MicroRNAs and ultraconserved genes as diagnostic markers and therapeutic targets in cancer and cardiovascular diseases

A first comprehensive analysis of Transcribed Ultra Conserved Regions uncovers important regulatory functions of novel non-coding transcripts in gliomas

Transcribed Ultra-Conserved Regions (TUCRs) represent a severely understudied class of putative non-coding RNAs (ncRNAs) that are 100% conserved across multiple species. We performed the first-ever analysis of TUCRs in glioblastoma (GBM) and low-grade gliomas (LGG). We leveraged large human datasets to identify the genomic locations, chromatin accessibility, transcription, differential expression, correlation with survival, and predicted functions of all 481 TUCRs, and identified TUCRs that are relevant to glioma biology. Of these, we investigated the expression, function, and mechanism of action of the most highly upregulated intergenic TUCR, uc.110, identifying it as a new oncogene. Uc.110 was highly overexpressed in GBM and LGG, where it promoted malignancy and tumor growth. Uc.110 activated the WNT pathway by upregulating the expression of membrane frizzled-related protein (MFRP), by sponging the tumor suppressor microRNA miR-544. This pioneering study shows important roles for TUCRs in gliomas and provides an extensive database and novel methods for future TUCR research.

Detection of miR-155 Using Peptide Nucleic Acid at Physiological-like Conditions by Surface Plasmon Resonance and Bio-Field Effect Transistor

MicroRNAs are small ribonucleotides that act as key gene regulators. Their altered expression is often associated with the onset and progression of several human diseases, including cancer. Given their potential use as biomarkers, there is a need to find detection methods for microRNAs suitable for use in clinical setting. Field-effect-transistor-based biosensors (bioFETs) appear to be valid tools to detect microRNAs, since they may reliably quantitate the specific binding between the immobilized probe and free target in solution through an easily detectable electrical signal. We have investigated the detection of human microRNA 155 (miR-155) using an innovative capturing probe constituted by a synthetic peptide nucleic acid (PNA), which has the advantage to form a duplex even at ionic strengths approaching the physiological conditions. With the aim to develop an optimized BioFET setup, the interaction kinetics between miR-155 and the chosen PNA was preliminarily investigated by using surface plasmon resonance (SPR). By exploiting both these results and our custom-made bioFET system, we were able to attain a low-cost, real-time, label-free and highly specific detection of miR-155 in the nano-molar range.

Studies on the application of single-stranded DNA and PNA probes for electrochemical detection of miRNA 141

The abnormal concentration of microRNAs (miRNAs) can be associated with occurrence of various diseases including cancer, cardiovascular and neurodegenerative, hence they can be considered as potential biomarkers. An attractive approach could be the application of electrochemical methods, particularly where hybridization event between single-stranded deoxyribonucleic acid (ssDNA) or peptide-nucleic acid (PNA) with miRNA strand happens. Recently, the use of various nanomaterials such as gold nanoparticles, graphene oxide, quantum dots as well as catalyzed hairpin assembly or hybridization chain reaction were proposed to further enhance the performance of elaborated sensors. Herein, we present the studies on selection of receptor layer composition for detection of miRNA 141. The possibility of formation of receptor layer and further duplex monolayer between ssDNA or PNA with miRNA was analyzed by atomic force microscopy (AFM) technique. The interaction of ssDNA and PNA probes with miRNA was further verified using surface plasmon resonance (SPR) and quartz - crystal microbalance (QCM) techniques. On the basis of impedance spectroscopy it was shown that the use of unlabelled ssDNA as receptor layer provided 0.1 pM detection limit. This shows that proposed biosensor that is simple in preparation and use is an attractive alternative to other recently presented approaches.

Transcribed Ultraconserved Regions in Cancer

Transcribed ultraconserved regions are putative lncRNA molecules that are transcribed from DNA that is 100% conserved in human, mouse, and rat genomes. This is notable, as lncRNAs are typically poorly conserved. TUCRs remain very understudied in many diseases, including cancer. In this review, we summarize the current literature on TUCRs in cancer with respect to expression deregulation, functional roles, mechanisms of action, and clinical perspectives.

Micro-RNA Implications in Type-1 Diabetes Mellitus: A Review of Literature

Type-1 diabetes mellitus (T1DM) is one of the most well-defined and complex metabolic disorders, characterized by hyperglycemia, with a constantly increasing incidence in children and adolescents. While current knowledge regarding the molecules related to the pathogenesis and diagnosis of T1DM is vast, the discovery of new molecules, such as micro ribonucleic acids (micro-RNAs, miRNAs), as well as their interactions with T1DM, has spurred novel prospects in the diagnosis of the disease. This review aims at summarizing current knowledge regarding miRNAs' biosynthesis and action pathways and their role as gene expression regulators in T1DM. MiRNAs follow a complex biosynthesis pathway, including cleaving and transport from nucleus to cytoplasm. After assembly of their final form, they inhibit translation or cause messenger RNA (mRNA) degradation, resulting in the obstruction of protein synthesis. Many studies have reported miRNA involvement in T1DM pathogenesis, mainly through interference with pancreatic b-cell function, insulin production and secretion. They are also found to contribute to β-cell destruction, as they aid in the production of autoreactive agents. Due to their elevated accumulation in various biological specimens, as well as their involvement in T1DM pathogenesis, their role as biomarkers in early preclinical T1DM diagnosis is widely hypothesized, with future studies concerning their diagnostic value deemed a necessity.

