Altered MicroRNA Expression Is Associated with Tumor Grade, Molecular Background and Outcome in Childhood Infratentorial Ependymoma

Crosstalk between Noncoding RNAs and the Epigenetics Machinery in Pediatric Tumors and Their Microenvironment

According to the World Health Organization, every year, an estimated 400,000+ new cancer cases affect children under the age of 20 worldwide. Unlike adult cancers, pediatric cancers develop very early in life due to alterations in signaling pathways that regulate embryonic development, and environmental factors do not contribute much to cancer development. The highly organized complex microenvironment controlled by synchronized gene expression patterns plays an essential role in the embryonic stages of development. Dysregulated development can lead to tumor initiation and growth. The low mutational burden in pediatric tumors suggests the predominant role of epigenetic changes in driving the cancer phenotype. However, one more upstream layer of regulation driven by ncRNAs regulates gene expression and signaling pathways involved in the development. Deregulation of ncRNAs can alter the epigenetic machinery of a cell, affecting the transcription and translation profiles of gene regulatory networks required for cellular proliferation and differentiation during embryonic development. Therefore, it is essential to understand the role of ncRNAs in pediatric tumor development to accelerate translational research to discover new treatments for childhood cancers. This review focuses on the role of ncRNA in regulating the epigenetics of pediatric tumors and their tumor microenvironment, the impact of their deregulation on driving pediatric tumor progress, and their potential as effective therapeutic targets.

The clinical utility of dysregulated microRNA expression in paediatric solid tumours

MicroRNAs (miRNAs) are short, non-protein-coding genes that regulate the expression of numerous protein-coding genes. Their expression is dysregulated in cancer, where they may function as oncogenes or tumour suppressor genes. As miRNAs are highly resistant to degradation, they are ideal biomarker candidates to improve the diagnosis and clinical management of cancer, including prognostication. Furthermore, miRNAs dysregulated in malignancy represent potential therapeutic targets. The use of miRNAs for these purposes is a particularly attractive option to explore for paediatric malignancies, where the mutational burden is typically low, in contrast to cancers affecting adult patients. As childhood cancers are rare, it has taken time to accumulate the necessary body of evidence showing the potential for miRNAs to improve clinical management across this group of tumours. Here, we review the current literature regarding the potential clinical utility of miRNAs in paediatric solid tumours, which is now both timely and justified. Exploring such avenues is warranted to improve the management and outcomes of children affected by cancer.

Spectrum of microRNAs and their target genes in cancer: intervention in diagnosis and therapy

Till date, several groups have studied the mechanism of microRNA (miRNA) biogenesis, processing, stability, silencing, and their dysregulation in cancer. The miRNA coding genes recurrently go through abnormal amplification, deletion, transcription, and epigenetic regulation in cancer. Some miRNAs function as tumor promoters while few others are tumor suppressors based on the transcriptional regulation of target genes. A review of miRNAs and their target genes in a wide range of cancers is attempted in this article, which may help in the development of new diagnostic tools and intervention therapies. The contribution of miRNAs for drug sensitivity or resistance in cancer therapy and opportunities of miRNAs in cancer prognosis or diagnosis and therapy is also presented in detail.

Noncoding RNAs in pediatric brain tumors: Molecular functions and pathological implications

Brain tumors are common solid pediatric malignancies and the main reason for cancer-related death in the pediatric setting. Recently, evidence has revealed that noncoding RNAs (ncRNAs), including microRNAs (miRNAs), long ncRNAs (lncRNAs), and circular RNAs (circRNAs), play a critical role in brain tumor development and progression. Therefore, in this review article, we describe the functions and molecular mechanisms of ncRNAs in multiple types of cancer, including medulloblastoma, pilocytic astrocytoma, ependymoma, atypical teratoid/rhabdoid tumor, glioblastoma, diffuse intrinsic pontine glioma, and craniopharyngioma. We also mention the limitations of using ncRNAs as therapeutic targets because of the nonspecificity of ncRNA targets and the delivery methods of ncRNAs. Due to the critical role of ncRNAs in brain oncogenesis, targeting aberrantly expressed ncRNAs might be an effective strategy to improve the outcomes of pediatric patients with brain tumors.

