MicroRNAs as novel biological targets for detection and regulation

MicroRNA expression profile of HCT-8 cells in the early phase of Cryptosporidium parvum infection

Background

Cryptosporidium parvum is an important zoonotic parasitic disease worldwide, but the molecular mechanisms of the host–parasite interaction are not fully understood. Noncoding microRNAs (miRNAs) are considered key regulators of parasitic diseases. Therefore, we used microarray, qPCR, and bioinformatic analyses to investigate the intestinal epithelial miRNA expression profile after Cryptosporidium parvum infection.

Results

Twenty miRNAs were differentially expressed after infection (four upregulated and 16 downregulated). Further analysis of the differentially expressed miRNAs revealed that many important cellular responses were triggered by Cryptosporidium parvum infection, including cell apoptosis and the inflammatory and immune responses.

Conclusions

This study demonstrates for the first time that the miRNA expression profile of human intestinal epithelium cells is altered by C. parvum infection. This dysregulation of miRNA expression may contribute to the regulation of host biological processes in response to C. parvum infection, including cell apoptosis and the immune responses. These results provide new insight into the regulatory mechanisms of host miRNAs during cryptosporidiosis, which may offer potential targets for future C. parvum control strategies.

Electronic supplementary material

The online version of this article (10.1186/s12864-018-5410-6) contains supplementary material, which is available to authorized users.

MicroRNA‑192 acts as a tumor suppressor in colon cancer and simvastatin activates miR‑192 to inhibit cancer cell growth

Colon cancer is one of the most common malignant tumors worldwide. Understanding the underlying molecular mechanisms is crucial for the development of therapeutic strategies for the treatment of patients with colon cancer. In the present study, a novel tumor suppressive microRNA, miR‑192, was demonstrated to be markedly downregulated in colon cancer cells compared with normal colon cells. By overexpressing miR‑192 in colon cancer HCT‑116 cells, the results of the present study revealed that miR‑192 inhibits cell proliferation, migration and invasion. Bioinformatics were used to determine the target gene of miR‑192 and Ras‑related protein Rab‑2A (RAB2A) was identified as a downstream target of miR‑192. Following the determination of the role of the miR‑192‑RAB2A pathway in colon cancer, small molecules that may regulate miR‑192 were screened and the results demonstrated that simvastatin is an activator of miR‑192. Furthermore, simvastatin upregulated miR‑192 and inhibited the expression of downstream targets of miR‑192, which subsequently led to suppressed proliferation, migration and invasion of colon cancer cells. In conclusion, the present study identified a novel colon cancer cell suppressor, as well as a small‑molecule activator of the tumor suppressor miR‑192, which may represent a therapeutic strategy for the treatment of patients with colon cancer.

The construction of DNAzyme-based logic gates for amplified microRNA detection and cancer recognition

A series of duplex-specific nuclease-based DNAzyme logic gates was established for detecting multiple low-abundance microRNAs.

A novel ratiometric SERS biosensor with one Raman probe for ultrasensitive microRNA detection based on DNA hydrogel amplification

A ratiometric SERS biosensor with DNA hydrogel-captured glucose oxidase amplification method was fabricated to detect microRNA 122.

Recent advances in nanomaterial-based electrochemical and optical sensing platforms for microRNA assays

This review describes recent efforts in the application of nanomaterials as sensing elements in electrochemical and optical miRNAs assays.

Non-viral nanocarriers for intracellular delivery of microRNA therapeutics

MicroRNAs are small regulatory noncoding RNAs that regulate various biological processes. Herein, we will present the development of the strategies for intracellular miRNAs delivery, and specially focus on the rational designed routes, their mechanisms of action, as well as potential therapeutics used in the host cells orin vivostudies.

MicroRNA-384 regulates cell proliferation and apoptosis through directly targeting WISP1 in laryngeal cancer

Laryngeal cancer (LC) is an increasingly common malignant tumors of head and neck cancer. Aberrant expression of microRNA (miRNA) is closely related with LC development. In the current study, we investigated the biological function and underlying molecular mechanism of miR-384 in LC. The results showed that the miR-384 expression was markedly downregulated in LC tissue and cell lines (TU212 and TU686) as compared with that of adjacent nontumor tissues and a normal human bronchial epithelial cell line. Next, we performed gain-of-function and loss-of-function experiments in the TU212 and TU686 cells by transfecting the cells with miR-384 mimics, miR-384 inhibitor, or miRNA control. Moreover, results showed that miR-384 mimic remarkably inhibited LC cell proliferation, which was notably decreased by miR-384 inhibitor. Furthermore, miR-384 mimics notably increased the amounts of DNA fragmentation from the apoptotic cells (a hallmark of apoptosis) and the caspase-3 activity, whereas miR-384 inhibitor resulted in a decline of DNA fragmentation and the caspase-3 activity compared with its control. In addition, a dual-luciferase reporter assay confirmed that Wnt-induced secreted protein-1 (WISP1) gene was a direct target of miR-384. MiR-384 mimic remarkably inhibited the messenger RNA and protein expression of WISP1, which was upregulated by miR-384 inhibitor as compared to its control. WISP1 knockdown by small interfering RNA inhibited LC cell proliferation and promoted cell apoptosis. WISP1 overexpression partly abrogates the effect of miR-384 overexpression. Taken together, these data indicate that miR-384 regulates LC cell proliferation and apoptosis through targeting WISP1 signaling pathway, providing a novel insight into the LC treatment.

