblastoma multiforme (GBM). Vascular cell adhesion molecule-1 (VCAM-1) is a cytokine-induced adhesion molecule expressed on the surface of cancer cells, which is involved in interactions with immune cells. Analysis of the glioma patient database and tissue immunohistochemistry showed that VCAM-1 expression correlated with the clinico-pathological grade of gliomas. Here, we found that VCAM-1 expression correlated positively with monocyte adhesion to GBM, and knockdown of VCAM-1 abolished the enhancement of monocyte adhesion. Importantly, upregulation of VCAM-1 is dependent on epidermal-growth-factor-receptor (EGFR) expression, and inhibition of EGFR effectively reduced VCAM-1 expression and monocyte adhesion activity. Moreover, GBM possessing higher EGFR levels (U251 cells) had higher VCAM-1 levels compared to GBMs with lower levels of EGFR (GL261 cells). Using two- and three-dimensional cultures, we found that monocyte adhesion to GBM occurs via integrin α4β1, which promotes tumor growth and invasion activity. Increased proliferation and tumor necrosis factor-α and IFN-γ levels were also observed in the adherent monocytes. Using a genetic modification approach, we demonstrated that VCAM-1 expression and monocyte adhesion were regulated by the miR-181 family, and lower levels of miR-181b correlated with high-grade glioma patients. Our results also demonstrated that miR-181b/protein phosphatase 2A-modulated SP-1 de-phosphorylation, which mediated the EGFR-dependent VCAM-1 expression and monocyte adhesion to GBM. We also found that the EGFR-dependent VCAM-1 expression is mediated by the p38/STAT3 signaling pathway. Our study suggested that VCAM-1 is a critical modulator of EGFR-dependent interaction of monocytes with GBM, which raises the possibility of developing effective and improved therapies for GBM.

Migration-prone glioma cells show curcumin resistance associated with enhanced expression of miR-21 and invasion/anti-apoptosis-related proteins

In study, the expression patterns and functional differences between an original glioma cell population (U251 and U87) and sublines (U251-P10, U87-P10) that were selected to be migration-prone were investigated. The expressions levels of VEGF and intracellular adhesion molecule-1 (ICAM-1) were increased in the migration-prone sublines as well as in samples from patients with high-grade glioma when compared to those with low-grade glioma. In addition, cells of the migration-prone sublines showed increased expression of the oncogenic microRNA. miR-21, which was also associated with more advanced clinical pathological stages in the patient tissue specimens. Treatment of U251 cells with an miR-21 mimic dramatically enhanced the migratory activity and expression of anti-apoptotic proteins. Furthermore, treatment with curcumin decreased the miR-21 level and anti-apoptotic protein expression, and increased the expression of pro-apoptosis proteins and microtubule-associated protein light chain 3-II (LC3-II) in U251 cells. The migration-prone sublines showed decreased induction of cell death markers in response to curcumin treatment. Finally, U251-P10 cells showed resistance against curcumin treatment. These results suggest that miR-21 is associated with regulation of the migratory ability and survival in human glioma cells. These findings suggest novel mechanisms of malignancy and new potential combinatorial strategies for the management of malignant glioma.

An update on the epigenetics of glioblastomas

Glioblastomas, also known as glioblastoma multiforme (GBM), are the most aggressive and malignant type of primary brain tumor in adults, exhibiting notable variability at the histopathological, genetic and epigenetic levels. Recently, epigenetic alterations have emerged as a common hallmark of many tumors, including GBM. Considering that a deeper understanding of the epigenetic modifications that occur in GBM may increase the knowledge regarding the tumorigenesis, progression and recurrence of this disease, in this review we discuss the recent major advances in GBM epigenetics research involving histone modification, glioblastoma stem cells, DNA methylation, noncoding RNAs expression, including their main alterations and the use of epigenetic therapy as a valid option for GBM treatment.

