Label-free high-throughput microRNA expression profiling from total RNA

Invading stacking primer: A trigger for high-efficiency isothermal amplification reaction with superior selectivity for detecting microRNA variants

Searching for a strategy to enhance the efficiency of nucleic acid amplification and achieve exquisite discrimination of nucleic acids at the single-base level for biological detection has become an exciting research direction in recent years. Here, we have developed a simple and universal primer design strategy which produces a fascinating effect on isothermal strand displacement amplification (iSDA). We refer to the resultant primer as "invading stacking primer (IS-Primer)" which is based on contiguous stacking hybridization and toehold-mediated exchange reaction and function by merely changing the hybridization location of the primer. Using the IS-Primer, the sensitivity in detecting the target miR-21 is improved approximately five fold compared with the traditional iSDA reaction. It was further demonstrated that the IS-Primer acts as an invading strand to initiate branch migration which can increase the efficiency of the untwisting of the hairpin probe. This effect is equivalent to reducing the free energy of the stem, and the technique shows superior selectivity for single-base mismatches. By demonstrating the enhanced effect of the IS-Primer in the iSDA reaction, this work may provide a potentially new avenue for developing more sensitive and selective nucleic acids assays.

Highly sensitive and selective miRNA detection based on a closed ring probe and multiple signal amplification

A highly sensitive and selective miRNA detection approach based on a small circular probe and dual signal amplification has been reported.

A review: microRNA detection methods

MicroRNA (miRNA) detection is of considerable significance in both disease diagnosis and in the study of miRNA function. The importance of miRNA itself is due to the complicated regulatory functions it plays in various life processes and its close relationship with some diseases. Traditional methods for miRNA detection do not meet the current demands, so various novel methods have been developed with a special focus on sensitivity and specificity. Herein, we summarize and discuss the newly developed miRNA detection methods.

MiR-221 and miR-26b Regulate Chemotactic Migration of MSCs Toward HGF Through Activation of Akt and FAK

The chemotactic migration of mesenchymal stem cells (MSCs) is fundamental for their use in cell-based therapies, but little is known about the molecular mechanisms that regulate their directed migration. MicroRNAs (miRNAs) participate in the regulation of a large variety of cellular processes. However, their roles in regulating the responses of MSCs to hepatocyte growth factor (HGF) remain elusive. Here, we found that microRNA-221 (miR-221) and microRNA-26b (miR-26b) were upregulated in MSCs subjected to HGF. Overexpression of miR-221 or miR-26b enhanced MSC migration through activation of PI3K/Akt signaling. Phosphatase and tensin homolog deleted on chromosome ten (PTEN) was identified as a potential target of miR-221 and miR-26b; overexpression of miR-221 or miR-26b decreased PTEN expression at both mRNA and protein levels. Overexpression of miR-221 or miR-26b in MSCs increased the phosphorylation of focal adhesion kinase (FAK), a downstream effector of PTEN, which regulates cell migration through assembly and distribution of focal adhesions (FAs), and more dot-like FAs were localized at the periphery of these cells. Altering miR-221 or miR-26b expression influenced the directed migration of MSCs toward HGF. Inhibition of miR-221 or miR-26b suppressed the phosphorylation of Akt and FAK and upregulated PTEN expression, which was partly restored by HGF treatment. Collectively, these results demonstrate that miR-221 and miR-26b participate in regulating the chemotactic response of MSCs toward HGF.

Coupling hybridization chain reaction with catalytic hairpin assembly enables non-enzymatic and sensitive fluorescent detection of microRNA cancer biomarkers

The identification and quantification of sequence-specific microRNAs (miRNAs) plays an important role in early diagnosis of different diseases. In this work, by integrating two independent signal amplification approaches, hybridization chain reaction and catalytic hairpin assembly, we report an enzyme-free and dual amplified approach for highly sensitive detection of a human prostate cancer biomarker, miR-141. The presence of miR-141 triggers the self-assembly of two hairpin DNAs into dsDNA polymers, which co-localize two split segments of ssDNA into proximity. Subsequently, these co-localized ssDNA sequences further act as triggers to initiate catalytic assembly of two fluorescently quenched hairpin DNAs to form numerous dsDNA strands, resulting in the recovery of the fluorescent emissions and remarkably amplified signals for highly sensitive detection of miR-141 down to 0.3 fM. In addition, this method is also selective for the target miRNA against other control sequences. With the advantages of high sensitivity and nanomaterial/enzyme-free detection format, the developed method can be a general sensing platform for the detection of trace amounts of sequence-specific nucleic acid targets.

