MicroRNA signatures as biomarkers and therapeutic target for CNS embryonal tumors: the pros and the cons

Integrative Predictive Modeling of Metastasis in Melanoma Cancer Based on MicroRNA, mRNA, and DNA Methylation Data

Introduction: Despite the significant progress in understanding cancer biology, the deduction of metastasis is still a challenge in the clinic. Transcriptional regulation is one of the critical mechanisms underlying cancer development. Even though mRNA, microRNA, and DNA methylation mechanisms have a crucial impact on the metastatic outcome, there are no comprehensive data mining models that combine all transcriptional regulation aspects for metastasis prediction. This study focused on identifying the regulatory impact of genetic biomarkers for monitoring metastatic molecular signatures of melanoma by investigating the consolidated effect of miRNA, mRNA, and DNA methylation.

Method: We developed multiple machine learning models to distinguish the metastasis by integrating miRNA, mRNA, and DNA methylation markers. We used the TCGA melanoma dataset to differentiate between metastatic melanoma samples by assessing a set of predictive models. For this purpose, machine learning models using a support vector machine with different kernels, artificial neural networks, random forests, AdaBoost, and Naïve Bayes are compared. An iterative combination of differentially expressed miRNA, mRNA, and methylation signatures is used as a candidate marker to reveal each new biomarker category’s impact. In each iteration, the performances of the combined models are calculated. During all comparisons, the choice of the feature selection method and under and oversampling approaches are analyzed. Selected biomarkers of the highest performing models are further analyzed for the biological interpretation of functional enrichment.

Results: In the initial model, miRNA biomarkers can identify metastatic melanoma with an 81% F-score. The addition of mRNA markers upon miRNA increased the F-score to 92%. In the final integrated model, the addition of the methylation data resulted in a similar F-score of 92% but produced a stable model with low variance across multiple trials.

Conclusion: Our results support the role of miRNA regulation in metastatic melanoma as miRNA markers model metastasis outcomes with high accuracy. Moreover, the integrated evaluation of miRNA with mRNA and methylation biomarkers increases the model’s power. It populates selected biomarkers on the metastasis-associated pathways of melanoma, such as the “osteoclast”, “Rap1 signaling”, and “chemokine signaling” pathways.

Source Code:https://github.com/aysegul-kt/MelonomaMetastasisPrediction/

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.

The Role of Liquid Biopsies in Pediatric Brain Tumors

Early detection and serial therapeutic monitoring for pediatric brain tumors are essential for diagnosis and therapeutic intervention. Currently, neuropathological diagnosis relies on biopsy of tumor tissue and surgical intervention. There is a great clinical need for less invasive methods to molecularly characterize the tumor and allow for more reliable monitoring of patients during treatment and to identify patients that might potentially benefit from targeted therapies, particularly in the setting where diagnostic tissue cannot be safely obtained. In this literature review, we highlight recent studies that describe the use of circulating tumor DNA, circulating tumor cells, circulating RNA and microRNA, and extracellular vesicles as strategies to develop liquid biopsies in pediatric central nervous system tumors. Liquid biomarkers have been demonstrated using plasma, urine, and cerebrospinal fluid. The use of liquid biopsies to help guide diagnosis, determine treatment response, and analyze mechanisms of treatment resistance is foreseeable in the future. Continued efforts to improve signal detection and standardize liquid biopsy procedures are needed for clinical application.

Circulating non-coding RNAs as potential diagnostic biomarkers in liver diseases

The liver plays a principal role in the human body as a metabolic and detoxifying unit. Liver diseases are the world's major health problems and affect millions of people worldwide. Early detection of liver diseases is certainly effective in timely treatment and prevention of their progression. Liver injury is associated with significant alterations in immune responses and pattern changes in various tissue-related gene expressions and cytokine production. Increasing or decreasing the specific spectrum of non-coding RNAs in different phases of liver disease can be a criterion for diagnosis. Novel diagnostic biomarkers are needed for liver diseases. Currently, micro-RNAs (miRNAs) are known to play important roles in the diagnosis of liver diseases. Circulating biomarkers such as miRNA-assisted diagnosis can conceivably be helpful for the early treatment of liver diseases. In this review, we look at miRNAs and their potential applications in liver diseases as diagnostic biomarkers were investigated.

Micro-RNA Analysis in Pulmonary Arterial Hypertension: Current Knowledge and Challenges

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The role of miRNAs in PAH is fast expanding, and it is increasingly difficult to identify which molecules have the highest translational potential.