Expression level of miRNAs on chromosome 14q32.31 region correlates with tumor aggressiveness and survival of glioblastoma patients

The 54 microRNAs (miRNAs) within the DLK-DIO3 genomic region on chromosome 14q32.31 (cluster-14-miRNAs) are organized into sub-clusters 14A and 14B. These miRNAs are downregulated in glioblastomas and might have a tumor suppressive role. Any association between the expression levels of cluster-14-miRNAs with overall survival (OS) is undetermined. We randomly selected miR-433, belonging to sub-cluster 14A and miR-323a-3p and miR-369-3p, belonging to sub-cluster 14B, and assessed their role in glioblastomas in vitro and in vivo. We also determined the expression level of cluster-14-miRNAs in 27 patients with newly diagnosed glioblastoma, and analyzed the association between their level of expression and OS. Overexpression of miR-323a-3p and miR-369-3p, but not miR-433, in glioblastoma cells inhibited their proliferation and migration in vitro. Mice implanted with glioblastoma cells overexpressing miR323a-3p and miR369-3p, but not miR433, exhibited prolonged survival compared to controls (P = .003). Bioinformatics analysis identified 13 putative target genes of cluster-14-miRNAs, and real-time RT-PCR validated these findings. Pathway analysis of the putative target genes identified neuregulin as the most enriched pathway. The expression level of cluster-14-miRNAs correlated with patients' OS. The median OS was 8.5 months for patients with low expression levels and 52.7 months for patients with high expression levels (HR 0.34; 95 % CI 0.12-0.59, P = .003). The expression level of cluster-14-miRNAs correlates directly with OS, suggesting a role for this cluster in promoting aggressive behavior of glioblastoma, possibly through ErBb/neuregulin signaling.

Prognostic role of microRNA-21 expression in gliomas: a meta-analysis

MicroRNA-21 (miRNA-21) has recently been shown to be a promising prognostic tumor biomarker. However, few studies have not supported this idea and have shown inconsistent data. Thus, we conducted a meta-analysis to elucidate the predictive value of miRNA-21 in gliomas. The relevant studies were identified by performing online search in PubMed, EMBASE and Web of Science databases up to Apr 2016. This meta-analysis study included seven eligible studies, consisting of 1121 gliomas and 533 glioblastoma multiforme (GBM) patients. Heterogeneity between studies was assessed using Egger's and Begg's test. Hazard ratios (HRs) with 95 % confidence intervals (CIs) for overall survival (OS), which compared the expression levels of miRNA-21 in patients with gliomas, were extracted and estimated. Our analysis revealed that the high expression of miRNA-21 is associated with the worse OS in gliomas. Further subgroup analysis indicated that increased expression of miRNA-21 was also associated with OS in GBM patients. Moreover, we observed a correlation between miRNA-21 expression and the World Health Organization defined gliomas grading system (WHO grade). Besides, high miRNA-21 expression was significantly correlated with lowered OS both in the Asian group and non-Asian group. In the cut-off subgroup analysis, both mean cut off value and median cut off value were significantly associated with OS. The expression level of miRNA-21 was not high in low KPS (Karnofsky score) group. miRNA-21 appears to be a promising biomarker for predicting the progression of patients with gliomas or GBM. However, due to the limited sample size, further prospective or retrospective multi-center well designed studies with adequate sample size should be conducted to verify its definite prognostic value.

MicroRNAs in glioblastoma multiforme pathogenesis and therapeutics

Glioblastoma multiforme (GBM) is the most common and lethal cancer of the adult brain, remaining incurable with a median survival time of only 15 months. In an effort to identify new targets for GBM diagnostics and therapeutics, recent studies have focused on molecular phenotyping of GBM subtypes. This has resulted in mounting interest in microRNAs (miRNAs) due to their regulatory capacities in both normal development and in pathological conditions such as cancer. miRNAs have a wide range of targets, allowing them to modulate many pathways critical to cancer progression, including proliferation, cell death, metastasis, angiogenesis, and drug resistance. This review explores our current understanding of miRNAs that are differentially modulated and pathologically involved in GBM as well as the current state of miRNA-based therapeutics. As the role of miRNAs in GBM becomes more well understood and novel delivery methods are developed and optimized, miRNA-based therapies could provide a critical step forward in cancer treatment.