MicroRNA-Responsive Cancer Cell Imaging and Therapy with Functionalized Gold Nanoprobe

Integration of cancer cell imaging and therapy is critical to enhance the theranostic efficacy and prevent under- or overtreatment. Here, a multifunctional gold nanoprobe is designed for simultaneous miRNA-responsive fluorescence imaging and therapeutic monitoring of cancer. By assembling with folic acid as the targeted moiety and a dye-labeled molecular beacon (MB) as the recognition element and signal switch, the gold nanoprobe is folate receptor-targeted delivered into the cancer cells, and the fluorescence is lighted with the unfolding of MB by intracellular microRNA (miRNA), resulting in an efficient method for imaging and detecting nucleic acid. The average quantity of miRNA-21 is measured to be 1.68 pg in a single HeLa cell. Upon the near-infrared irradiation at 808 nm, the real-time monitoring and assessing of photothermal therapeutic efficacy is achieved from the further enhanced fluorescence of the dye-labeled MB, caused by the high photothermal transformation efficiency of the gold nanocarrier to unwind the remaining folded MB and depart the dye from the nanocarrier. The fluorescence monitoring is also feasible for applications in vivo. This work provides a simple but powerful protocol with great potential in cancer imaging, therapy, and therapeutic monitoring.

MicroRNA Detection: Current Technology and Research Strategies

The relatively new field of microRNA (miR) has experienced rapid growth in methodology associated with its detection and bioanalysis as well as with its role in -omics research, clinical diagnostics, and new therapeutic strategies. The breadth of this area of research and the seemingly exponential increase in number of publications on the subject can present scientists new to the field with a daunting amount of information to evaluate. This review aims to provide a collective overview of miR detection methods by relating conventional, established techniques [such as quantitative reverse transcription polymerase chain reaction (RT-qPCR), microarray, and Northern blotting (NB)] and relatively recent advancements [such as next-generation sequencing (NGS), highly sensitive biosensors, and computational prediction of microRNA/targets] to common miR research strategies. This should guide interested readers toward a more focused study of miR research and the surrounding technology.

Establishing biodegradable single-layer MnO2 nanosheets as a platform for live cell microRNA sensing

We have established a simple and effective biosensing platform based on the non-covalent assembly of biodegradable single-layer MnO₂ nanosheet and target-specific oligonucleotide, and demonstrated its application for sensing miRNA in living cells.

Differential microRNA expression profiles in HCT116 colorectal cancer cell lines located in the lung and colon

Colorectal cancer (CRC) is one of the most common types of cancer worldwide. The majority of mortalities caused by colorectal cancer are due to metastatic disease. As numerous CRC patients experience metastasis to the liver or lung and fail to respond to curative therapies, intensive research efforts have sought to identify the molecular changes or regulatory mechanisms underlying CRC metastasis. In the present study, a stable CRC cell line, HCT16, overexpressing firefly luciferase was constructed and an in vivo metastasis model was established via intravenous injection of this cell line. Using an imaging system, tumor tissue located in the lung and colon was separated and cells were prepared. The microRNA (miRNA) expression profiles of these lung homing or colon homing cells were assessed and compared. A total of 38 differentially expressed miRNAs were selected and confirmed our previous results; several of these have been reported to be involved in the regulation of cancer progression. However, the remaining miRNAs require further investigation. The present profiling may be the first step toward delineating the differential expression of miRNAs in the CRC cells located in the colon and the lung, enabling the elucidation of the regulation associated with miRNAs in colorectal lung metastases. These miRNAs require further validation and functional analysis to evaluate whether they are important in the pathogenesis of colorectal lung metastases or are adopted as markers to predict colorectal metastasis.

Rapid sub-attomole microRNA detection on a portable microfluidic chip

Microfluidic devices are an attractive choice for meeting the requirements of point-of-care microRNA detection. A method using a microfluidic device can drastically shorten the incubation time because the device conveys sample molecules right straight to the surface-immobilized probe DNAs by hydrodynamic force. In this review, we present an overview of a new method for rapid and sensitive microRNA detection from a small sample volume using a power-free microfluidic device driven by degassed poly-dimethylsiloxane (PDMS). Two key technologies for this detection method are summarized. One of the methods relies on the coaxial stacking effect of nucleic acids during sandwich hybridization. This effect is also efficient for stabilizing sandwich hybridization consisting of small DNA and microRNA. The other is the laminar flow-assisted dendritic amplification, which increases the fluorescent signal by supplying two amplification reagents from laminar streams to surface-bound molecules. Utilizing both technologies, microRNA detection is possible with a 0.5 pM detection limit from a 0.5 μL sample corresponding to 0.25 attomoles, with a detection time of 20 min. Since microRNAs are associated with various human diseases, future studies of these technologies might contribute to improved healthcare and may have both industrial and societal impacts.