Monocyte and Macrophage miRNA: Potent Biomarker and Target for Host-Directed Therapy for Tuberculosis

The end TB strategy reinforces the essentiality of readily accessible biomarkers for early tuberculosis diagnosis. Exploration of microRNA (miRNA) and pathway analysis opens an avenue for the discovery of possible therapeutic targets. miRNA is a small, non-coding oligonucleotide characterized by the mechanism of gene regulation, transcription, and immunomodulation. Studies on miRNA define their importance as an immune marker for active disease progression and as an immunomodulator for innate mechanisms, such as apoptosis and autophagy. Monocyte research is highly advancing toward TB pathogenesis and biomarker efficiency because of its innate and adaptive response connectivity. The combination of monocytes/macrophages and their relative miRNA expression furnish newer insight on the unresolved mechanism for Mycobacterium survival, exploitation of host defense, latent infection, and disease resistance. This review deals with miRNA from monocytes, their relative expression in different disease stages of TB, multiple gene regulating mechanisms in shaping immunity against tuberculosis, and their functionality as biomarker and host-mediated therapeutics. Future collaborative efforts involving multidisciplinary approach in various ethnic population with multiple factors (age, gender, mycobacterial strain, disease stage, other chronic lung infections, and inflammatory disease criteria) on these short miRNAs from body fluids and cells could predict the valuable miRNA biosignature network as a potent tool for biomarkers and host-directed therapy.

Electrochemical nano-genosensor for highly sensitive detection of miR-21 biomarker based on SWCNT-grafted dendritic Au nanostructure for early detection of prostate cancer

MicroRNAs (miRNAs) appear as a novel reliable candidate in biomarkers for early diagnosis of cancer. Due to their roles in various types of cancer, their potential as a diagnostic biomarker is getting more attention. Here, a novel electrochemical biosensor for detection of miR-21 was demonstrated, through combining the advantages of electrochemical methods and nanomaterials with the selectivity of oligonucleotides, based on thiolated receptor probe-functionalized dendritic gold nanostructures (den-Au) via the self-assembly monolayer (SAM) process which grafted on the single-wall carbon nanotubes (SWCNTs) platform on the surface of the fluorine-doped tin oxide (FTO) electrode. Cadmium ions (Cd²⁺) were used as signal units and also signal amplification substance which labeled before on miR-21 target. The oxidation signal of Cd²⁺ as a signal unit was measured by differential pulse voltammetry (DPV) technique that had a very wide linear relationship with the concentration of miR-21 target (0.01 fmol L^-1 to 1 μmol L^-1) and low experimental detection limit of 0.01 fmol L^-1. Furthermore, fabricated biosensor showed acceptable performance in human serum samples and also good selectivity indiscriminate between the complementary target and non-complementary one, so this nano-genosensor can clinically be used for prostate cancer diagnosis through the detection of miR-21 in human serum samples.

An ultrasensitive detection of miRNA-155 in breast cancer via direct hybridization assay using two-dimensional molybdenum disulfide field-effect transistor biosensor

MicroRNAs (miRNAs), critical biomarkers of acute and chronic diseases, play key regulatory roles in many biological processes. As a result, robust assay platforms to enable an accurate and efficient detection of low-level miRNAs in complex biological samples are of great significance. In this work, a label-free and direct hybridization assay using molybdenum disulfide (MoS₂) field-effect transistor (FET) biosensor has been developed for ultrasensitive detection of miRNA-155 as a breast cancer biomarker in human serum and cell-line samples. MoS₂, the novel 2D layered material with excellent physical and chemical properties, was prepared through sequential solvent exchange method and was used as an active channel material. MoS₂ was comprehensively characterized by spectroscopic and microscopic methods and it was applied for fabrication of FET device by drop-casting MoS₂ flacks suspension onto the FET surface. MoS₂ FET device showed a relatively low subthreshold swing of 48.10mV/decade and a high mobility of 1.98 × 10³cm²V^-1s^-1. Subsequently, probe miRNA-155 strands were immobilized on the surface of the MoS₂ FET device. Under optimized conditions detection limit of 0.03fM and concentration range 0.1fM to 10nM were achieved. The developed biosensor not only was capable to identification of fully matched versus one-base mismatch miRNA-155 sequence, but also it could detect target miRNA-155 in spiked real human serum and extracts from human breast cancer cell-line samples. This approach paves a way for label-free, early detection of miRNA as a biomarker in cancer diagnostics with very high sensitivity and good specificity, thus offering a significant potential for clinical application.

Upregulation of miR-146a increases cisplatin sensitivity of the non-small cell lung cancer A549 cell line by targeting JNK-2

The aim of the present study was to investigate the effects of microRNA (miR-)146a on the cisplatin sensitivity of the non-small cell lung cancer (NSCLC) A549 cell line and study the underlying molecular mechanism. The differences in expression of miRNAs between A549 and A549/cisplatin (A549/DDP) cells were determined, and miR-146a was selected to study its effect on cisplatin sensitivity of A549/DDP cells. miR-146a mimic and inhibitor transient transfection systems were constructed using vectors, and A549/DDP cells were infected with miR-146a mimic and inhibitor to investigate growth, apoptosis and migration. The directed target of miR-146a was determined and the underlying molecular mechanism was validated in the present study. The results of the present study demonstrated that miR-146a was downregulated in NSCLC A549/DDP cells, compared with A549 cells. The overexpression of miR-146a induced apoptosis and inhibited the growth and invasion of A549/DDP cells, which resulted in increased cisplatin sensitivity in NSCLC cells. The JNK2 gene was determined as the direct target of miR-146a, and may be activated by the overexpression of miR-146a. Additionally, JNK2 activated the expression of p53 and inhibited B cell lymphoma 2. The upregulation of miR-146a increased cisplatin sensitivity of the A549 cell line by targeting JNK2, which may provide a novel method for treating NSCLC cisplatin resistance.