MicroRNA-124-3p regulates cell proliferation, invasion, apoptosis, and bioenergetics by targeting PIM1 in astrocytoma

The PIM1 protein is an important regulator of cell proliferation, the cell cycle, apoptosis, and metabolism in various human cancers. MicroRNAs (miRNAs) are powerful post‐transcriptional gene regulators that function through translational repression or transcript destabilization. Therefore, we aimed to identify whether a close relationship exists between PIM1 and miRNAs. PIM1 protein levels and mRNA levels were significantly upregulated in astrocytoma tissues, indicating the oncogenic role of PIM1 in astrocytoma. Further bioinformatics analysis indicated that miR‐124‐3p targeted the 3′‐UTR of PIM1. We also observed an inverse correlation between the miR‐124‐3p levels and PIM1 protein or mRNA levels in astrocytoma samples. Next, we experimentally confirmed that miR‐124‐3p directly recognizes the 3′‐UTR of the PIM1 transcript and regulates PIM1 expression at both the protein and mRNA levels. Furthermore, we examined the biological consequences of miR‐124‐3p targeting PIM1 in vitro. We showed that the repression of PIM1 in astrocytoma cancer cells by miR‐124‐3p suppressed proliferation, invasion, and aerobic glycolysis and promoted apoptosis. We observed that the restoration or inhibition of PIM1 activity resulted in effects that were similar to those induced by miR‐124‐3p inhibitors or mimics in cancer cells. Finally, overexpression of PIM1 rescued the inhibitory effects of miR‐124‐3p. In summary, these findings aid in understanding the tumor‐suppressive role of miR‐124‐3p in astrocytoma pathogenesis through the inhibition of PIM1 translation.

Systems medicine in colorectal cancer: from a mathematical model toward a new type of clinical trial

Current colorectal cancer (CRC) treatment guidelines are primarily based on clinical features, such as cancer stage and grade. However, outcomes may be improved using molecular treatment guidelines. Potentially useful biomarkers include driver mutations and somatically inherited alterations, signaling proteins (their expression levels and (post) translational modifications), mRNAs, micro‐RNAs and long noncoding RNAs. Moving to an integrated system is potentially very relevant. To implement such an integrated system: we focus on an important region of the signaling network, immediately above the G1‐S restriction point, and discuss the reconstruction of a Molecular Interaction Map and interrogating it with a dynamic mathematical model. Extensive model pretraining achieved satisfactory, validated, performance. The model helps to propose future target combination priorities, and restricts drastically the number of drugs to be finally tested at a cellular, in vivo, and clinical‐trial level. Our model allows for the inclusion of the unique molecular profiles of each individual patient's tumor. While existing clinical guidelines are well established, dynamic modeling may be used for future targeted combination therapies, which may progressively become part of clinical practice within the near future. WIREs Syst Biol Med 2016, 8:314–336. doi: 10.1002/wsbm.1342

This article is categorized under: 1

Biological Mechanisms > Cell Signaling

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Analytical and Computational Methods > Computational Methods

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Translational, Genomic, and Systems Medicine > Translational Medicine

Network analysis of microRNAs, transcription factors, target genes and host genes in human anaplastic astrocytoma

Numerous studies have investigated the roles played by various genes and microRNAs (miRNAs) in neoplasms, including anaplastic astrocytoma (AA). However, the specific regulatory mechanisms involving these genes and miRNAs remain unclear. In the present study, associated biological factors (miRNAs, transcription factors, target genes and host genes) from existing studies of human AA were combined methodically through the interactions between genes and miRNAs, as opposed to studying one or several. Three regulatory networks, including abnormally expressed, related and global networks were constructed with the aim of identifying significant gene and miRNA pathways. Each network is composed of three associations between miRNAs targeted at genes, transcription factors (TFs) regulating miRNAs and miRNAs located on their host genes. Among these, the abnormally expressed network, which involves the pathways of previously identified abnormally expressed genes and miRNAs, partially indicated the regulatory mechanism underlying AA. The network contains numerous abnormal regulation associations when AA emerges. By modifying the abnormally expressed network factors to a normal expression pattern, the faulty regulation may be corrected and tumorigenesis of AA may be prevented. Certain specific pathways are highlighted in AA, for example PTEN which is targeted by miR-21 and miR-106b, regulates miR-25 which in turn targets TP53. PTEN and miR-21 have been observed to form feedback loops. Furthermore, by comparing and analyzing the pathway predecessors and successors of abnormally expressed genes and miRNAs in three networks, similarities and differences of regulatory pathways may be identified and proposed. In summary, the present study aids in elucidating the occurrence, mechanism, prevention and treatment of AA. These results may aid further investigation into therapeutic approaches for this disease.