The mechanism of non-coding RNAs in medulloblastoma

Medulloblastoma (MB) is one of the most common malignant tumors of the central nervous system in children. Although surgery, radiotherapy and chemotherapy have resulted in considerable progress in the treatment of this disease, the prognosis of patients with MB remains very poor. Therefore, highly specific molecular targeted treatment, which can improve the therapeutic efficacy and reduce the side effects of MB, has become a research hotspot. In recent years, non-coding RNAs (ncRNAs), which were initially considered to be transcriptional noise, have been shown to possess regulatory functions. A series of ncRNAs have been identified, including microRNAs and circular RNAs, which affect the expression of specific genes in a variety of tumors. These genes lead to the formation of a specific complex of proteins or they directly participate in protein synthesis in order to regulate the occurrence and development of tumors. The aim of the present review article was to summarize the recent research studies that have explored the ability of ncRNAs to regulate the occurrence and development of MB.

Co-Deregulated miRNA Signatures in Childhood Central Nervous System Tumors: In Search for Common Tumor miRNA-Related Mechanics

Simple Summary

Childhood tumors of the central nervous system (CNS) constitute a grave disease and their diagnosis is difficult to be handled. To gain better knowledge of the tumor’s biology, it is essential to understand the underlying mechanisms of the disease. MicroRNAs (miRNAs) are small noncoding RNAs that are dysregulated in many types of CNS tumors and regulate their occurrence and development through specific signal pathways. However, different types of CNS tumors’ area are characterized by different deregulated miRNAs. Here, we hypothesized that CNS tumors could have commonly deregulated miRNAs, i.e., miRNAs that are simultaneously either upregulated or downregulated in all tumor types compared to the normal brain tissue, irrespectively of the tumor sub-type and/or diagnosis. The only criterion is that they are present in brain tumors. This approach could lead us to the discovery of miRNAs that could be used as pan-CNS tumoral therapeutic targets, if successful.

Abstract

Despite extensive experimentation on pediatric tumors of the central nervous system (CNS), related to both prognosis, diagnosis and treatment, the understanding of pathogenesis and etiology of the disease remains scarce. MicroRNAs are known to be involved in CNS tumor oncogenesis. We hypothesized that CNS tumors possess commonly deregulated miRNAs across different CNS tumor types. Aim: The current study aims to reveal the co-deregulated miRNAs across different types of pediatric CNS tumors. Materials: A total of 439 CNS tumor samples were collected from both in-house microarray experiments as well as data available in public databases. Diagnoses included medulloblastoma, astrocytoma, ependydoma, cortical dysplasia, glioblastoma, ATRT, germinoma, teratoma, yoc sac tumors, ocular tumors and retinoblastoma. Results: We found miRNAs that were globally up- or down-regulated in the majority of the CNS tumor samples. MiR-376B and miR-372 were co-upregulated, whereas miR-149, miR-214, miR-574, miR-595 and miR-765 among others, were co-downregulated across all CNS tumors. Receiver-operator curve analysis showed that miR-149, miR-214, miR-574, miR-595 and miR765 could distinguish between CNS tumors and normal brain tissue. Conclusions: Our approach could prove significant in the search for global miRNA targets for tumor diagnosis and therapy. To the best of our knowledge, there are no previous reports concerning the present approach.

Non-coding RNAs in Wilms' tumor: biological function, mechanism, and clinical implications

Non-coding RNAs are involved with maintenance and regulation of physiological mechanisms and are involved in pathological processes, such as cancer. Among the small ncRNAs, miRNAs are the most explored in tumorigenesis, metastasis development, and resistance to chemotherapy. These small molecules of ~ 22 nucleotides are modulated during early renal development, involved in the regulation of gene expression and Wilms' tumor progression. Wilms' tumors are embryonic tumors with few mutations and complex epigenetic dysregulation. In recent years, the small ncRNAs have been explored as potentially related both in physiological development and in the tumorigenesis of several types of cancer. Besides, genes regulated by miRNAs are related to biological pathways as PI3K, Wnt, TGF-β, and Hippo signaling pathways, among others, which may be involved with the underlying mechanisms of resistance to chemotherapy, and in this way, it has emerged as potential targets for cancer therapies, including for Wilms' tumors.

