The regulation of microRNA in each of cancer stage from two different ethnicities as potential biomarker for breast cancer

miRNA has recently emerged as a potential biomarker for breast cancer. Even though many studies have identified ethnic variation affecting miRNA regulation, the effect of cancer stage within specific ethnicities on miRNA epigenetic remains unclear. The present study is designed to investigate miRNA regulation from two distinct ethnicities in specific cancer stages (non-Hispanic white and non-Hispanic black) using the TCGA dataset. Differentially expressed miRNAs were calculated by using the edgeR package. miRNAs with the highest or lowest log fold Change from each cancer stage were selected as a potential biomarker. miRNA-gene interaction was analyzed by using spearman correlation analysis, CLUEGO, and DIANA-mirpath. The association of biomarker candidates with diagnostic and prognostic performance was assessed using ROC and Kaplan-Meier survival analysis. miRNA-gene interaction analysis revealed the involvement of selected miRNAs in cancer progression. From eleven selected aberrant miRNAs, four of the miRNAs (hsa-mir-495, hsa-mir-592, hsa-mir-6501, and hsa-mir-937) are significantly detrimental to breast cancer diagnosis and prognosis. Hence, our result provides valuable information to explore miRNA’s role in each cancer stage between non-Hispanic white and non-Hispanic black.     

Recent Applications of Carbon Nanomaterials for microRNA Electrochemical Sensing

MicroRNA (miRNA) is an important tumor marker in the human body, and its early detection has a great influence on the survival rate of patients. Although there are many detection methods for miRNA at present such as northern blotting, real-time quantitative polymerase chain reaction, microarrays, and others, electrochemical biosensors have the advantages of low detection cost, small instrument size, simple operation, non-invasive detection and low consumption of reagents and solvents, and thus they play an important role in the early detection of cancer. In addition, with the development of nanotechnology, nano-biosensors show great potential. The application of various nanomaterials in the development of electrochemical biosensor has greatly improved the detection sensitivity of electrochemical biosensor. Among them, carbon nanomaterials which have unique electrical, optical, physical and chemical properties have attracted increasing attention. In particular, they have a large surface area, good biocompatibility and conductivity. Therefore, carbon nanomaterials combined with electrochemical methods can be used to detect miRNA quickly, easily and sensitively. In this review, we systematically review recent applications of different carbon nanomaterials (carbon nanotubes, graphene and its derivatives, graphitic carbon nitride, carbon dots, graphene quantum dots and other carbon nanomaterials) for miRNA electrochemical detection. In addition, we demonstrate the future prospects of electrochemical biosensors modified by carbon nanomaterials for the detection of miRNAs, and some suggestions for their development in the near future.     

Entropy-driven reactions in living cells for assay let-7a microRNA

Imaging of microRNA (miRNA) in living cells could facilitate the monitoring of the expression and distribution of miRNA and research on miRNA-related diseases. Given the low expression levels and even down-regulation of cellular miRNA that is associated with some diseases, enzyme-free amplification strategies are imperative for intracellular miRNA assay. In this work, we report an entropy-driven reaction for amplification assay miRNA with a detection limit of 0.27 pM. The resulting signal amplification provides excellent recognition and signal enhancement of specific miRNAs in living cells. This method supplies accurate information regarding cellular miRNA-related biological events and provides a new tool for highly sensitive and simultaneous imaging of multiple low-level biomarkers, thereby improving the accuracy of early disease diagnosis.     

Solution-phase detection of dual microRNA biomarkers in serum

A strategy for the simultaneous detection of multiple microRNA (miRNA) targets was developed utilizing fluorophore/quencher-labeled oligonucleotide probe sets. Two miRNA targets (miR-155 and miR-103), whose misregulation has afforded them status as putative biomarkers in certain types of cancer, were detected using our assay design. In the absence of target, the complementary fluorophore-probe and quencher-probe hybridize, resulting in a fluorescence resonance energy transfer-based quenching of the fluorescence signal. In the presence of unlabeled target, however, the antisense quencher-probe can hybridize with the target, resulting in increased fluorescence intensity as the quencher-probe is sequestered beyond the Förster radius of the fluorescent-probe. The assay design was tested in multiple matrices of buffer, cellular extract, and serum; and detection limits were found to be matrix-dependent, ranging from 0.34 to 8.89 pmol (3.4–59.3 nM) for miR-155 and 2.90–11.8 pmol (19.3–79.0 nM) for miR-103. Single, double, and triple nucleotide selectivity was also tested. Additionally, miR-155 concentrations were assessed in serum samples obtained directly from breast cancer patients without the need for RNA extraction. This assay is quantitative, possesses a low detection limit, can be applied in multiple complex matrices, and can obtain single-nucleotide selectivity. This method can be employed for the multiplex detection of solution-phase DNA or RNA targets and, more specifically, for the direct detection of serum miRNA biomarkers.     