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This review discusses the challenges in miRNA analysis and interpretation in PAH and highlights 4 promising miRNAs in this field.

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Additional pre-clinical studies and clinical trials are urgently needed to bring miRNAs from the bench to the bedside soon.

Pulmonary arterial hypertension (PAH) is a rare, chronic disease of the pulmonary vasculature that is associated with poor outcomes. Its pathogenesis is multifactorial and includes micro-RNA (miRNA) deregulation. The understanding of the role of miRNAs in PAH is expanding quickly, and it is increasingly difficult to identify which miRNAs have the highest translational potential. This review summarizes the current knowledge of miRNA expression in PAH, discusses the challenges in miRNA analysis and interpretation, and highlights 4 promising miRNAs in this field (miR-29, miR-124, miR-140, and miR-204).

Medulloblastoma epigenetics and the path to clinical innovation

INTRODUCTION

In the last decade, a number of genomic and pharmacological studies have demonstrated the importance of epigenetic dysregulation in medulloblastoma initiation and progression. High throughput approaches including gene expression array, next-generation sequencing (NGS), and methylation profiling have now clearly identified at least four molecular subgroups within medulloblastoma, each with distinct clinical and prognostic characteristics. These studies have clearly shown that despite the overall paucity of mutations, clinically relevant events do occur within the cellular epigenetic machinery. Thus, this review aims to provide an overview of our current understanding of the spectrum of epi-oncogenetic perturbations in medulloblastoma.

METHODS

Comprehensive review of epigenetic profiles of different subgroups of medulloblastoma in the context of molecular features. Epigenetic regulation is mediated mainly by DNA methylation, histone modifications and microRNAs (miRNA). Importantly, epigenetic mis-events are reversible and have immense therapeutic potential.

CONCLUSION

The widespread epigenetic alterations present in these tumors has generated intense interest in their use as therapeutic targets. We provide an assessment of the progress that has been made towards the development of molecular subtypes-targeted therapies and the current status of clinical trials that have leveraged these recent advances.

MicroRNA-122a as a non-invasive biomarker for HCV genotype 4-related hepatocellular carcinoma in Egyptian patients

INTRODUCTION

Hepatitis C virus (HCV) infection persists in most infected individuals and can lead to the development of chronic hepatitis, cirrhosis and hepatocellular carcinoma (HCC). MicroRNAs (miRNAs) have a crucial role in various liver diseases, especially HCC. The expression profiles of circulating microRNAs have been studied aiming at the identification of novel non-invasive biomarkers. This study aims to develop a non-invasive diagnostic tool based on measuring the serum levels of different miRNAs in order to detect HCV-induced HCC at the early stages of the disease.

MATERIAL AND METHODS

Five main miRNAs (miRNA-122a, miRNA-125a, miRNA-139, miRNA-145, and miRNA-199a) were selected according to the literature that demonstrated their unique expression pattern during HCC development. Serum samples were collected from 42 cases of chronic hepatitis C (CHC) without cirrhosis, 45 cases of CHC with cirrhosis (LC), 38 cases of HCC with HCV, and 40 healthy individuals serving as a control. The five miRNAs were measured using real-time reverse transcription PCR. The conventional HCC markers α-fetoprotein (AFP) and des-γ-carboxyprothrombin (DCP) were measured with commercial kits.

RESULTS

Serum levels of miRNA-122a, miRNA-125a, miRNA-139, miRNA-145, and miRNA-199a were significantly lower (p < 0.01) in HCC than in CHC and LC groups. As a single marker, miRNA-122a had the highest sensitivity for HCC, followed by miRNA-199a, miRNA-145, miRNA-139, and miRNA-125a.

CONCLUSIONS

These findings indicate that measurement of serum levels of miRNA-122a, miRNA-125a, miRNA-139, miRNA-145, and miRNA-199a can differentiate HCC from CHC and LC. Our results suggest that serum miR-122 might serve as a novel and potential noninvasive biomarker for HCV-induced HCC.