MicroRNAs as novel biological targets for detection and regulation

MicroRNAs are being considered as a novel type of bio-markers and potential therapeutic targets for various diseases. Diverse chemical tools are being developed for the detection or regulation of microRNAs with bio-medical implications. Chemical probes have been developed for use in combination with in situ signal amplification strategies to realize sensitive detection of microRNAs of low abundance. Regulation of microRNAs aberrantly expressed in tumours represents a new approach to cancer chemotherapy. Synthetic oligonucleotides including antisense oligonucleotides and microRNA mimics have been successfully delivered into cells or tissues to inhibit or enhance the function of specific endogenous microRNAs. Small-molecule modifiers of microRNAs that modify the expression or function of endogenous microRNAs are emerging not only as useful probes to explore microRNA-involved regulatory networks, but also as potential therapeutic reagents. In this tutorial review, we discuss the strategies developed by chemists in recent years for microRNA detection and regulation, with a focus on the potential of these chemical tools in microRNA-related biomedical applications.

Rapid and reliable microRNA detection by stacking hybridization on electrochemiluminescent chip system

MicroRNAs play pivotal roles in many fundamental aspects of life. Because microRNAs have the characteristics of small size, similar sequence, and low abundance, it is challenging to identify microRNAs rapidly and specifically with high sensitivity. Herein, we developed an electrochemiluminescent (ECL) chip system for microRNA detection based on base-stacking hybridization and magnetic microparticle enrichment technology. In the designed system, the integration of the microfluidic system with ECL detection made it easy to assemble the multiple assay steps and allowed the construction of a device that is convenient to carry. A limit of detection of 1fmol was achieved with this assay. The proposed direct optical microRNA detection technique demonstrated an acceptable sensitivity combined with the advantages of reliability and rapidity.

Label-free quantification of microRNAs using ligase-assisted sandwich hybridization on a DNA microarray

MicroRNAs (miRNAs) can be used as biomarkers for cancer and other human diseases; therefore, high-throughput and reliable miRNA-quantification methods are required to exploit these markers for diagnostic testing. In this report, we describe the construction of a platform for miRNA-quantification using ligase-assisted sandwich hybridization (LASH) without miRNA-labeling. T4 DNA ligase was used to compensate for the low affinity between miRNAs and two short complementary DNA probes, and it improved the hybridization yield ∼50,000 times. The LASH assay enabled synthesized miR-143 to be quantified at concentrations ranging from 30 fM to 30 pM. The LASH assay could also quantify endogenous miR-143 released from cultured cells as well as some miRNAs in total RNAs derived from blood. Furthermore, multi-color detection enabled us to distinguish between the highly homologous miR-141 and miR-200a. This simple label-free quantification technique is an easy-to-use approach that can be applied to disease diagnosis.

Noninvasive micromarkers

BACKGROUND

The recent revolutionary advances made in genome-wide sequencing technology have transformed biology and molecular diagnostics, allowing new sRNA (small RNA) classes to be discovered as potential disease-specific biological indicators. Cell-free microRNAs (miRNAs) have been shown to exist stably in a wide spectrum of body fluids and their expression profiles have been shown to reflect an assortment of physiological conditions, underscoring the utility of this new class of molecules to function as noninvasive biomarkers of disease.

CONTENT

We summarize information on the known mechanisms of miRNA protection and release into extracellular space and compile the current literature on extracellular miRNAs that have been investigated as biomarkers of 20 different cancers, 11 organ damage conditions and 10 diverse disease states. We also discuss the various strategies involved in the miRNA biomarker discovery workflow and provide a critical opinion on the impediments faced by this advancing field that need to be overcome in the laboratory.

SUMMARY

The field of miRNA-centered diagnostics is still in its infancy, and basic questions with regard to the exact role of miRNAs in the pathophysiology of diseases, and the mechanisms of their release from affected cells into biological fluids are yet to be completely understood. Nevertheless, these noninvasive micromarkers have immense potential in translational medicine not only for use in monitoring the efficacy and safety of therapeutic regimens but also to guide the diagnosis of diseases, to determine the risk of developing diseases or conditions, and more importantly, to inform treatment options.