Ratiometric Detection of microRNA Using Hybridization Chain Reaction and Fluorogenic Silver Nanoclusters

miRNA (miR)-155 is a potential biomarker for breast cancers. We aimed at developing a nanosensor for miR-155 detection by integrating hybridization chain reaction (HCR) and silver nanoclusters (AgNCs). HCR serves as an enzyme-free and isothermal amplification method, whereas AgNCs provide a built-in fluorogenic detection probe that could simplify the downstream analysis. The two components were integrated by adding a nucleation sequence of AgNCs to the hairpin of HCR. The working principle was based on the influence of microenvironment towards the hosted AgNCs, whereby unfolding of hairpin upon HCR has manipulated the distance between the hosted AgNCs and cytosine-rich toehold region of hairpin. As such, the dominant emission of AgNCs changed from red to yellow in the absence and presence of miR-155, enabling a ratiometric measurement of miR with high sensitivity. The limit of detection (LOD) of our HCR-AgNCs nanosensor is 1.13 fM in buffered solution. We have also tested the assay in diluted serum samples, with comparable LOD of 1.58 fM obtained. This shows the great promise of our HCR-AgNCs nanosensor for clinical application.     

Graphene Oxide Modified Chemically Activated Graphite Electrodes for Detection of microRNA

In our study, graphene oxide (GO) modified graphite electrodes were used for sensitive and selective impedimetric detection of miRNA. After chemical activation of pencil graphite electrode (PGE) surface using covalent agents (CA), GO modification was performed at the surface of chemically activated PGE. Then, CA‐GO‐PGEs were applied for impedimetric miRNA detection. The microscopic and electrochemical characterization of CA‐GO‐PGEs was performed by scanning electron microscopy (SEM) and electrochemical impedance spectroscopy (EIS). The optimization of experimental conditions; such as GO concentration, DNA probe concentration and miRNA target concentration was performed by using EIS technique. After the hybridization occurred between miRNA‐34a RNA target and its complementary DNA probe, the hybrid was immobilized onto the surface of CA‐GO‐PGEs. Then, the impedimetric detection of miRNA‐DNA hybridization was performed by EIS. The selectivity of our assay was also tested under the optimum experimental conditions.     

Plant microRNA detection using the circular code information

In this paper we present a new computational method leading to the identification of a new property in the plant microRNAs. This property which is based on the circular code information is then used to detect microRNAs in plants. The common C(3) circular code X is a set of 20 trinucleotides identified in the reading frames of both eukaryotic and prokaryotic genes allowing retrieval of any frame in genes, locally anywhere in the three frames (reading frame and its two shifted frames) and automatically with the same window length of 13 nucleotides in each frame. This code X is detected around the beginning of microRNAs. This method based only on the internal structure of genes, i.e. the circular code, allows sensible and precise microRNA site identification in precursor microRNAs with a sliding window of only 14 nucleotides.     

Multiplexed detection methods for profiling microRNA expression in biological samples

The recent discovery of short, non-protein coding RNA molecules, such as microRNA molecules (miRNAs), that can control gene expression has unveiled a whole new layer of complexity in the regulation of cell function. Since 2001, there has been a surge of interest in understanding the regulatory role of the hundreds to thousands of miRNAs expressed in both plants and animals. Significant progress in this area requires the development of quantitative bioanalytical methods for the rapid, multiplexed detection of all miRNAs that are present in a particular cell or tissue sample. In this Minireview, we discuss some of the latest methods for high-throughput miRNA profiling and the unique technological challenges that must be surmounted in this endeavor.     