Identification of a Specific miRNA Profile in HIV-Exposed Seronegative Individuals

OBJECTIVE

MicroRNAs (miRNAs) are small noncoding RNAs involved in the posttranscriptional regulation of gene expression that play important roles in viral infections. Alterations of specific miRNAs are described in HIV infection, suggesting a role for miRNAs in pathogenesis of this disease. We verified whether a particular miRNA signature could be identified in natural resistance to HIV-1.

METHODS

Expression level of 84 miRNAs was analyzed by RT-qPCR in plasma and unstimulated peripheral blood mononuclear cell (PBMC) of 30 seronegative individuals repeatedly exposed to HIV-1 (HESN), 30 HIV seropositive subjects (HIV+), and 30 healthy controls (HC). Results were confirmed by individual RT-qPCR in in vitro HIV-1-infected PBMC and in their cell culture medium. Dicer and Drosha expression was analyzed in basal PBMC.

RESULTS

Whereas Dicer and Drosha expression was comparable in HESN, HIV+ and HC, several miRNAs were upregulated both in HESN and HIV+ compared with HC. Furthermore, miRNA-29a and miR-223 were upregulated in both unstimulated PBMC and plasma of HESN alone; their expression was reduced upon in vitro HIV-1 infection of HESN PBMC indicating that, upon infection, they are secreted in the extracellular milieu. These results were confirmed by individual qPCR.

CONCLUSIONS

Our studies demonstrate that HIV-1 exposure modifies miRNAs expression even in the absence of productive infection. Because those miRNAs that are specifically increased only in HESN have been known to reduce HIV-1 replication, their modulation could represent an important mechanism in resistance to HIV-1 infection.

Roles of MicroRNA-195 in cardiomyocyte apoptosis induced by myocardial ischemia-reperfusion injury

This study aims to investigate microRNA-195 (miR-195) expression in myocardial ischaemia-reperfusion (I/R) injury and the roles of miR-195 in cardiomyocyte apoptosis though targeting Bcl-2. A mouse model of I/R injury was established. MiR- 195 expression levels were detected by real-time quantitative PCR (qPCR), and the cardiomyocyte apoptosis was detected by TUNEL assay. After cardiomyocytes isolated from neonatal rats and transfected with miR-195 mimic or inhibitor, the hypoxia/reoxygenation (H/R) injury model was established. Cardiomyocyte apoptosis and mitochondrial membrane potential were evaluated using flow cytometry. Bcl-2 and Bax mRNA expressions were detected by RT-PCR. Bcl-2, Bax and cytochrome c (Cyt-c) protein levels were determined by Western blot. Caspase-3 and caspase-9 activities were assessed by luciferase assay. Compared with the sham group, miR-195 expression levels and rate of cardiomyocyte apoptosis increased significantly in I/R group (both P < 0.05). Compared to H/R + negative control (NC) group, rate of cardiomyocyte apoptosis increased in H/R + miR-195 mimic group while decreased in H/R + miR-195 inhibitor group (both P <0.05). MiR-195 knockdown alleviated the loss of mitochondrial membrane potential (P <0.05). MiR-195 overexpression decreased Bcl-2 mRNA and protein expression, increased BaxmRNA and protein expression, Cyt-c protein expression and caspase-3 and caspase-9 activities (all P <0.05).While, downregulated MiR-195 increased Bcl-2 mRNA and protein expression, decreased Bax mRNA and protein expression, Cyt-c protein expression and caspase-3 and caspase-9 activities (all P < 0.05). Our study identified that miR-195 expression was upregulated in myocardial I/R injury, and miR-195 overexpression may promote cardiomyocyte apoptosis by targeting Bcl-2 and inducing mitochondrial apoptotic pathway.

Circulating miRNAs are generic and versatile therapeutic monitoring biomarkers in muscular dystrophies

The development of medical approaches requires preclinical and clinical trials for assessment of therapeutic efficacy. Such evaluation entails the use of biomarkers, which provide information on the response to the therapeutic intervention. One newly-proposed class of biomarkers is the microRNA (miRNA) molecules. In muscular dystrophies (MD), the dysregulation of miRNAs was initially observed in muscle biopsy and later extended to plasma samples, suggesting that they may be of interest as biomarkers. First, we demonstrated that dystromiRs dysregulation occurs in MD with either preserved or disrupted expression of the dystrophin-associated glycoprotein complex, supporting the utilization of dystromiRs as generic biomarkers in MD. Then, we aimed at evaluation of the capacity of miRNAs as monitoring biomarkers for experimental therapeutic approach in MD. To this end, we took advantage of our previously characterized gene therapy approach in a mouse model for α-sarcoglycanopathy. We identified a dose-response correlation between the expression of miRNAs on both muscle tissue and blood serum and the therapeutic benefit as evaluated by a set of new and classically-used evaluation methods. This study supports the utility of profiling circulating miRNAs for the evaluation of therapeutic outcome in medical approaches for MD.

