Detection of miRNA expression in intact cells using activatable sensor oligonucleotides

Programmable, Universal DNAzyme Amplifier Supporting Pancreatic Cancer-Related miRNAs Detection

The abnormal expression of miRNA is closely related to the occurrence of pancreatic cancer. Herein, a programmable DNAzyme amplifier for the universal detection of pancreatic cancer-related miRNAs was proposed based on its programmability through the rational design of sequences. The fluorescence signal recovery of the DNAzyme amplifier showed a good linear relationship with the concentration of miR-10b in the range of 10–60 nM, with a detection limit of 893 pM. At the same time, this method displayed a high selectivity for miR-10b, with a remarkable discrimination of a single nucleotide difference. Furthermore, this method was also successfully used to detect miR-21 in the range of 10–60 nM based on the programmability of the DNA amplifier, exhibiting the universal application feasibility of this design. Overall, the proposed programmable DNAzyme cycle amplifier strategy shows promising potential for the simple, rapid, and universal detection of pancreatic cancer-related miRNAs, which is significant for improving the accuracy of pancreatic cancer diagnosis.

Candida albicans Induces Cross-Kingdom miRNA Trafficking in Human Monocytes To Promote Fungal Growth

In response to infections, human immune cells release extracellular vesicles (EVs) that carry a situationally adapted cocktail of proteins and nucleic acids, including microRNAs (miRNAs), to coordinate the immune response. In this study, we identified hsa-miR-21-5p and hsa-miR-24-3p as the most common miRNAs in exosomes released by human monocytes in response to the pathogenic fungus Candida albicans. Functional analysis of miRNAs revealed that hsa-miR-24-3p, but not hsa-miR-21-5p, acted across species and kingdoms, entering C. albicans and inducing fungal cell growth by inhibiting translation of the cyclin-dependent kinase inhibitor Sol1. Packaging of hsa-miR-24-3p into monocyte exosomes required binding of fungal soluble β-glucan to complement receptor 3 (CR3) and binding of mannan to Toll-like receptor 4 (TLR4), resulting in receptor colocalization. Together, our in vitro and in vivo findings reveal a novel cross-species evasion mechanism by which C. albicans exploits a human miRNA to promote fungal growth and survival in the host. IMPORTANCE Over the last decade, communication between immune cells by extracellular vesicle-associated miRNAs has emerged as an important regulator of the coordinated immune response. Therefore, a thorough understanding of the conversation occurring via miRNAs, especially during infection, may provide novel insights into both the host reaction to the microbe as well as the microbial response. This study provides evidence that the pathogenic fungus C. albicans communicates with human monocytes and induces the release of a human miRNA that promotes fungal growth. This mechanism represents an unexpected cross-species interaction and implies that an inhibition of specific miRNAs offers new possibilities for the treatment of human fungal infections.

Peritumoral Microenvironment in High-Grade Gliomas: From FLAIRectomy to Microglia-Glioma Cross-Talk

Cellular composition and molecular signatures of the glioma core compared with infiltrative margins are different, and it is well known that the tumor edge is enriched in microglia. In this review of the literature, we summarize the role of the peritumoral area in high-grade gliomas (HGGs) from surgical and biological points of view. There is evidence on the dual role of microglia in HGGs-a scavenger-tumoricidal role when microglia are activated in an M1 phenotype and a role favoring tumor growth and infiltration/migration when microglia are activated in an M2 phenotype. Microglia polarization is mediated by complex pathways involving cross-talk with glioma cells. In this scenario, extracellular vesicles and their miRNA cargo seem to play a central role. The switch to a specific phenotype correlates with prognosis and the pathological assessment of a specific microglial setting can predict a patient's outcome. Some authors have designed an engineered microglial cell as a biologically active vehicle for the delivery of intraoperative near-infrared fluorescent dye with the aim of helping surgeons detect peritumoral infiltrated areas during resection. Furthermore, the pharmacological modulation of microglia-glioma cross-talk paves the way to more effective therapies.

MiRNA10b-directed nanotherapy effectively targets brain metastases from breast cancer

RNA interference represents one of the most appealing therapeutic modalities for cancer because of its potency, versatility, and modularity. Because the mechanism is catalytic and affects the expression of disease-causing antigens at the post-transcriptional level, only small amounts of therapeutic need to be delivered to the target in order to exert a robust therapeutic effect. RNA interference is also advantageous over other treatment modalities, such as monoclonal antibodies or small molecules, because it has a much broader array of druggable targets. Finally, the complementarity of the genetic code gives us the opportunity to design RNAi therapeutics using computational, rational approaches. Previously, we developed and tested an RNAi-targeted therapeutic, termed MN-anti-miR10b, which was designed to inhibit the critical driver of metastasis and metastatic colonization, miRNA-10b. We showed in animal models of metastatic breast cancer that MN-anti-miR10b accumulated into tumors and metastases in the lymph nodes, lungs, and bone, following simple intravenous injection. We also found that treatment incorporating MN-anti-miR10b was effective at inhibiting the emergence of metastases and could regress already established metastases in the lymph nodes, lungs, and bone. In the present study, we extend the application of MN-anti-miR10b to a model of breast cancer metastatic to the brain. We demonstrate delivery to the metastatic lesions and obtain evidence of a therapeutic effect manifested as inhibition of metastatic progression. This investigation represents an additional step towards translating similar RNAi-targeted therapeutics for the systemic treatment of metastatic disease.