Multiplexed microRNA detection by capillary electrophoresis with laser-induced fluorescence

In this study, we developed a novel assay that simultaneously detects multiple miRNAs (microRNAs) within a single capillary by combining a tandem adenosine-tailed DNA bridge-assisted splinted ligation with denaturing capillary gel electrophoresis with laser-induced fluorescence. This proposed method not only represents a significant improvement in resolution but also allows for the detection of multiple miRNAs within a single capillary based on the length differences of specified target bridge DNA. The assay's linear range covers three orders of magnitude (1.0 nM to 1.0 pM) with a limit of detection (S/N=3) as low as 190 fM (2.5 zmol). Five miRNAs of Epstein-Barr virus (EBV) were also detected in EBV-infected nasopharyngeal carcinoma cells, while they did not appear in non-virus infected cells. Moreover, the electropherogram indicated that the screening of isomiRs (isomer of miRNA) of BART2 by CE-LIF is feasible by our proposed method. The developed electrophoresis-based method for miRNA detection is fast, amplification-free, multiplexed and cost-effective, making it potentially applicable to large-scale screening of isomiRs.     

Temperature-dependent photoluminescence of water-soluble quantum dots for a bioprobe

The photoluminescence of water-soluble CdSe/ZnS core/shell quantum dots is found to be temperature-dependent: as temperature arising from 280 K to 351 K, the photoluminescence declines with emission peak shifting towards the red at a rate of ∼0.11 nm K⁻¹. And the studies show that the photoluminescence of water-soluble CdSe/ZnS quantum dots with core capped by a thinner ZnS shell is more sensitive to temperature than that of ones with core capped by a thicker one. That is, with 50% decrement of the quantum yield the temperature of the former need to arise from 280 K to 295 K, while the latter requires much higher temperature (315.6 K), which means that the integrality of shell coverage is a very important factor on temperature-sensitivity to for the photoluminescence of water-soluble CdSe/ZnS quantum dots. Moreover, it is found that the water-soluble CdSe quantum dots with different core sizes, whose cores are capped by thicker ZnS shells, possess almost the same sensitivity to the temperature. All of the studies about photoluminescence temperature-dependence of water-soluble CdSe/ZnS core/shell quantum dots show an indispensable proof for their applications in life science.     

Magnetic bead-based hybridization assay for electrochemical detection of microRNA

Aberrant expression of microRNAs (miRNAs), short non-coding RNA molecules regulating gene expression, is often found in tumor cells, making the miRNAs suitable candidates as cancer biomarkers. Electrochemistry is an interesting alternative to current standard methods of miRNA detection by offering cheaper instrumentation and faster assays times. In this paper, we labeled miRNA in a quick, simple, two-step procedure with electroactive complex of osmium(VI) and 2,2′-bipyridine, Os(VI)bipy, which specifically binds to the ribose at the 3′-end of the miRNA, and hybridized such labeled miRNA with biotinylated capture probe attached to the streptavidin magnetic beads. Labeled miRNA was then detected at hanging mercury drop electrode at femtomole level due to an electrocatalytic nature of the peak from the Os(VI)bipy label. We obtained good selectivity of the assay using elevated hybridization temperatures for better discrimination of perfect duplex from single and double mismatches. After optimization of the protocol, we demonstrated feasibility of our assay by detecting target miRNA in real total RNA samples isolated from human cancer cells.     

An electrochemical signal 'off-on' sensing platform for microRNA detection

The abnormal expression of microRNAs (miRNAs) in many solid tumors makes miRNAs potential biomarkers for disease diagnosis and highlights the need for the sensitive and selective detection of miRNAs. In the present work, an 'off-on' signaling genosensor platform for miRNA-21 detection was well developed. This tactic was based on a locked nucleic acid-integrated nucleic acid hairpin probe, a biotin-labeled bridge DNA-AuNPs-bio-barcode signal amplification unit and enzymatic signal amplification. The test is simple, fast and ultrasensitive with a linear range of 0.01-700 pM. The detection limit was estimated to be 6 fM. The overexpression of miRNA-21 was confirmed in total RNA extracted from human hepatocarcinoma cells BEL-7402 and human HeLa cells compared with the control sample extracted from normal human hepatic L02 cells. This method does not need miRNA-21 labeling, isolation, enrichment or PCR amplification. The performance of the assay developed here could satisfy the need for rapid, easy, sensitive and specific early cancer diagnosis in clinical diagnostics.     

Development of a Urea Bioprobe Based on Platinized Boron‐Doped Diamond Electrodes

Urea (CH₆ON₂) is one of the main human nitrogen‐based metabolic wastes. The concentration of urea in blood lies between 2.5–7 mM for healthy individuals, and is commonly used as an indicator for several diseases that may alter this value. Spectrophotometric methods are employed for the determination of blood urea concentration during clinical assays. Although these methods are sensitive, they make use of toxic reagents and complex reaction schemes. Therefore, in this research we present the bioelectrochemical determination of urea by the use of the protein urease (E.C.3.1.1.5) along with a nano‐platinized boron‐doped diamond electrode. This approach has been proven to be efficient and sensitive providing a platform with detection limits of 1.79 mM (S/N=3). The linear range resulted from 1 mM to 25 mM for the determination of urea, and response time of five minutes.     