Exploiting microRNA Specificity and Selectivity: Paving a Sustainable Path Towards Precision Medicine

In his State of the Union address before both chambers of the US Congress, President Barack Obama called for increased investment in US infrastructure and research and announced the launch of a new Precision Medicine Initiative, aiming to accelerate biomedical discovery. Due to their well-established selectivity and specificity, microRNAs can represent a useful tool, both in diagnosis and therapy, in forging the path towards the achievement of precision medicine. This introductory chapter represents a guide for the Reader in examining the functional roles of microRNAs in the most diverse aspects of clinical practice, which will be explored in this third volume of the microRNA trilogy.

Molecular pathways: microRNAs, cancer cells, and microenvironment

One of the most unexpected discoveries in molecular oncology over the last decade is the interplay between abnormalities in protein-coding genes and short noncoding microRNAs (miRNA) that are causally involved in cancer initiation, progression, and dissemination. This phenomenon was initially defined in malignant cells; however, in recent years, more data have accumulated describing the active participation of miRNAs produced by microenvironment cells. As hormones, miRNAs can be released by a donor cell in various forms of vesicles or as "free" molecules secreted by active mechanisms. These miRNAs spread as signaling molecules that are uptaken either as exosomes or as "free" RNAs, by cells located in other parts of the organism. Here, we discuss the communication between cancer cells and the microenvironment through miRNAs. We further expand this in a more translational context and present miRNAs as predictors of treatment response, as crucial agents in targeted therapeutics, and as significant molecules to target.

Epithelial mesenchymal transition of non-small-cell lung cancer cells A549 induced by SPHK1

OBJECTIVE

To explore the effect and molecular mechanism of SPHK1 in the invasion and metastasis process of non-small-cell lung cancer cells (A549).

METHODS

Recombinant retrovirus was used to mediate the production of A549/vector, A549/SPHK1, A549/scramble, and A549/SPHKl/RNAi that stably expressed or silenced SPHK1. The invasion and migration capacities of A549 cells overexpressing or silencing SPHK1 were determined using Transwell invasion assay and scratch wound repair experiment. The protein and mRNA expression levels of E-cadherin, fibronectin, vimentin in A549/vector, A549/SPHK1, A549/scramble, A549/SPHK1/RNAi were detected with Western blot (WB) and quantitative PCR (QPCR) methods, respectively.

RESULTS

Transwell invasion assay and scratch wound repair experiments showed that over-expression of SPHK1 obviously enhanced the invasion and migration capacities of A549 cells. WB and QPCR detection results showed that, the expression of E-cadherin (a molecular marker of epithelial cells) and fibronectin, vimentin (molecular markers of mesenchymal cells) in A549 cells was upregulated after overexpression of SPHK1; while SPHK1 silencing significantly reduced the invasion and metastasis capacities of A549 cells, upregulated the expression of molecular marker of epithelial cells, and downregulated the expression of molecular marker of mesenchymal cells.

CONCLUSIONS

SPHK1 promotes epithelial mesenchymal transition of non-small-cell lung cancer cells and affects the invasion and metastasis capacities of these cells.

Electrochemical sensing of microRNAs: avenues and paradigms

Twenty years has passed since the first discovery of microRNA (miRNA) lin-4 in Caenorhabditis elegans. Over the last two decades, the study of miRNAs has attracted tremendous attention. These new stars of biomarkers are naturally occurring non-coding RNAs that regulate gene expression posttranscriptionally and have been demonstrated to be dysregulated in many diseases. Since their profiles reflect pathological conditions, miRNAs have recently been proposed as biomarkers of the onset, prognosis and risk of diseases, as well as in the classification of different types of cancer. The establishment of miRNA profiles for diseases and the detection of different types and levels of miRNAs in biological samples are therefore critical milestones in diagnostics. This provides powerful impetus and a growing demand for researchers to develop simple analytical techniques to allow for an accurate, sensitive, selective, and cost effective miRNA analysis at point-of-care settings. Among several methods proposed for miRNA detection, electrochemical nucleic acid biosensors exhibit many attractive features and could play a leading role in future miRNA detection and quantification. This review gives an overview of recent advances in the rapidly growing area of electrochemical detection of miRNAs. The fundamentals of the different strategies adopted for miRNA detection are discussed and some examples of relevant approaches are highlighted, along with future prospects and challenges.

Ultra-specific zeptomole microRNA detection by plasmonic nanowire interstice sensor with Bi-temperature hybridization

MicroRNAs (miRNAs) are emerging new biomarkers for many human diseases. To fully employ miRNAs as biomarkers for clinical diagnosis, it is most desirable to accurately determine the expression patterns of miRNAs. The optimum miRNA profiling method would feature 1) highest sensitivity with a wide dynamic range for accurate expression patterns, 2) supreme specificity to discriminate single nucleotide polymorphisms (SNPs), and 3) simple sensing processes to minimize measurement variation. Here, an ultra-specific detection method of miRNAs with zeptomole sensitivity is reported by applying bi-temperature hybridizations on single-crystalline plasmonic nanowire interstice (PNI) sensors. This method shows near-perfect accuracy of SNPs and a very low detection limit of 100 am (50 zeptomole) without any amplification or labeling steps. Furthermore, multiplex sensing capability and wide dynamic ranges (100 am-100 pm) of this method allows reliable observation of the expression patterns of miRNAs extracted from human tissues. The PNI sensor offers combination of ultra-specificity and zeptomole sensitivity while requiring two steps of hybridization between short oligonucleotides, which could present the best set of features for optimum miRNA sensing method.