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.

Aberrantly expressed microRNAs and their implications in childhood central nervous system tumors

Even though the treatment of childhood cancer has evolved significantly in recent decades, aggressive central nervous system (CNS) tumors are still a leading cause of morbidity and mortality in this population. Consequently, the identification of molecular targets that can be incorporated into diagnostic practice, effectively predict prognosis, follow treatment response, and materialize into potential targeted therapeutic approaches are still warranted. Since the first evidence of the participation of miRNAs in cancer development and progression 20 years ago, notable progress has been made in the basic understanding of the contribution of their dysregulation as epigenetic driver of tumorigenesis. Nevertheless, among the plethora of articles in the literature, microRNA profiling of pediatric tumors are scarce. This article gives an overview of the recent advances in the diagnostic/prognostic potential of miRNAs in a selection of pediatric CNS tumors: medulloblastoma, ependymoma, pilocytic astrocytoma, glioblastoma, diffuse intrinsic pontine glioma, atypical teratoid/rhabdoid tumors, and choroid plexus tumors.

MicroRNA Signature in Human Normal and Tumoral Neural Stem Cells

MicroRNAs, also called miRNAs or simply miR-, represent a unique class of non-coding RNAs that have gained exponential interest during recent years because of their determinant involvement in regulating the expression of several genes. Despite the increasing number of mature miRNAs recognized in the human species, only a limited proportion is engaged in the ontogeny of the central nervous system (CNS). miRNAs also play a pivotal role during the transition of normal neural stem cells (NSCs) into tumor-forming NSCs. More specifically, extensive studies have identified some shared miRNAs between NSCs and neural cancer stem cells (CSCs), namely miR-7, -124, -125, -181 and miR-9, -10, -130. In the context of NSCs, miRNAs are intercalated from embryonic stages throughout the differentiation pathway in order to achieve mature neuronal lineages. Within CSCs, under a different cellular context, miRNAs perform tumor suppressive or oncogenic functions that govern the homeostasis of brain tumors. This review will draw attention to the most characterizing studies dealing with miRNAs engaged in neurogenesis and in the tumoral neural stem cell context, offering the reader insight into the power of next generation miRNA-targeted therapies against brain malignances.

Serum miR-338-5p has potential for use as a tumor marker for retinoblastoma

The aim of the present study was to investigate the expression of microRNA (miR)-338-5p in retinoblastoma(RB), thereby evaluating whether it could have potential as a biomarker to screen patients with RB from healthy controls. The results revealed that miR-338-5p was significantly upregulated in patients with RB compared with in healthy controls. There was no significant difference in the expression of miR-338-5p between patients with RB of different age, sex, tumor stage or binocular disease. Receiver operator characteristic analysis indicated that serum miR-338-5p combined with neuron-specific enolase (NSE) had a larger area under the curve compared with serum miR-338-5p alone when diagnosing RB. In addition, suppression of miR-338-5p induced slower proliferation of ACBRI-181 and Y79 cells at 2, 3, 4 and 5 days compared with the negative control group. Flow cytometric analysis indicated that transfection with miR-338-5p inhibitor leads to significant cell cycle arrest in ACBRI-181 and Y79 cells compared with in the negative control group. Furthermore, transfection with miR-338-5p inhibitor significantly decreased ACBRI-181 and Y79 cell migration and invasion, suggesting that miR-338-5p may serve an oncogenic role in the progression of RB. In conclusion, the low expression of miR-338-5p in the serum of patients with RB suggests that it may be involved in the formation of RB. Serum miR-338-5p has the potential to be a tumor marker of RB, and, in combination with NSE, miR-338-5p may improve the early diagnosis rate of RB.