An innovative strategy for direct electrochemical detection of microRNA biomarkers

We report an electrochemical method for direct, reagentless, and label-free detection of microRNA, based on a conjugated copolymer, poly(5-hydroxy-1,4-naphthoquinone-co-5-hydroxy-2-carboxyethyl-1,4-naphthoquinone), acting as hybridization transducer. Hybridization between the oligonucleotide capture probe and a microRNA target of 22 base pairs generates an increase in the redox current (“signal-on”), which is evidenced by square wave voltammetry. Selectivity is good, with little hybridization for non-complementary targets, and the limit of detection reaches 650 fM. It is also evidenced that this sensitivity benefits from the high affinity of DNA for RNA.

Enzyme-free and multiplexed microRNA detection using microRNA-initiated DNA molecular motor

In this work, we have developed a sensitive, simple, and enzyme-free assay for detection of microRNAs (miRNAs) by means of a DNA molecular motor consisting of two stem-loop DNAs with identical stems and complementary loop domains. In the presence of miRNA target, it can hybridize with one of the stem-loop DNA to open the stem and to produce a miRNA/DNA hybrid and a single strand (ss) DNA, the ssDNA will in turn hybridize with another stem-loop DNA and finally form a double strand (ds) DNA to release the miRNA. One of the stem-loop DNA is double-labeled by a fluorophore/quencher pair with efficiently quenched fluorescence. The formation of dsDNA can produced specific fluorescence signal for miRNA detection. The released miRNA will continuously initiate the next hybridization of the two stem-loop DNAs to form a cycle-running DNA molecular motor, which results in great fluorescence amplification. With the efficient signal amplification, as low as 1 pmol/L miRNA target can be detected and a wide dynamic range from 1 pmol/L to 2 nmol/L is also obtained. Moreover, by designing different stem-loop DNAs specific to different miRNA targets and labeling them with different fluorophores, multiplexed miRNAs can be simultaneously detected in one-tube reaction with the synchronous fluorescence spectrum (SFS) technique.     

Mass spectrometric detection in chromatography. Trends and perspectives

The newest results in the use of miscellaneous mass spectrometric detection methods in various chromatographic techniques are compiled and critically evaluated. Examples of application in clinical chemistry, health care, and in the analysis of pharmaceuticals, environmental pollutants, foods and food products are given. The benefits and drawbacks of MS detection are discussed, and future trends are briefly discussed.     

Highly sensitive detection of microRNA by chemiluminescence based on enzymatic polymerization

We have developed a new methodology for miRNA assay using chemiluminescence imaging by poly(U) polymerase catalyzed miRNA polymerization. This method is very sensitive with a 50 fM limit of detection, which is comparable to or better than current assay methods. Multiplex detection for miRNA can be easily realized by introducing different capture probes onto the biosensor array, which will make it highly versatile for various research purposes.     

Study on molecular interactions between proteins on live cell membranes using quantum dot-based fluorescence resonance energy transfer

Mouse anti-human CD71 monoclonal antibody (anti-CD71) was conjugated with red quantum dots (QDs; 5.3 nm, emission wavelength λ _em = 614 nm) and used to label HeLa cells successfully. Then green QD-labeled goat anti-mouse immunoglobulin G (IgG; the size of the green QDs was 2.2 nm; λ _em = 544 nm) was added to bind the red-QD-conjugated anti-CD71 on the cell surface by immunoreactions. Such interaction between anti-CD71 and IgG lasted 4 min and was observed from the fluorescence spectra: the fluorescence intensity of the “red” peak at 614 nm increased by 32%; meanwhile that of the “green” one at 544 nm decreased by 55%. The ratio of the fluorescence intensities (I _544 nm/I _614 nm) decreased from 0.5 to 0.2. The fluorescence spectra as well as cell imaging showed that fluorescence resonance energy transfer took place between these two kinds of QDs on the HeLa cells through interactions between the primary antibody and the secondary antibody.     

生物探针与脱氧核糖核酸的结合模式及其分光光度法测定的进展

对生物探针与脱氧核糖核酸（DNA）的结合模式及有机染料分光光度法测定DNA的研究进展进行了综述。引用文献71篇。