Synergistic antitumor activity of resveratrol and miR-200c in human lung cancer

MicroRNAs have emerged as promising molecular factors with potential for clinical applications in cancer diagnosis and therapy. In the present study, we demonstrated that the level of miR-200c in lung cancer tissues was lower than that in normal tissues using real-time PCR. To further investigate the effects of miR-200c expression in lung cancer cells, we upregulated miR-200c levels in H460 cells using transfection. We found that the percentage of apoptotic cells was higher in the cells expressing miR-200c than that in the untransfected cells. Furthermore, the antitumor activities of miR-200c were demonstrated in vivo. Notably, we confirmed that reservatol (RESV) showed stronger antitumor activities in miR-200c-positive cells than in miR-200c-negative cells. Finally, we demonstrated that expression of miR-200c in H460 cells suppressed cell growth by targeting RECK, followed by activation of the JNK signaling pathway and ER stress. Collectively, these data show that miR-200c expression sensitizes H460 cells to RESV and this is likely due to RECK expression.

Characterization and regulation of mechanical loading-induced compensatory muscle hypertrophy

In mammalian systems, skeletal muscle exists in a dynamic state that monitors and regulates the physiological investment in muscle size to meet the current level of functional demand. This review attempts to consolidate current knowledge concerning development of the compensatory hypertrophy that occurs in response to a sustained increase in the mechanical loading of skeletal muscle. Topics covered include: defining and measuring compensatory hypertrophy, experimental models, loading stimulus parameters, acute responses to increased loading, hyperplasia, myofiber-type adaptations, the involvement of satellite cells, mRNA translational control, mechanotransduction, and endocrinology. The authors conclude with their impressions of current knowledge gaps in the field that are ripe for future study.

Flank sequences of miR-145/143 and their aberrant expression in vascular disease: mechanism and therapeutic application

BACKGROUND

Many microRNAs (miRNAs) are downregulated in proliferative vascular disease. Thus, upregulation of these miRNAs has become a major focus of research activity. However, there is a critical barrier in gene therapy to upregulate some miRNAs such as miR-145 and miR-143 because of their significant downregulation by the unclear endogenous mechanisms under disease conditions. The purpose of this study was to determine the molecular mechanisms responsible for their downregulation and to overcome the therapeutic barrier.

METHODS AND RESULTS

In cultured proliferative rat vascular smooth muscle cells (VSMCs) in vitro and in diseased rat and mouse arteries in vivo, we have identified that the impairment of pri-miR-145 into pre-miR-145 is the critical step related to the downregulation of miR-145, in which the PI3-kinase/Akt/p53 pathway is involved. We further identified that the flank sequences of pri-miR-145 are the critical structural components responsible for the aberrant miR-145 expression. Switching of the flank sequence of downregulated miR-145 and miR-143 to the flank sequence of miR-31 confers resistance to their downregulation. The genetically engineered miR-145 (smart miR-145) restored the downregulated miR-145 in proliferative rat VSMCs and in rat carotid arteries with balloon injury and mouse atherosclerotic aortas and demonstrated much better therapeutic effects on the abnormal growth of VSMCs, expression of its target gene, KLF5 expression, VSMC marker gene expression, and vascular neointimal growth.

CONCLUSIONS

The flank sequences of miR-145 and miR-143 play a critical role in their aberrant expression in VSMCs and vascular walls. The genetically engineered "smart" miRNAs based on their flank sequences may have broadly therapeutic applications for many vascular diseases.

miRNAs and long noncoding RNAs as biomarkers in human diseases

Noncoding RNAs (ncRNAs) are transcripts that have no apparent protein-coding capacity; however, many ncRNAs have been found to play a major biological role in human physiology. Their deregulation is implicated in many human diseases, but their exact roles are only beginning to be elucidated. Nevertheless, ncRNAs are extensively studied as a novel source of biomarkers, and the fact that they can be detected in body fluids makes them extremely suitable for this purpose. The authors mainly focus on ncRNAs as biomarkers in cancer, but also touch on other human diseases such as cardiovascular diseases, autoimmune diseases, neurological disorders and infectious diseases. The authors discuss the established methods and provide a selection of emerging new techniques that can be used to detect and quantify ncRNAs. Finally, the authors discuss ncRNAs as a new strategy for therapeutic interventions.

The microRNA-200 family targets multiple non-small cell lung cancer prognostic markers in H1299 cells and BEAS-2B cells