Recent advances in high-performance fluorescent and bioluminescent RNA imaging probes

RNA plays an important role in life processes. Imaging of messenger RNAs (mRNAs) and micro-RNAs (miRNAs) not only allows us to learn the formation and transcription of mRNAs and the biogenesis of miRNAs involved in various life processes, but also helps in detecting cancer. High-performance RNA imaging probes greatly expand our view of life processes and enhance the cancer detection accuracy. In this review, we summarize the state-of-the-art high-performance RNA imaging probes, including exogenous probes that can image RNA sequences with special modification and endogeneous probes that can directly image endogenous RNAs without special treatment. For each probe, we review its structure and imaging principle in detail. Finally, we summarize the application of mRNA and miRNA imaging probes in studying life processes as well as in detecting cancer. By correlating the structures and principles of various probes with their practical uses, we compare different RNA imaging probes and offer guidance for better utilization of the current imaging probes and the future design of higher-performance RNA imaging probes.

In Vivo Detection of miRNA Expression in Tumors Using an Activatable Nanosensor

PURPOSE

The development of tools for the analysis of microRNA (miRNA) function in tumors can advance our diagnostic and prognostic capabilities. Here, we describe the development of technology for the profiling of miRNA expression in the tumors of live animals.

PROCEDURES

The approach is based on miRNA nanosensors consisting of sensor oligonucleotides conjugated to magnetic nanoparticles for systemic delivery. Feasibility was demonstrated for the detection of miR-10b, implicated in epithelial to mesenchymal transition and the development of metastasis. The miR-10b nanosensor was tested in vivo in two mouse models of cancer. In the first model, mice were implanted subcutaneously with MDA-MB-231-luc-D3H2LN tumors, in which miR-10b was inhibited. In the second model, mice were implanted bilaterally with metastatic MDA-MB-231 and nonmetastatic MCF-7 cells. The nanosensors were injected intravenously, and fluorescence intensity in the tumors was monitored over time.

RESULTS

We showed that the described nanosensors are capable of discriminating between tumors based on their expression of miR-10b. Radiant efficiency was higher in the miR-10b-active tumors than in the miR-10b-inhibited tumors and in the MDA-MB-231 tumors relative to the MCF-7 tumors.

CONCLUSIONS

The described technology provides an important tool that could be used to answer questions about microRNA function in cancer.

A DNA Circuit for IsomiR Detection

A synthetic DNA oligonucleotide has been programmed to function as a biological circuit to detect 5'-IsomiRs. The circuit consists of two integrated DNA switches. The first is "activated" when a DNA probe is enzymatically modified by a reverse transcriptase that incorporates nucleotides complementary to the 5'-region of a microRNA (miRNA). Addition of the correct number and sequence of nucleotides enables the probe to assemble into an asymmetric DNA hairpin. The reconfigured hairpin probe then primes an internal polymerisation reaction, resulting in the synthesis of a symmetrical DNA hairpin. This activates the second switch, which then initiates the amplification of reverse-transcribed miRNA through a continuous cycle of DNA nicking and polymerisation. The DNA circuit enables sensitive and rapid detection of femtomoles of a miRNA transcript under isothermal conditions.

MicroRNA-Responsive Drug Release System for Selective Fluorescence Imaging and Photodynamic Therapy In Vivo

Photodynamic therapy (PDT) is a noninvasive strategy to treat diseases by light-triggered activation of a photosensitizer (PS). One aim of the recent researches on PDT is to overcome the limitation of conventional PDT by improving selective activation of PS on targeted region. Here, a microRNA (miRNA)-responsive drug activation system is developed which focuses on the role of endogenous miRNA as an internal cancer specific stimulus for initiating drug release in cancer treatment. The present system consists of PS chlorin e6 (Ce6) conjugated to peptide nucleic acid (PNA) having complementary sequence to cancer specific miRNA and dextran coated reduced graphene oxide nanocolloid (Dex-RGON). In the presence of oncogenic miR-21 in cancer cells, Ce6-PNA drug gets hybridized with miR-21, resulting in the release of Ce6-PNA from Dex-RGON and subsequent recovery of Ce6 fluorescence and activation of Ce6 as a photosensitizer under near IR irradiation. It is demonstrated that the Ce6-PNA/Dex-RGON complex shows sequence-specific fluorescence in response to miR-21 and selective cytotoxic effect for tumor growth inhibition. The present study will pave a new way for utilizing PDT in cancer treatment with tightly regulated activation of a photosensitizer by oncogenic miRNA as an internal stimulus to reduce potential risk associated with conventional PDT.