The Application of microRNAs in Biomaterial Scaffold-Based Therapies for Bone Tissue Engineering

In recent years, the application of microRNAs (miRNAs) or anti-microRNAs (anti-miRNAs) that can induce expression of the runt-related transcription factor 2 (RUNX2), a master regulator of osteogenesis, has been investigated as a promising alternative bone tissue engineering strategy. In this review, biomaterial scaffold-based applications that have been used to deliver cells expressing miRNAs or anti-miRNAs that induce expression of RUNX2 for bone tissue engineering are discussed. An overview of the components of the scaffold-based therapies including the miRNAs/anti-miRNAs, cell types, gene delivery vectors, and scaffolds that have been applied are provided. To date, there have been nine miRNAs/anti-miRNAs (i.e., miRNA-26a, anti-miRNA-31, anti-miRNA-34a, miRNA-135, anti-miRNA-138, anti-miRNA-146a, miRNA-148b, anti-miRNA-221, and anti-miRNA-335) that have been incorporated into scaffold-based bone tissue engineering applications and investigated in an in vivo bone critical-sized defect model. For all of the biomaterial scaffold-based miRNA therapies that have been developed thus far, cells that are transfected or transduced with the miRNA/anti-miRNA are loaded into the scaffolds and implanted at the site of interest instead of locally delivering the miRNA/anti-miRNAs directly from the scaffolds. Thus, future work may focus on developing biomaterial scaffolds to deliver miRNAs or anti-miRNAs into cells in vivo.

Long Non-coding Ribonucleic Acid as a Novel Diagnosis and Prognosis Biomarker of Bladder Cancer

Long non-coding ribonucleic acids (lncRNAs) are the largest group of non-coding RNAs and supposedly have a broad spectrum of diverse functions in normal cellular processes. This study was carried out to review the biological functions of candidate lncRNAs (i.e., H19, MALAT-1, TUG1, UCA-1, MEG-3, HOTAIR, CCAT2, AATBC, and the like) with aberrant expressions that play critical roles in bladder cancer (BC) initiation, progression, and metastasis. A formal narrative review was performed by searching the PubMed database for English articles using a combination of keywords such as "long non-coding RNA", "lncRNA", "cancer", "bladder cancer", "screening", "prognosis", "diagnosis", and "response to therapy". In addition, the existing literature was studied on biological function, aberrant expression, and the clinical applications of candidate lncRNAs in BC. By a better understanding of the molecular mechanisms of lncRNAs, they can be used as biomarkers for tumor signatures in urologic malignancies, which can improve screening, prognosis, diagnosis, and the treatment of BC.

The role of miRNAs as biomarkers in prostate cancer

There is an urged need of non-invasive biomarkers for the implementation of precision medicine. These biomarkers are required to these days for improving prostate cancer (PCa) screening, treatment or stratification in current clinical strategies. There are several commercial kits (Oncotype DX genomic prostate score^®, Prolaris^®, among others) that use genomic changes, rearrangement or even non-coding RNA events. However, none of them are currently used in the routine clinical practice. Many recent studies indicate that miRNAs are relevant molecules (small single-stranded non-coding RNAs that regulate gene expression of more than 30% of human genes) to be implement non-invasive biomarkers. However, contrasting to others tumors, such as breast cancer where miR-21 seems to be consistently upregulated; PCa data are controversial. Here we reported an extended revision about the role of miRNAs in PCa including data of AR signaling, cell cycle, EMT process, CSCs regulation and even the role of miRNAs as PCa diagnostic, prognostic and predictive tool. It is known that current biomedical research uses big-data analysis like Next Generation Sequencing (NGS) analysis. We also conducted an extensive online search, including the main platforms and kits for miRNAs massive analysis (like MiSeq, Nextseq 550, or Ion S5™ systems) indicating their pros, cons and including pre-analytical and analytical issues of miRNA studies.

A New Eye Dual-readout Method for MiRNA Detection based on Dissolution of Gold nanoparticles via LSPR by CdTe QDs Photoinduction

Breast cancer (BC) is the most frequent cancer that affects one in eight women worldwide. Recent advances in early cancer diagnosis anticipates more efficient treatment and prolong patient survival. MicroRNAs expression profiling plays a key role in diagnosis of cancer such as BC in early stages. For the first time we describe direct injection of hot electrons from plasmonic gold nanoparticles (AuNPs) to adsorbed water molecules with photoinduction of CdTe quantum dots (QDs) with emission wavelength at ~560 nm. As a result of hot electrons exiting from AuNPs with red color, gold cations (holes) are gradually discharged (AuNPs dissolution) leading to a colorless solution. Our group applied this phenomenon to propose a spectral method for miRNA recognition based on different responsive disaggregation and aggregation of CdTe QDs interacted with single strand DNA probes and DNA/RNA heteroduplex respectively resulting in a detection limit of 4.4 pM. This method has been applied also for the determination of miR-155 in the human breast carcinoma MCF-7 cells and normal human embryonic kidney cell line (HEK 293).