Lung cancer remains the leading cause of cancer-related mortality for both men and women. Tumor recurrence and metastasis is the major cause of lung cancer treatment failure and death. The microRNA‑200 (miR-200) family is a powerful regulator of the epithelial-mesenchymal transition (EMT) process, which is essential in tumor metastasis. Nevertheless, miR-200 family target genes that promote metastasis in non-small cell lung cancer (NSCLC) remain largely unknown. Here, we sought to investigate whether the microRNA-200 family regulates our previously identified NSCLC prognostic marker genes associated with metastasis, as potential molecular targets. Novel miRNA targets were predicted using bioinformatics tools based on correlation analyses of miRNA and mRNA expression in 57 squamous cell lung cancer tumor samples. The predicted target genes were validated with quantitative RT-PCR assays and western blot analysis following re-expression of miR-200a, -200b and -200c in the metastatic NSCLC H1299 cell line. The results show that restoring miR-200a or miR-200c in H1299 cells induces downregulation of DLC1, ATRX and HFE. Reinforced miR-200b expression results in downregulation of DLC1, HNRNPA3 and HFE. Additionally, miR-200 family downregulates HNRNPR3, HFE and ATRX in BEAS-2B immortalized lung epithelial cells in quantitative RT-PCR and western blot assays. The miR-200 family and these potential targets are functionally involved in canonical pathways of immune response, molecular mechanisms of cancer, metastasis signaling, cell-cell communication, proliferation and DNA repair in Ingenuity pathway analysis (IPA). These results indicate that re-expression of miR-200 downregulates our previously identified NSCLC prognostic biomarkers in metastatic NSCLC cells. These results provide new insights into miR-200 regulation in lung cancer metastasis and consequent clinical outcome, and may provide a potential basis for innovative therapeutic approaches for the treatment of this deadly disease.

Upregulation of miR-15b in NAFLD models and in the serum of patients with fatty liver disease

AIM

In the present study, we examined the expression and function of miR-15b in a rat model of non-alcoholic fatty liver disease (NAFLD), and we determined whether the presence of miR-15b in serum can be used as a biomarker for this disease.

METHODS

We measured the expression of miR-15b in both the high-fat-induced non-alcoholic fatty liver disease (NAFLD) SD rat model and in the palmitate-induced NAFLD L02 cell model. Following transfection of miR-15b into QSG7701 cells, cell proliferation, glucose consumption and intracellular triglyceride levels were measured. We also measured the levels of miR-15b in the serum of fatty liver disease patients using real-time PCR.

RESULTS

We found that miR-15b was upregulated in the livers of NAFLD SD rats as well as in NAFLD L02 cells. Increased miR-15b levels could cause decreased cell proliferation and glucose consumption as well as induce the storage of intracellular triglyceride in QSG7701 cells. The expression of miR-15b was also significantly elevated in the serum of fatty liver disease patients compared with healthy subjects.

CONCLUSIONS

Increased miR-15b expression in NAFLD models may lead to decreased cell proliferation and glucose consumption while inducing the storage of intracellular triglyceride, which are all hazards of NAFLD. Therefore, increased serum miR-15b level is a potentially biomarker for the diagnosis of fatty liver disease.

Principles of microRNA involvement in human cancers

Naturally occurring microRNAs (miRNAs), small non-coding RNAs of 19 to 24 nucleotides (nt), are encoded in the genomes of invertebrates, vertebrates, and plants. miRNAs act as regulators of gene expression during development and differentiation at the transcriptional, posttranscriptional, and/or translational levels, although most target genes are still elusive. Many miRNAs are conserved in sequence between distantly related organisms, suggesting that these molecules participate in essential processes. In this review, we present principles related to the basic and translational research that has emerged in the last decade, a period that can be truly considered the “miRNA revolution” in molecular oncology. These principles include the regulation mechanism of miRNA expression, functions of miRNAs in cancers, diagnostic values and therapeutic potentials of miRNAs. Furthermore, we present a compendium of information about the main miRNAs that have been identified in the last several years as playing important roles in cancers. Also, we orient the reader to several additional reviews that may provide a deeper understanding of this new and exciting field of research.

Bioinformatics, non-coding RNAs and its possible application in personalized medicine

Non-coding RNAs are important actors in human biology. A massive amount of data has been created and manipulated, and important findings have been extracted thanks in part to bioinformatics approaches and consequent experimental validation; many of these results are for a specific class of non-coding RNAs, the microRNAs (miRNAs), that are important regulators of gene expression although their transcriptional regulation is not yet well understood. Their involvement in cancer development and progression makes the related research field an integrated one, composed of bioinformaticians, clinicians, statisticians and biologists, as well as informaticians and data miners that cure data manipulation and storage especially due to the output of the latest technologies, like the Next Generation Sequencers.In this chapter we report the main miRNA findings of the last 10 years in terms of identification and prediction techniques, data generation and manipulation methods, as well as possible use in clinical practice.

MicroRNA-125a inhibits cell growth by targeting glypican-4

Heparan sulfate proteoglycan (HSPG), such as glypican, plays a role as a co-receptor for growth factor to influence cells proliferation. However the mechanism is still vague. Micro-RNAs (miRNAs) regulate cell proliferation. Their capacity to direct the translation and stability of targeted transcripts can dramatically influence cellular physiological function. To explore how the function of glypican is regulated involved in cell proliferation, glypican-4 was chosen with a bioinformatics search identifying targeting seed sequences for miR-125a within the 3'-untranslated regions (3'UTR). Indeed, luciferase constructs containing the 3'UTR of glypican-4 demonstrated around 54% less activity in miR-125a expressing cells relative to the controls. The expression of glypican-4 at both the transcript and protein level was down-regulated by transition trasfection of miR-125a in the human embryonic kidney cell line 293T (HEK293T). Although cell proliferation of HEK293T was not influenced by the silence of glypican-4, DNA synthesis in response to FGF2 in the cells was attenuated by knockdown of glypican-4 using siRNA technique. Further study showed that phosphorylation of ERK(1/2) and AKT was suppressed by overexpressing miR-125a, whereas the suppressed MAPK and AKT signaling could be recovered by anti-miR-125a treatment. Both DNA synthesis and cell proliferation were impaired by the inhibitor of ERK(1/2) signaling. MTT assay demonstrated that the cell proliferation was impaired by miR-125a overexpression, however, rescued by anti-miR-125a in HEK293T cells. These results disclosed new function of miR-125a by targeting gene glypican-4 in cell growth process and illustrated the feasibility of using miRNAs as a therapeutic strategy to suppress cells proliferation.