Fluorescent miRNA analysis enhanced by mesopore effects of polydopamine nanoquenchers

The combination of fluorophore-labelled single-strand DNA probes and nanomaterial quenchers has shown great potential in miRNA detection. The development of advanced detection systems by understanding and controlling the fluorescence quenching/recovery via nanoquenchers' microstructures and local morphologies is an attractive area warranting further investigations. Inspired by nanopore sequencing, we present a novel miRNA sensing strategy using fluorophore-labeled DNA as probes and a type of large-pore-sized mesoporous polydopamine nanoparticles (MPDA-L, 70 nm in diameter) as fluorescence quenchers. It is revealed that the quenching efficiency of MPDA-L towards the fluorophore labelled on the probe, reached more than 99% at a relatively low particle concentration. Moreover, the mesopores effectively protected the probe DNA from cleavage by DNase I which was used for signal amplification. Sensitive detection of miRNA with a low detection limit of 32-40 pM, as well as a linear detection range of up to 5 nM, was realized by the mesopore effects via a greatly improved differential affinity of ssDNA and the probe-miRNA heteroduplex toward the surface of nanoquenchers. Interestingly, enhanced DLVO (Derjaguin-Landau-Verwey-Overbeek) repulsion generated inside the pore surface by the negative surface-curvature effect correlates with the improved duplex detachment and fluorescence recovery. The developed strategy can be successfully applied to quantify down-regulated let-7a and up-regulated miRNA-21 in different types of cancer cells by using total RNA samples from cell lysate. These findings are expected to inspire strategies and pave a way for utilizing porous nanomaterials for constructing miRNA detection systems.

Regulation of capillary tubules and lipid formation in vascular endothelial cells and macrophages via extracellular vesicle-mediated microRNA-4306 transfer

Objective

This study aimed to examine regulation of capillary tubules and lipid formation in vascular endothelial cells and macrophages via extracellular vesicle-mediated microRNA (miRNA)-4306 transfer

Methods

Whole blood samples (12 mL) were collected from 53 patients, and miR-4306 levels in extracellular vesicles (EVs) were analyzed by reverse transcription-polymerase chain reaction. Human coronary artery vascular endothelial cells (HCAECs) and human monocyte-derived macrophages (HMDMs) were transfected with a scrambled oligonucleotide, an miR-4306 mimic, or an anti-miR-4306 inhibitor. The direct effect of miR-4306 on the target gene was analyzed by a dual-luciferase reporter assay.

Results

EV-contained miR-4306 released from HMDMs was significantly upregulated in coronary artery disease. Oxidized low-density lipoprotein (ox-LDL)-stimulated HMDM-derived EVs inhibited proliferation, migration, and angiogenesis abilities of HCAECs in vitro. However, ox-LDL-stimulated HCAEC-derived EVs enhanced lipid formation of HMDMs. The possible mechanism of these findings was partly due to EV-mediated miR-4306 upregulation of the Akt/nuclear factor kappa B signaling pathway.

Conclusions

Paracrine cellular crosstalk between HCAECs and HMDMs probably supports the pro-atherosclerotic effects of EVs under ox-LDL stress.

Upconversion nanocrystal 'armoured' silica fibres with superior photoluminescence for miRNA detection

We have fabricated a flexible membrane, consisting of SiO2 nanofibres armoured with upconversion nanoparticles, exhibiting intense photoluminescence. These assemblies were subsequently grafted with molecular beacons to produce a biosensor suitable for the detection of specific microRNA and with applications in early cancer detection and point-of-care diagnosis.

Upregulated miR-1258 regulates cell cycle and inhibits cell proliferation by directly targeting E2F8 in CRC

OBJECTIVES

MicroRNAs (miRNAs) as small noncoding RNA molecules function by regulating their target genes negatively. MiR-1258 was widely researched in multicancers, but its role remains unclear in colorectal cancer (CRC).