MiRNA Influences in Neuroblast Modulation: An Introspective Analysis

Neuroblastoma (NB) is the most common occurring solid paediatric cancer in children under the age of five years. Whether of familial or sporadic origin, chromosome abnormalities contribute to the development of NB and cause dysregulation of microRNAs (miRNAs). MiRNAs are small non-coding, single stranded RNAs that target messenger RNAs at the post-transcriptional levels by repressing translation within all facets of human physiology. Such gene 'silencing' activities by miRNAs allows the development of regulatory feedback loops affecting multiple functions within the cell, including the possible differentiation of neural stem cell (NSC) lineage selection. Neurogenesis includes stages of self-renewal and fate specification of NSCs, migration and maturation of young neurones, and functional integration of new neurones into the neural circuitry, all of which are regulated by miRNAs. The role of miRNAs and their interaction in cellular processes are recognised aspects of cancer genetics, and miRNAs are currently employed as biomarkers for prognosis and tumour characterisation in multiple cancer models. Consequently, thorough understanding of the mechanisms of how these miRNAs interplay at the transcriptomic level will definitely lead to the development of novel, bespoke and efficient therapeutic measures, with this review focusing on the influences of miRNAs on neuroblast modulations leading to neuroblastoma.

Human salivary microRNAs in Cancer

Circulating microRNAs (miRNAs) have emerged as excellent candidates for cancer biomarkers. Several recent studies have highlighted the potential use of saliva for the identification of miRNAs as novel biomarkers, which represents a great opportunity to improve diagnosis and monitor general health and disease. This review summarises the mechanisms of miRNAs deregulation in cancer, the value of targeting them with a therapeutic intention and the evidence of the potential clinical use of miRNAs expressed in saliva for the detection of different cancer types. We also provide a comprehensive review of the different methods for normalising the levels of specific miRNAs present in saliva, as this is a critical step in their analysis, and the challenge to validate salivary miRNAs as a reality to manage cancer patients.

Tumor-derived exosomes in ovarian cancer - liquid biopsies for early detection and real-time monitoring of cancer progression

Ovarian cancer usually has a poor prognosis because it predominantly presents as high stage disease. New approaches are required to develop more effective early detection strategies and real-time treatment response monitoring. Nano-sized extracellular vesicles (EVs, including exosomes) may provide an approach to enrich tumor biomarker detection and address this clinical need. Exosomes are membranous extracellular vesicles of approximately 100 nm in diameter that have potential to be used as biomarkers and therapeutic delivery tools for ovarian cancer. Exosomal content (proteins and miRNA) is often parent cell specific thus providing an insight or "fingerprint" of the intracellular environment. Furthermore, exosomes can aid cell-cell communication and have the ability to modify target cells by transferring their content. Additionally, via the capacity to evade the immune system and remain stable over long periods in circulation, exosomes have potential as natural drug agents. This review examines the potential role of exosomes in diagnosis, drug delivery and real-time monitoring in ovarian cancer.

Tissue Elasticity Bridges Cancer Stem Cells to the Tumor Microenvironment Through microRNAs: Implications for a "Watch-and-Wait" Approach to Cancer

BACKGROUND

Targeting the tumor microenvironment (TME) through which cancer stem cells (CSCs) crosstalk for cancer initiation and progression, may open new treatments different from those centered on the original hallmarks of cancer genetics thereby implying a new approach for suppression of TME driven activation of CSCs. Cancer is dynamic, heterogeneous, evolving with the TME and can be influenced by tissue-specific elasticity. One of the mediators and modulators of the crosstalk between CSCs and mechanical forces is miRNA, which can be developmentally regulated, in a tissue- and cellspecific manner.

OBJECTIVE

Here, based on our previous data, we provide a framework through which such gene expression changes in response to external mechanical forces can be understood during cancer progression. Recognizing the ways mechanical forces regulate and affect intracellular signals with applications in cancer stem cell biology. Such TME-targeted pathways shed new light on strategies for attacking cancer stem cells with fewer side effects than traditional gene-based treatments for cancer, requiring a "watchand- wait" approach. We attempt to address both normal brain microenvironment and tumor microenvironment as both works together, intertwining in pathology and physiology - a balance that needs to be maintained for the "watch-and-wait" approach to cancer.