Sunitinib causes dose-dependent negative functional effects on myocardium and cardiomyocytes

OBJECTIVES

To examine the acute effects of sunitinib on inotropic function, intracellular Ca(2+) transients, myofilament Ca(2+) sensitivity and generation of reactive oxygen species (ROS) in human multicellular myocardium and isolated mouse cardiomyocytes. To search for microRNAs as suitable biomarkers for indicating toxic cardiac effects.

PATIENTS AND METHODS

After exposure to sunitinib (0.1-10 µg/mL) developed force, diastolic tension and kinetic variables were assessed in isolated human myocardium. Changes in myocyte sarcomere length, whole-cell calcium transients, myofilament force-Ca(2+) relationship, and ROS generation were examined in isolated ventricular mouse cardiomyocytes. Microarray and realtime-PCR were used to screen for differentially expressed microRNAs in cultured cardiomyocytes that were exposed for 24 h to sunitinib.

RESULTS

We found that higher concentrations of sunitinib (1 and 10 µg/mL) decreased developed force at 30 minutes 76.9 + 2.8 and 54.5 + 6.3%, compared to 96.1 + 2.6% in controls (P < 0.01). Sunitinib exposure significantly decreased sarcomere shortening and Ca2+ transients. Myofilament Ca(2+) sensitivity was not altered, while ROS levels were significantly increased after exposure to the drug. MicroRNA expression patterns were not altered by sunitinib.

CONCLUSIONS

Sunitinib elicits a dose-dependent negative inotropic effect in myocardium, accompanied by a decline in intracellular Ca(2+) and increased ROS generation. In clinical practice, these cardiotoxic effects should be considered in cases where cardiac concentrations of sunitinib could be increased.

Non-coding RNAs with essential roles in neurodegenerative disorders

The importance of various classes of regulatory non-protein-coding RNA molecules (ncRNAs) in the normal functioning of the CNS is becoming increasingly evident. ncRNAs are involved in neuronal cell specification and patterning during development, but also in higher cognitive processes, such as structural plasticity and memory formation in the adult brain. We discuss advances in understanding of the function of ncRNAs in the CNS, with a focus on the potential involvement of specific species, such as microRNAs, endogenous small interfering RNAs, long intergenic non-coding RNAs, and natural antisense transcripts, in various neurodegenerative disorders. This emerging field is anticipated to profoundly affect clinical research, diagnosis, and therapy in neurology.

Relationships of PBMC microRNA expression, plasma viral load, and CD4+ T-cell count in HIV-1-infected elite suppressors and viremic patients

Background

HIV-1-infected elite controllers or suppressors (ES) maintain undetectable viral loads (< 50 copies/mL) without antiretroviral therapy. The mechanisms of suppression are incompletely understood. Modulation of HIV-1 replication by miRNAs has been reported, but the role of small RNAs in ES is unknown. Using samples from a well-characterized ES cohort, untreated viremic patients, and uninfected controls, we explored the PBMC miRNA profile and probed the relationships of miRNA expression, CD4+ T-cell counts, and viral load.

Results

miRNA profiles, obtained using multiple acquisition, data processing, and analysis methods, distinguished ES and uninfected controls from viremic HIV-1-infected patients. For several miRNAs, however, ES and viremic patients shared similar expression patterns. Differentially expressed miRNAs included those with reported roles in HIV-1 latency (miR-29 family members, miRs -125b and -150). Others, such as miR-31 and miR-31*, had no previously reported connection with HIV-1 infection but were found here to differ significantly with uncontrolled HIV-1 replication. Correlations of miRNA expression with CD4+ T-cell count and viral load were found, and we observed that ES with low CD4+ T-cell counts had miRNA profiles more closely related to viremic patients than controls. However, expression patterns indicate that miRNA variability cannot be explained solely by CD4+ T-cell variation.

Conclusions

The intimate involvement of miRNAs in disease processes is underscored by connections of miRNA expression with the HIV disease clinical parameters of CD4 count and plasma viral load. However, miRNA profile changes are not explained completely by these variables. Significant declines of miRs-125b and -150, among others, in both ES and viremic patients indicate the persistence of host miRNA responses or ongoing effects of infection despite viral suppression by ES. We found no negative correlations with viral load in viremic patients, not even those that have been reported to silence HIV-1 in vitro, suggesting that the effects of these miRNAs are exerted in a focused, cell-type-specific manner. Finally, the observation that some ES with low CD4 counts were consistently related to viremic patients suggests that miRNAs may serve as biomarkers for risk of disease progression even in the presence of viral suppression.

A plasma microRNA signature of acute lentiviral infection: biomarkers of central nervous system disease

OBJECTIVE

Plasma microRNAs (miRNAs) are modulated during disease and are emerging biomarkers; they have not been characterized in HIV infection. Using our macaque/simian immunodeficiency virus (SIV) model of HIV, we sought to identify a plasma miRNA profile of acute lentiviral infection, evaluate its relationship with known cellular and viral determinants of lentivirus-associated central nervous system (CNS) disease, and explore the potential of miRNAs to predict CNS disease.