Sensing miRNA: Signal Amplification by Cognate RISC for Intracellular Detection of miRNA in Live Cells

The ability to detect miRNA expression in live cells would leave these cells available for further manipulation or culture. Here, we describe the design of a miRNA sensor oligonucleotide whose sequence mimics the target mRNA. The sensor has a fluorescent label on one end of the oligo and a quencher on the other. When inside the cell, the sensor is recognized by its cognate miRNA-RISC and gets cleaved, setting the fluorophore free from its quencher. This results in fluorescence "turn on." Since cleavage by the RISC complex is an enzymatic process, the described approach has a very high level of sensitivity (nM). The rate of nonspecific cleavage of the sensor is very slow permitting the collection of meaningful signal over a long period of time.

Tiny giants of gene regulation: experimental strategies for microRNA functional studies

The discovery over two decades ago of short regulatory microRNAs (miRNAs) has led to the inception of a vast biomedical research field dedicated to understanding these powerful orchestrators of gene expression. Here we aim to provide a comprehensive overview of the methods and techniques underpinning the experimental pipeline employed for exploratory miRNA studies in animals. Some of the greatest challenges in this field have been uncovering the identity of miRNA-target interactions and deciphering their significance with regard to particular physiological or pathological processes. These endeavors relied almost exclusively on the development of powerful research tools encompassing novel bioinformatics pipelines, high-throughput target identification platforms, and functional target validation methodologies. Thus, in an unparalleled manner, the biomedical technology revolution unceasingly enhanced and refined our ability to dissect miRNA regulatory networks and understand their roles in vivo in the context of cells and organisms. Recurring motifs of target recognition have led to the creation of a large number of multifactorial bioinformatics analysis platforms, which have proved instrumental in guiding experimental miRNA studies. Subsequently, the need for discovery of miRNA-target binding events in vivo drove the emergence of a slew of high-throughput multiplex strategies, which now provide a viable prospect for elucidating genome-wide miRNA-target binding maps in a variety of cell types and tissues. Finally, deciphering the functional relevance of miRNA post-transcriptional gene silencing under physiological conditions, prompted the evolution of a host of technologies enabling systemic manipulation of miRNA homeostasis as well as high-precision interference with their direct, endogenous targets. For further resources related to this article, please visit the WIREs website.

A conformation-induced fluorescence method for microRNA detection

MicroRNAs play important roles in a large variety of biological systems and processes through their regulation of target mRNA expression, and show promise as clinical biomarkers. However, their small size presents challenges for tagging or direct detection. Innovation in techniques to sense and quantify microRNAs may aid research into novel aspects of microRNA biology and contribute to the development of diagnostics. By introducing an additional stem loop into the fluorescent RNA Spinach and altering its 3' and 5' ends, we have generated a new RNA, Pandan, that functions as the basis for a microRNA sensor. Pandan contains two sequence-variable stem loops that encode complementary sequence for a target microRNA of interest. In its sensor form, it requires the binding of a target microRNA in order to reconstitute the RNA scaffold for fluorophore binding and fluorescence. Binding of the target microRNA resulted in large changes in fluorescence intensity. The median fold change in fluorescence observed for the sensors tested was ∼50-fold. Pandan RNA sensors exhibit good signal-to-noise ratios, and can detect their target microRNAs within complex RNA mixtures.

Analysis of MicroRNA Function in Drosophila

MicroRNAs are short noncoding, ~22-nucleotide RNAs that regulate protein abundance. The growth in our understanding of this class of RNAs has been rapid since their discovery just over a decade ago. We now appreciate that miRNAs are deeply embedded within the genetic networks that control basic features of metazoan cells including their identity, metabolism, and reproduction. The Drosophila melanogaster model system has made and will continue to make important contributions to this analysis. Intended as an introductory overview, here we review the current methods and resources available for functional analysis of fly miRNAs for those interested in performing this type of analysis.

Single Cell Real-Time miRNAs Sensing Based on Nanomotors

A nanomotor-based strategy for rapid single-step intracellular biosensing of a target miRNA, expressed in intact cancer cells, at the single cell level is described. The new concept relies on the use of ultrasound (US) propelled dye-labeled single-stranded DNA (ssDNA)/graphene-oxide (GO) coated gold nanowires (AuNWs) capable of penetrating intact cancer cells. Once the nanomotor is internalized into the cell, the quenched fluorescence signal (produced by the π-π interaction between GO and a dye-labeled ssDNA) is recovered due to the displacement of the dye-ssDNA probe from the motor GO-quenching surface upon binding with the target miRNA-21, leading to an attractive intracellular "OFF-ON" fluorescence switching. The faster internalization process of the US-powered nanomotors and their rapid movement into the cells increase the likelihood of probe-target contacts, leading to a highly efficient and rapid hybridization. The ability of the nanomotor-based method to screen cancer cells based on the endogenous content of the target miRNA has been demonstrated by measuring the fluorescence signal in two types of cancer cells (MCF-7 and HeLa) with significantly different miRNA-21 expression levels. This single-step, motor-based miRNAs sensing approach enables rapid "on the move" specific detection of the target miRNA-21, even in single cells with an extremely low endogenous miRNA-21 content, allowing precise and real-time monitoring of intracellular miRNA expression.