MicroRNAs and the cancer phenotype: profiling, signatures and clinical implications

MicroRNAs (miRNAs) have emerged as key genetic regulators of a wide variety of biological processes, including growth, proliferation, and survival. Recent advances have led to the recognition that miRNAs can act as potent oncogenes and tumor suppressors, playing crucial roles in the initiation, maintenance, and progression of the oncogenic state in a variety of cancers. Determining how miRNA expression and function is altered in cancer is an important goal, and a necessary prerequisite to the development and adoption of miRNA-based therapeutics in the clinic. Highly promising clinical applications of miRNAs are the use of miRNA signatures as biomarkers for cancer (for example, for early detection or diagnosis), and therapeutic supplementation or inhibition of specific miRNAs to alter the cancer phenotype. In this review, we discuss the main methods used for miRNA profiling, and examine key miRNAs that are commonly altered in a variety of tumors. Current studies underscore the functional versatility and potency of miRNAs in various aspects of the cancer phenotype, pointing to their potential clinical applications. Consequently, we discuss the application of miRNAs as biomarkers, clinical agents, and therapeutic targets, highlighting both the enormous potential and major challenges in this field.

Detection methods for microRNAs in clinic practice

MicroRNAs (miRNA) are short non-coding RNA molecules that regulate gene expression. miRNAs profiles are specific for cell lineages and tissues, and their changes reflect pathological processes. This fact introduces the possibility of their use in diagnostics. The application of miRNAs in diagnostics is critically dependent on the establishment of miRNA profiles that can discriminate patients from normal healthy individuals with good sensitivity and specificity and on the development of methods for their accurate and high-throughput quantification. In this review, we present an overview of some of the different techniques and methods currently used to detect miRNAs. We focus on methods that can be employed in routine clinic diagnostics indicating their advantages as well as their shortcomings, with special attention being paid to the most innovative ones. Since disease-specific miRNAs can be found in blood serum, we also present emerging methods for the detection of circulating miRNAs as a way of fast, reliable and non-invasive diagnostic.

DNA Nanostructure-based Interfacial engineering for PCR-free ultrasensitive electrochemical analysis of microRNA

MicroRNAs (miRNAs) have been identified as promising cancer biomarkers due to their stable presence in serum. As an alternative to PCR-based homogenous assays, surface-based electrochemical biosensors offer great opportunities for low-cost, point-of-care tests (POCTs) of disease-associated miRNAs. Nevertheless, the sensitivity of miRNA sensors is often limited by mass transport and crowding effects at the water-electrode interface. To address such challenges, we herein report a DNA nanostructure-based interfacial engineering approach to enhance binding recognition at the gold electrode surface and drastically improve the detection sensitivity. By employing this novel strategy, we can directly detect as few as attomolar (<1, 000 copies) miRNAs with high single-base discrimination ability. Given that this ultrasensitive electrochemical miRNA sensor (EMRS) is highly reproducible and essentially free of prior target labeling and PCR amplification, we also demonstrate its application by analyzing miRNA expression levels in clinical samples from esophageal squamous cell carcinoma (ESCC) patients.

Rapid and sensitive microRNA detection with laminar flow-assisted dendritic amplification on power-free microfluidic chip

Detection of microRNAs, small noncoding single-stranded RNAs, is one of the key topics in the new generation of cancer research because cancer in the human body can be detected or even classified by microRNA detection. This report shows rapid and sensitive microRNA detection using a power-free microfluidic device, which is driven by degassed poly(dimethylsiloxane), thus eliminating the need for an external power supply. MicroRNA is detected by sandwich hybridization, and the signal is amplified by laminar flow-assisted dendritic amplification. This method allows us to detect microRNA of specific sequences at a limit of detection of 0.5 pM from a 0.5 µL sample solution with a detection time of 20 min. Together with the advantages of self-reliance of this device, this method might contribute substantially to future point-of-care early-stage cancer diagnosis.

Potential pitfalls in microRNA profiling

MicroRNAs (miRNAs) are small, noncoding RNAs that post-transcriptionally influence a wide range of cellular processes such as the host response to viral infection, innate immunity, cell cycle progression, migration, and apoptosis through the inhibition of target mRNA translation. Owing to the growing number of miRNAs and identification of their functional roles, miRNA profiling of many different sample types has become more expansive, especially with relevance to disease signatures. In this review, we address some of the advantages and potential pitfalls of the currently available methods for miRNA expression profiling. Some of the topics discussed include isomiRNAs, comparison of different profiling platforms, normalization strategies, and issues with regard to sample preparation and experimental analyses.