DESIGN

Plasma samples were obtained before inoculation and 10 days after inoculation from SIV-infected macaques.

METHODS

Plasma miRNA expression profiles were determined by TaqMan low-density array for six individuals. miRNA expression was compared with levels of cytokines, virus, and plasma platelet count. miRNA results were confirmed by single miRNA-specific assays for 10 macaques. Nineteen individuals were used to validate a disease prediction test.

RESULTS

A 45-miRNA signature of acute infection (differential expression with P < 0.05 after multiple comparison correction) classified plasma as infected or not. Several differentially expressed miRNAs correlated with CNS disease-associated cytokines interleukin-6 and CCL2 and included predicted and/or validated regulators of the corresponding mRNAs. miRNAs tracked with viral load and platelet count were also predictors of CNS disease. At least six miRNAs were significantly differentially expressed in individuals with severe versus no CNS disease; in an unweighted expression test, they predicted CNS disease.

CONCLUSION

Acute-phase differential expression of plasma miRNAs predicts CNS disease and suggests that CNS damage or predisposition to disease progression begins in the earliest phase of infection. Plasma miRNAs should be investigated further as leading indicators of HIV diseases as early as acute infection.

Cardiac insulin resistance and microRNA modulators

Cardiac insulin resistance is a metabolic and functional disorder that is often associated with obesity and/or the cardiorenal metabolic syndrome (CRS), and this disorder may be accentuated by chronic alcohol consumption. In conditions of over-nutrition, increased insulin (INS) and angiotensin II (Ang II) activate mammalian target for rapamycin (mTOR)/p70 S6 kinase (S6K1) signaling, whereas chronic alcohol consumption inhibits mTOR/S6K1 activation in cardiac tissue. Although excessive activation of mTOR/S6K1 induces cardiac INS resistance via serine phosphorylation of INS receptor substrates (IRS-1/2), it also renders cardioprotection via increased Ang II receptor 2 (AT2R) upregulation and adaptive hypertrophy. In the INS-resistant and hyperinsulinemic Zucker obese (ZO) rat, a rodent model for CRS, activation of mTOR/S6K1signaling in cardiac tissue is regulated by protective feed-back mechanisms involving mTOR↔AT2R signaling loop and profile changes of microRNA that target S6K1. Such regulation may play a role in attenuating progressive heart failure. Conversely, alcohol-mediated inhibition of mTOR/S6K1, down-regulation of INS receptor and growth-inhibitory mir-200 family, and upregulation of mir-212 that promotes fetal gene program may exacerbate CRS-related cardiomyopathy.

Analytical aspects of microRNA in diagnostics: a review

MicroRNAs (miRNA) are short (∼22 nucleotides) non-coding RNA molecules that regulate gene expression at the post-transcriptional level. Their expression is specific to cells and tissues and is temporally regulated. miRNAs are known to be involved in developmental and physiological processes, and their dysregulation leads to development of diseases. Since their profiles reflect pathological processes, miRNAs have recently been proposed as being useful in diagnostics as biomarkers of the onset, prognosis and risk of diseases, as well as in the classification of different types of cancer. The establishment of miRNA profiles that are representative of diseases and the detection of different types and levels of miRNA in samples are therefore critical milestones in diagnostics. miRNAs can be detected in blood and body fluids as well as in tissues, thus making non-invasive collection of samples possible. For a method to be useful in diagnostics, it should be simple, inexpensive and highly sensitive. Here, we will review current methods of detecting miRNAs and indicate the advantages and disadvantages of each techniques. We will then summarize some of the clinical evidence for the potential application of miRNAs as biomarkers in diagnostics. We conclude providing some general perspectives on the use of miRNAs in clinical situations, including therapeutic applications.

MicroRNA history: discovery, recent applications, and next frontiers

Since 1993, when the first small non-coding RNA was identified, our knowledge about microRNAs has grown exponentially. In this review, we focus on the main progress in this field and discuss the most important findings under a historical perspective. In addition, we examine microRNAs as markers of disease diagnosis and prognosis, and as new therapeutic targets.

Upregulation of microRNA-451 increases cisplatin sensitivity of non-small cell lung cancer cell line (A549)

Background

Recently, miR-451 as a tumor suppressor has been reported in other studies. However, whether miR-451 can affect the sensitivity of non-small cell lung cancer (NSCLC) cells to cisplatin (DDP) remains unclear. The aim of this study is to evaluate the roles of miR-451 in the sensitivity of NSCLC cells to DDP.

Methods

Quantitative RT-PCR assay was performed to detect the expression of miR-451 in 10 pairs of NSCLC and noncancerous tissue samples. pcDNA-GW/EmGFP-miR-451 was stably transfected into NSCLC cell line (A549). Then, the effects of miR-451 upregulation on growth, colony formation and apoptosis of A549 cells were investigated. Finally, the effects of miR-451 upregulation on in vitro and in vivo sensitivity of A549 cells of DDP were also determined.

Results

The level of miR-451 expression in NSCLC tissues was significantly higher than that in corresponding noncancerous tissues. Ectopic overexpression of miR-451 could significantly inhibit growth and induce apoptosis of A549 cells. Moreover, ectopic overexpression of miR-451 could sensitize A549 cells to DDP possibly by increasing DDP-induced apoptosis which might be associated with the inactivation of Akt signaling pathway.

Conclusions

This study demonstrated for the first time that combination of DDP application with miR-451 upregulation might be a potential strategy for the treatment of human NSCLC.