MicroRNA expression in pediatric intracranial ependymomas and their potential value for tumor grading

Intracranial ependymoma represents one of the most common pediatric central nervous system malignancies, and exhibits a wide range of clinical behavior from relatively indolent lesions to highly malignant anaplastic ependymomas. Due to the heterogeneous nature of this disease there is lack of prognostic markers, which would reliably predict the outcome of patients. MicroRNAs (miRNAs) have emerged as important molecules in cancer biology during past decade; however, very little is known about their role in ependymomas. The aim of the present study was to evaluate expression of miRNAs in archived formalin-fixed paraffin-embedded (FFPE) samples of pediatric intracranial ependymomas. The expression of miRNAs were examined in 29 samples of ependymoma and we observed that miR-135a-3p, miR-137, miR-17-5p, miR-181d and let-7d-5p were upregulated. In addition, a significantly higher expression of miR-203a was detected in Grade III tumors suggesting its possible use as a prognostic or diagnostic marker. The present study also demonstrated that storage of (FFPE) ependymoma samples for >20 years did not result in a deterioration of miRNAs. The present findings broaden the presently available knowledge regarding miRNA expression in ependymomas and provide further evidence for the employment of miRNA analysis as a supplementary method for the morphological assessment of ependymoma samples.

Prognostic value of miR-17-5 p in gastrointestinal cancers: a systematic review and meta-analysis

BACKGROUND

There are accumulating studies investigating the aberrant expression of microRNAs in tumor patients. As an important member of miR-17/92 cluster, miR-17-5 p has been identified as a potential prognostic factor for survival in tumor patients. We conducted this meta-analysis aimed to assess the effect of miR-17-5 p as a prognostic biomarker for gastrointestinal tumor patients.

MATERIALS AND METHODS

Eligible studies were enrolled by searching the online databases of PubMed, Embase, Web of Science, China National Knowledge Infrastructure, and WanFang Data until September 2017. We calculated pooled hazard ratios (HRs) and 95% CI of miR-17-5 p for overall survival and disease-free survival.

RESULTS

In the categorical variable analysis, we identified 11 studies with 1,279 patients. The pooled analyses suggested that overexpression of miR-17-5 p may predict poor overall survival (HR = 1.86, 95% CI: 1.55-2.25, P<0.001) and disease-free survival (HR = 1.43, 95% CI: 1.01-2.03, P=0.046) in patients with gastrointestinal tumors. Subgroup analysis showed the pooled HR of overall survival was more significant in tissue specimen, Asian patients, and digestive tract tumors. But there was no correlation between the outcomes and European patients.

CONCLUSIONS

This meta-analysis suggested that miR-17-5 p has predictive effects on overall survival and disease-free survival of patients with gastrointestinal tumors.

Prognostic value of miR-17-5p in cancers: a meta-analysis

Background

Studies have shown that miR-17-5p plays an important role in the development of cancer. The aim of this meta-analysis was to quantitatively analyze the association of miR-17-5p with prognosis in various cancers.

Materials and methods

We searched the PubMed, EMBASE, Web of Science, and Cochrane library databases for relevant studies through August 2017. The prognostic data and clinico-pathological features of overall survival (OS) and disease-free survival (DFS) were extracted to investigate the association between miR-17-5p expression and tumor prognosis. In addition, odds ratios (ORs) were used to assess the correlations between miR-17-5p expression and clinicopathological characteristics.

Results

A total of ten studies were incorporated into this systematic review, and we found that high miR-17-5p expression can predict poor OS for malignancies (combined hazard ratio [HR]=1.87; 95% confidence interval [CI], 1.37–2.55; P=0.000) as well as poor DFS (combined HR=1.60; 95% CI, 1.05–2.44; P=0.027). Further subgroup analyses suggested that high miR-17-5p expression was related to poor OS in Asian patients (combined HR=1.92; 95% CI, 1.37–2.71; P=0.000) and the serum/plasma sample source subgroup (combined HR=2.13; 95% CI, 1.36–3.31; P=0.001). The combined OR indicated that the expression of miR-17-5p was associated with lymph node invasion (OR=1.28; 95% CI, 1.05–1.56; P=0.016) and venous invasion (OR=1.92; 95% CI, 1.40–2.63; P=0.000).

Conclusion

Elevated expression of miR-17-5p suggested a poor prognosis in cancer patients and may serve as a new tumor marker to monitor cancer development and progression.