CONCLUSION

This review connected the subjects of tissue elasticity, tumor microenvironment, epigenetic of miRNAs, and stem-cell biology that are very relevant in cancer research and therapy. It attempts to unify apparently separate entities in a complex biological web, network, and system in a realistic and practical manner, i.e., to bridge basic research with clinical application.

Circulating microRNAs in cancer: Hope or hype?

Circulating miRNAs are a novel class of stable, minimally invasive disease biomarkers that are considered to be valuable in diagnosis, prognosis and treatment response monitoring. Unlike intracellular miRNAs, circulating miRNAs are released from their producer cells and, based on their targeted functions, they may shuttle in and out of circulation. Their discovery has opened up new avenues for clinical realms and led to a quest for targeted biomarkers. Subsequently, as more cell-free miRNAs are being discovered, their expression is expected to provide precise information regarding disease progression and treatment outcomes, thereby fostering personalized therapeutic strategies. The significance of circulating miRNAs capitalizes on the fact that they are highly stable in body fluids and their expression levels can be detected by common techniques such as qPCR and microarray. However, discrepancies have started to emerge in terms of their reliability and their response under physiological and pathological conditions. Functional studies are still pending, which may determine whether circulating miRNAs play a role as a central component or just as an auxiliary tuner. Also, the distinct clinical signatures that they display have never been subjected to an extensive critical review and experimental validation. As a consequence, the applicability of circulating miRNAs remains a matter of deliberation, despite many intriguing perspectives about their competency. In this review, we highlight some ambiguous issues with the application of circulating miRNAs, which may warrant an immediate consideration. We propose that the circulating miRNA domain needs to be reevaluated to authenticate their specific role and to probe whether they actually carry any clinical weightage.

Mir-449a, a potential diagnostic biomarker for WNT group of medulloblastoma

Medulloblastoma (MB) is the most common malignant brain tumor in childhood. The 5 year disease-free survival rate is rather low. There is a consensus that MB can be divided into at least four clinically, transcriptionally, and genetically distinct molecular variants, being designated as wingless (WNT), sonic hedgehog (SHH), Group 3 and Group 4. It poses a great challenge to the design of therapeutic strategy for MB patients. Intensive clinical intervention, including high dose radiotherapy, is commonly used in treatment of high risk MB, most of which are considered to be Group 3 patients. But such intensive therapy should be avoided to protect neurologic function of patients in the lower risk WNT group. In present study, MB subgroup assignment in formalin-fixed paraffin embedded (FFPE) specimens from 45 Chinese patients were performed by Nanostring platform using 22 well-known signature genes. Based on comparative expression profiles of miRNA real-time PCR microarray in MB cells with and without treatment of demethylation reagent, as well as MSP assay, miR-449a was demonstrated to be significantly silenced by aberrant DNA methylation in tumor cells. Real-time PCR showed that expression level of miR-449a in WNT group was significantly different from other subgroups, although it was down-regulated in most of the MB samples. In conclusion, current study demonstrates for the first time the feasibility of using the Nanostring assay for subgrouping of MBs in Chinese patients. In addition, MiR-449a, a candidate tumor suppressor regulated by hypermethylation, is a novel potential diagnostic marker for WNT group of MBs.

High expression of microRNA-183/182/96 cluster as a prognostic biomarker for breast cancer

More sensitive and effective diagnostic markers for the detection of breast cancer are urgently needed. The microRNA-183/182/96 cluster has been reported to be involved in tumorigenesis and progression in a variety of cancers, and it is a promising cancer prognostic biomarker. The goal of this study was to determine the expression levels of the miR-183/182/96 cluster in breast cancer tissues and evaluate its prognostic role in breast cancer. Real-time quantitative polymerase chain reaction analysis (qRT-PCR) was used to detect the expression levels of the miR-183/182/96 cluster in 41 breast cancer tissues and adjacent normal tissues (control tissues) and also in different mammary cell lines. In situ hybridization (ISH) of the miR-183/182/96 cluster on 131 tissue microarrays (TMAs) was used to statistically analyze its prognostic role. The miR-183/182/96 cluster levels were significantly higher in breast cancer tissues than in control tissues. The miR-183/182/96 cluster was also upregulated in human breast cancer cell lines. An increased miR-183/182/96 cluster level was correlated with local relapse, distant metastasis and poor clinical outcomes. Our findings improve our understanding of the expression level of the miR-183/182/96 cluster in breast cancer and clarify the role of the miR-183/182/96 cluster as a novel prognostic biomarker for breast cancer.