ExRNA in Biofluids as Biomarkers for Brain Tumors

Patients with high-grade gliomas and glioblastomas (GBMs) have poor survival despite optimal surgical and drug therapy. Minimally invasive diagnostic biomarkers would enable early diagnosis and tumor-specific treatments for 'personalized targeted' therapy, and would create the basis for response tracking in patients with GBM. Extracellular vesicles (EVs) isolated from cerebrospinal fluid and blood contain glioma-specific molecules, including tumor-derived EV RNAs that are detectable in small copy numbers in these biofluids. EV RNA mutations or expression changes are also detectable, the analysis of which gives rise to 'liquid biopsy' tumor profiling.

Glioma Stem Cells and Their Microenvironments: Providers of Challenging Therapeutic Targets

Malignant gliomas are aggressive brain tumors with limited therapeutic options, possibly because of highly tumorigenic subpopulations of glioma stem cells. These cells require specific microenvironments to maintain their “stemness,” described as perivascular and hypoxic niches. Each of those niches induces particular signatures in glioma stem cells (e.g., activation of Notch signaling, secretion of VEGF, bFGF, SDF1 for the vascular niche, activation of HIF2α, and metabolic reprogramming for hypoxic niche). Recently, accumulated knowledge on tumor-associated macrophages, possibly delineating a third niche, has underlined the role of immune cells in glioma progression, via specific chemoattractant factors and cytokines, such as macrophage-colony stimulation factor (M-CSF). The local or myeloid origin of this new component of glioma stem cells niche is yet to be determined. Such niches are being increasingly recognized as key regulators involved in multiple stages of disease progression, therapy resistance, immune-escaping, and distant metastasis, thereby substantially impacting the future development of frontline interventions in clinical oncology. This review focuses on the microenvironment impact on the glioma stem cell biology, emphasizing GSCs cross talk with hypoxic, perivascular, and immune niches and their potential use as targeted therapy.

MicroRNA as potential biomarkers in Glioblastoma

Glioblastoma is the most aggressive and lethal tumour of the central nervous system and as such the identification of reliable prognostic and predictive biomarkers for patient survival and tumour recurrence is paramount. MicroRNA detection has rapidly emerged as potential biomarkers, in patients with glioblastoma. Over the last decade, analysis of miRNA in laboratory based studies have yielded several candidates as potential biomarkers however, the accepted use of these candidates in the clinic is yet to be validated. Here we will examine the use of miRNA signatures to improve glioblastoma stratification into subgroups and summarise recent advances made in miRNA examination as potential biomarkers for glioblastoma progression and recurrence.

Upregulation of miR-181s reverses mesenchymal transition by targeting KPNA4 in glioblastoma

The goal of this work was to explore the most effective miRNAs affecting glioblastoma multiforme (GBM) phenotype transition and malignant progression. We annotated 491 TCGA samples’ miRNA expression profiles according to their mRNA-based subtypes and found that the mesenchymal tumors had significantly decreased miR-181 family expression compared with the other three subtypes while the proneural subtype harbored extremely high miR-181 family expression. Patients with high miR-181 family expression had longer overall survival (p = 0.0031). We also confirmed that NF-κB-targeting genes and the EMT (epithelial-mesenchymal transition) pathway were inversely correlated with miR-181 family expression and that the entire miR-181 family inhibited glioma cell invasion and proliferation; of these, miR-181b was the most effective suppressor. Furthermore, miR-181b was validated to suppress EMT by targeting KPNA4 and was associated with survival outcome in the TCGA and CGGA datasets and in another independent cohort. The EMT-inhibitory effect of miR-181b was lost after KPNA4 expression was restored. We also identified the antitumorigenic activity of miR-181b in vitro and in vivo. Our results showed that miR-181 family expression was closely correlated with TCGA subtypes and patients’ overall survival, indicating that miR-181b, a tumor-suppressive miRNA, could be a novel therapeutic candidate for treating gliomas.