Identification of microRNA signature in different pediatric brain tumors

Understanding pediatric brain tumor biology is essential to help on disease stratification, and to find novel markers for early diagnosis. MicroRNA (miRNA) expression has been linked to clinical outcomes and tumor biology. Here, we aimed to detect the expression of different miRNAs in different pediatric brain tumor subtypes to discover biomarkers for early detection and develop novel therapies. Expression of 82 miRNAs was detected in 120 pediatric brain tumors from fixed-formalin paraffin-embedded tissues, low-grade glioma, high-grade glioma, ependymoma, and medulloblastoma, using quantitative real-time PCR. Low-expression of miR-221, miR-9, and miR-181c/d and over-expression of miR-101, miR-222, miR-139, miR-1827, and miR-34c was found in medulloblastoma; low expression of miR-10a and over-expression of miR-10b and miR-29a in ependymoma; low expression of miR-26a and overexpression of miR-19a/b, miR-24, miR-27a, miR- 584, and miR-527 in low-grade glioma. Cox regression showed differential miRNA expression between responders and non-responders. The most specific were miR-10a and miR-29a low expression in LGG non-responders, miR-135a and miR-146b over-expression in ependymoma non-responders, and miR-135b overexpression in medulloblastoma non-responders. MicroRNAs are differentially expressed in subtypes of brain tumors suggesting that they may help diagnosis. A greater understanding of aberrant miRNA in pediatric brain tumors may support development of novel therapies.

The Oncogenic Relevance of miR-17-92 Cluster and Its Paralogous miR-106b-25 and miR-106a-363 Clusters in Brain Tumors

The fundamental function of ribonucleic acids is to transfer genetic information from DNA to protein during translation process, however, this is not the only way connecting active RNA sequences with essential biological processes. Up until now, many RNA subclasses of different size, structure, and biological function were identified. Among them, there are non-coding single-stranded microRNAs (miRNAs). This subclass comprises RNAs of 19–25 nucleotides in length that modulate the activity of well-defined coding RNAs and play a crucial role in many physiological and pathological processes. miRNA genes are located both in exons, introns, and also within non-translated regions. Several miRNAs that are transcribed from the adjacent miRNA genes are called cluster. One of the largest ones is miR-17-92 cluster known as OncomiR-1 due to its strong link to oncogenesis. Six miRNAs from the OncomiR-1 have been shown to play important roles in various physiological cellular processes but also through inhibition of cell death in many cancer-relevant processes. Due to the origin and similarity of the sequence, miR-17-92 cluster and paralogs, miR-106b-25 and miR-106a-363 clusters were defined. Here we discuss the oncogenic function of those miRNA subgroups found in many types of cancers, including brain tumors.

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.

MicroRNA expression patterns and signalling pathways in the development and progression of childhood solid tumours

The development of childhood solid tumours is tied to early developmental processes. These tumours may be complex and heterogeneous, and elucidating the aberrant mechanisms that alter the early embryonic environment and lead to disease is essential to our understanding of how these tumours function. MicroRNAs (miRNAs) are vital regulators of gene expression at all stages of development, and their crosstalk via developmental signalling pathways is essential for orchestrating regulatory control in processes such as proliferation, differentiation and apoptosis of cells. Oncogenesis, from aberrant miRNA expression, can occur through amplification and overexpression of oncogenic miRNAs (oncomiRs), genetic loss of tumour suppressor miRNAs, and global miRNA reduction from genetic and epigenetic alterations in the components regulating miRNA biogenesis. While few driver mutations have been identified in many of these types of tumours, abnormal miRNA expression has been found in a number of childhood solid tumours compared to normal tissue. An exploration of the network of key developmental pathways and interacting miRNAs may provide insight into the development of childhood solid malignancies and how key regulators are affected. Here we present a comprehensive introduction to the roles and implications of miRNAs in normal early development and childhood solid tumours, highlighting several tumours in depth, including embryonal brain tumours, neuroblastoma, osteosarcoma, Wilms tumour, and hepatoblastoma. In light of recent literature describing newer classifications and subtyping of tumours based on miRNA profiling, we discuss commonly identified miRNAs, clusters or families associated with several solid tumours and future directions for improving therapeutic approaches.