Tumor-Associated CSF MicroRNAs for the Prediction and Evaluation of CNS Malignancies

Cerebrospinal fluid (CSF) is a readily reachable body fluid that is reflective of the underlying pathological state of the central nervous system (CNS). Hence it has been targeted for biomarker discovery for a variety of neurological disorders. CSF is also the major route for seeding metastases of CNS malignancies and its analysis could be informative for diagnosis and risk stratification of brain cancers. Recently, modern high-throughput, microRNAs (miRNAs) measuring technology has enabled sensitive detection of distinct miRNAs that are bio-chemicallystable in the CSF and can distinguish between different types of CNS cancers. Owing to the fact that a CSF specimen can be obtained with relative ease, analysis of CSF miRNAs could be a promising contribution to clinical practice. In this review, we examine the current scientific knowledge on tumor associated CSF miRNAs that could guide diagnosis of different brain cancer types, or could be helpful in predicting disease progression and therapy response. Finally, we highlight their potential applications clinically as biomarkers and discuss limitations.

The Multiple Roles of Microrna-223 in Regulating Bone Metabolism

Bone metabolism is a lifelong process for maintaining skeletal system homeostasis, which is regulated by bone-resorbing osteoclasts and bone-forming osteoblasts. Aberrant differentiation of osteoclasts and osteoblasts leads to imbalanced bone metabolism, resulting in ossification and osteolysis diseases. MicroRNAs (miRNAs) are pivotal factors in regulating bone metabolism via post-transcriptional inhibition of target genes. Recent studies have revealed that miR-223 exerts multiple effects on bone metabolism, especially in the processes of osteoclast and osteoblasts differentiation. In this review, we highlight the roles of miR-223 during the processes of osteoclast and osteoblast differentiation, as well as the potential clinical applications of miR-223 in bone metabolism disorders.

Next generation sequencing profiling identifies miR-574-3p and miR-660-5p as potential novel prognostic markers for breast cancer

Background

Prognostication of Breast Cancer (BC) relies largely on traditional clinical factors and biomarkers such as hormone or growth factor receptors. Due to their suboptimal specificities, it is challenging to accurately identify the subset of patients who are likely to undergo recurrence and there remains a major need for markers of higher utility to guide therapeutic decisions. MicroRNAs (miRNAs) are small non-coding RNAs that function as post-transcriptional regulators of gene expression and have shown promise as potential prognostic markers in several cancer types including BC.

Results

In our study, we sequenced miRNAs from 104 BC samples and 11 apparently healthy normal (reduction mammoplasty) breast tissues. We used Case–control (CC) and Case-only (CO) statistical paradigm to identify prognostic markers. Cox-proportional hazards regression model was employed and risk score analysis was performed to identify miRNA signature independent of potential confounders. Representative miRNAs were validated using qRT-PCR. Gene targets for prognostic miRNAs were identified using in silico predictions and in-house BC transcriptome dataset. Gene ontology terms were identified using DAVID bioinformatics v6.7. A total of 1,423 miRNAs were captured. In the CC approach, 126 miRNAs were retained with predetermined criteria for good read counts, from which 80 miRNAs were differentially expressed. Of these, four and two miRNAs were significant for Overall Survival (OS) and Recurrence Free Survival (RFS), respectively. In the CO approach, from 147 miRNAs retained after filtering, 11 and 4 miRNAs were significant for OS and RFS, respectively. In both the approaches, the risk scores were significant after adjusting for potential confounders. The miRNAs associated with OS identified in our cohort were validated using an external dataset from The Cancer Genome Atlas (TCGA) project. Targets for the identified miRNAs were enriched for cell proliferation, invasion and migration.

Conclusions

The study identified twelve non-redundant miRNAs associated with OS and/or RFS. These signatures include those that were reported by others in BC or other cancers. Importantly we report for the first time two new candidate miRNAs (miR-574-3p and miR-660-5p) as promising prognostic markers. Independent validation of signatures (for OS) using an external dataset from TCGA further strengthened the study findings.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-1899-0) contains supplementary material, which is available to authorized users.