The Use of Three Long Non-Coding RNAs as Potential Prognostic Indicators of Astrocytoma

Long noncoding RNAs (lncRNAs) are pervasively transcribed and play a key role in tumorigenesis. The aim of the study was to determine the lncRNA expression profile in astrocytomas and to assess its potential clinical value. We performed a three-step analysis to establish the lncRNA profile for astrocytoma: a) the lncRNA expression was examined on 3 astrocytomas as well as 3 NATs (normal adjacent tissues) using the lncRNA microarray; b) the top-hits were validated in 40 astrocytomas (WHO grade II-IV) by quantitative real time-PCR (qRT-PCR); c) the hits with significant differences were re-evaluated using qRT-PCR in 90 astrocytomas. Finally, 7 lncRNAs were found to have a significantly different expression profile in astrocytoma samples compared to the NAT samples. Unsupervised clustering analysis further revealed the potential of the 7-lncRNA profile to differentiate between tumors and NAT samples. The upregulation of ENST00000545440 and NR_002809 was associated with advanced clinical stages of astrocytoma. Using Kaplan-Meier survival analysis, we showed that the low expression of BC002811 or XLOC_010967, or the high expression of NR_002809 was significantly associated with poor patient survival. Moreover, Cox proportional hazard regression analysis revealed that this prognostic impact was independent of other clinicopathological factors. Our results indicate that the lncRNA profile may be a potential prognostic biomarker for the prediction of post-surgical outcomes.

The role of microRNA in nutritional control

MicroRNAs (miRNAs) are one of a growing class of noncoding RNAs that are involved in the regulation of a wide range of metabolic processes including cellular differentiation, cell proliferation and apoptosis. The generation of miRNA is regulated in complex ways, for example by small interfering RNAs (small nucleolar and nuclear RNAs) and various other metabolites. This complexity of control is likely to explain how a relatively small part of the DNA that codes for proteins has enabled the evolution of such complex organisms as mammals. Non-protein-coding DNA is therefore thought to carry the memory of early evolutionary steps that led to progressively complex metabolic controls. Clinically, miRNAs are becoming increasingly important following the recognition that some congenital abnormalities can be traced to defects in miRNA processing. The potential for manipulating metabolism and affecting disease processes by the pharmaceutical or biological targeting of specific miRNA pathways is now being tested. miRNAs are also released into the extracellular milieu after packaging by cells into nano-sized extracellular vesicles. Such vesicles can be taken up by adjacent and possibly more distant cells, thereby allowing coordinated intercellular communication in specific tissues. Extracellular miRNAs found in the blood stream may also serve as novel biomarkers for both diagnosing specific forms of cancer and assessing the likelihood of metastasis, and as powerful prognostic indices for various cancers. Here, we discuss the role of intracellular and extracellular miRNAs in nutritional control of various (patho)physiological processes. In this review, we provide an update of the presentations from the 25th Marabou Symposium (Stockholm, 14-16 June 2013) entitled 'Role of miRNA in health and nutrition', attended by 50 international experts

Integrative Analysis with Monte Carlo Cross-Validation Reveals miRNAs Regulating Pathways Cross-Talk in Aggressive Breast Cancer

In this work an integrated approach was used to identify functional miRNAs regulating gene pathway cross-talk in breast cancer (BC). We first integrated gene expression profiles and biological pathway information to explore the underlying associations between genes differently expressed among normal and BC samples and pathways enriched from these genes. For each pair of pathways, a score was derived from the distribution of gene expression levels by quantifying their pathway cross-talk. Random forest classification allowed the identification of pairs of pathways with high cross-talk. We assessed miRNAs regulating the identified gene pathways by a mutual information analysis. A Fisher test was applied to demonstrate their significance in the regulated pathways. Our results suggest interesting networks of pathways that could be key regulatory of target genes in BC, including stem cell pluripotency, coagulation, and hypoxia pathways and miRNAs that control these networks could be potential biomarkers for diagnostic, prognostic, and therapeutic development in BC. This work shows that standard methods of predicting normal and tumor classes such as differentially expressed miRNAs or transcription factors could lose intrinsic features; instead our approach revealed the responsible molecules of the disease.