Dicer Is Required for Normal Cerebellar Development and to Restrain Medulloblastoma Formation

Dicer, a ribonuclease III enzyme, is required for the maturation of microRNAs. To assess its role in cerebellar and medulloblastoma development, we genetically deleted Dicer in Nestin-positive neural progenitors and in mice lacking one copy for the Sonic Hedgehog receptor, Patched 1. We found that conditional loss of Dicer in mouse neural progenitors induced massive Trp53-independent apoptosis in all proliferative zones of the brain and decreased proliferation of cerebellar granule progenitors at embryonic day 15.5 leading to abnormal cerebellar development and perinatal lethality. Loss of one copy of Dicer significantly accelerated the formation of mouse medulloblastoma of the Sonic Hedgehog subgroup in Patched1-heterozygous mice. We conclude that Dicer is required for proper cerebellar development, and to restrain medulloblastoma formation.

MicroRNA and pediatric tumors: Future perspectives

A better understanding of pediatric tumor biology is needed to allow the development of less toxic and more efficient therapies, as well as to provide novel reliable biomarkers for diagnosis and risk stratification. The emerging role of microRNAs in controlling key pathways implicated in tumorigenesis makes their use in diagnostics a powerful novel tool for the early detection, risk assessment and prognosis, as well as for the development of innovative anticancer therapies. This perspective would be more urgent for the clinical management of pediatric cancer. In this review, we focus on the involvement of microRNAs in the biology of the main childhood tumors, describe their clinical significance and discuss their potential use as novel therapeutic tools and targets.

MicroRNAs in pediatric central nervous system embryonal neoplasms: the known unknown

MicroRNAs (miRNAs) are endogenous short non-coding RNAs that repress post-transcriptional regulation of gene expression, while embryonal central nervous system tumors are the foremost cause of mortality in children suffering from a neoplasm. MiRNAs and their regulatory mechanisms are new to understand, while pediatric CNS tumors are difficult to comprehend. Therefore, identification of the link between them composes a major scientific challenge. The present study, reviewed the current knowledge on the role of miRNA in pediatric CNS embryonal tumors, attempting to collect the existing information in one piece of work that could ideally be used as a guide for future reference and research.

Microrna expression signatures predict patient progression and disease outcome in pediatric embryonal central nervous system neoplasms

Background

Although, substantial experimental evidence related to diagnosis and treatment of pediatric central nervous system (CNS) neoplasms have been demonstrated, the understanding of the etiology and pathogenesis of the disease remains scarce. Recent microRNA (miRNA)-based research reveals the involvement of miRNAs in various aspects of CNS development and proposes that they might compose key molecules underlying oncogenesis. The current study evaluated miRNA differential expression detected between pediatric embryonal brain tumors and normal controls to characterize candidate biomarkers related to diagnosis, prognosis and therapy.

Methods

Overall, 19 embryonal brain tumors; 15 Medulloblastomas (MBs) and 4 Atypical Teratoid/Rabdoid Tumors (AT/RTs) were studied. As controls, 13 samples were used; The First-Choice Human Brain Reference RNA and 12 samples from deceased children who underwent autopsy and were not present with any brain malignancy. RNA extraction was carried out using the Trizol method, whilst miRNA extraction was performed with the mirVANA miRNA isolation kit. The experimental approach included miRNA microarrays covering 1211 miRNAs. Quantitative Real-Time Polymerase Chain Reaction was performed to validate the expression profiles of miR-34a and miR-601 in all 32 samples initially screened with miRNA microarrays and in an additional independent cohort of 30 patients (21MBs and 9 AT/RTs). Moreover, meta-analyses was performed in total 27 embryonal tumor samples; 19 MBs, 8 ATRTs and 121 control samples. Twelve germinomas were also used as an independent validation cohort. All deregulated miRNAs were correlated to patients’ clinical characteristics and pathological measures.

Results

In several cases, there was a positive correlation between individual miRNA expression levels and laboratory or clinical characteristics. Based on that, miR-601 could serve as a putative tumor suppressor gene, whilst miR-34a as an oncogene. In general, miR-34a demonstrated oncogenic roles in all pediatric embryonal CNS neoplasms studied.

Conclusions

Deeper understanding of the aberrant miRNA expression in pediatric embryonal brain tumors might aid in the development of tumor-specific miRNA signatures, which could potentially afford promising biomarkers related to diagnosis, prognosis and patient targeted therapy.

Electronic supplementary material

The online version of this article (doi:10.1186/s13045-014-0096-y) contains supplementary material, which is available to authorized users.