METHODS

The expression of miR-1258 and its specific target gene were detected in human CRC specimens and cell lines by miRNA RT-PCR, qRT-PCR and Western blot. The effects of miR-1258 on CRC proliferation were evaluated using CCK-8 assays, EdU incorporation, colony formation assays and cell-cycle assays; in vitro and the in vivo effects were investigated using a mouse tumorigenicity model. Luciferase reporter and RIP assays were employed to identify interactions between miR-1258 and its specific target gene.

RESULTS

MiR-1258 was downregulated in CRC tissues and CRC cell lines, and upregulated miR-1258 was proved to inhibit proliferation and arrest cell cycle at G0/G1 in vitro and vivo. Luciferase reporter, RIP and western blot assays revealed E2F8 to be a direct target of miR-1258. The effects of miR-1258 in proliferation and cell cycle regulation can be abolished by E2F8 through rescue experiments. By directly targeting E2F8, miR-1258 influenced the expression of several cell-cycle factors, including cyclin D1 (CCND1) and cyclin dependent kinase inhibitor 1A (p21).

CONCLUSION

MiR-1258 may function as a suppressive factor by negatively controlling E2F8, thus, highlighting the potential role of miR-1258 as a therapeutic target for human CRC.

Integration of T7 exonuclease-triggered amplification and cationic conjugated polymer biosensing for highly sensitive detection of microRNA

A novel and highly sensitive method for detection of microRNA (miRNA) was developed by integration of T7 exonuclease-triggered amplification and cationic conjugated polymer (CCP) biosensing. First, a fluorescein-labeled probe was designed with the complementary sequence to the target miRNA. When target miRNA was absent in the solution, the fluorescence probe interacted with CCP through the strong electrostatic interactions, leading to the highly efficient fluorescence resonance energy transfer (FRET) from CCP to fluorescein. In the presence of target miRNA, the probe hybridized with the miRNA to form DNA/miRNA duplex hybrids. Then, T7 exonuclease digested cyclically the fluorescence probes in hybrids and triggered the enzyme amplification reaction, generating a large number of single nucleotides. Owing to the weak electrostatic interaction between CCP and the single nucleotide, the FRET from CCP to fluorescein would not take place, which effectively reduced the background and significantly enhanced the sensitivity and the dynamic range of miRNA detection. The linear range of the assay was 0.2-100 pM and the detection limit 0.08 pM was 58 times lower than that of the endonuclease-based assay. The method is simple, cost-effective, and with no need for the sophisticated instrument, and has broad application prospects for miRNA detection and early diagnosis.

Nicking-enhanced rolling circle amplification for sensitive fluorescent detection of cancer-related microRNAs

In this study, a biosensing system based on nicking-enhanced rolling circle amplification (N-RCA) was proposed for the highly sensitive detection of cancer-related let-7a microRNA (miRNA). The sensing system consists of a padlock probe (PP), which contains a target recognition sequence and two binding sites for nicking endonuclease (NEase), and molecular beacon (MB) as reporting molecule. Upon hybridization with let-7a, the PP can be circularized by ligase. Then, the miRNA acted as polymerization primer to initiate rolling circle amplification (RCA). With the assistance of NEase, RCA products can be nicked on the cyclized PP and are displaced during the subsequent duplication process, generating numerous nicked fragments (NFs). These NFs not only induce another RCA reaction but also open the molecular beacons (MBs) via hybridization, leading to significantly amplified fluorescence signal. Under the optimized conditions, this method exhibits high sensitivity toward target miRNA let-7a with a detection limit of as low as 10 pM, a dynamic range of three orders of magnitude is achieved, and its family member is easily distinguished even with only one mismatched base. Meanwhile, it displays good recovery and satisfactory reproducibility in fetal bovine serum (FBS). Therefore, these merits endow the newly proposed N-RCA strategy with powerful implications for miRNA detection. Graphical abstract A biosensing system based on nicking-enhanced rolling circle amplification (N-RCA) for the highly sensitive detection of cancer-related let-7a microRNA.

BMSCs and miR-124a ameliorated diabetic nephropathy via inhibiting notch signalling pathway

BMSCs are important in replacement therapy of diabetic nephropathy (DN). MiR‐124a exerts effect on the differentiation capability of pancreatic progenitor cells. The objective of this study was to explore the molecular mechanisms, the functions of miR‐124a and bone marrow mesenchymal stem cells (BMSCs) in the treatment of DN. Characterizations of BMSCs were identified using the inverted microscope and flow cytometer. The differentiations of BMSCs were analysed by immunofluorescence assay and DTZ staining. The expression levels of islet cell‐specific transcription factors, apoptosis‐related genes, podocytes‐related genes and Notch signalling components were detected using quantitative real‐time reverse transcription PCR (qRT‐PCR) and Western blot assays. The production of insulin secretion was detected by adopting radioimmunoassay. Cell proliferation and apoptosis abilities were detected by CCK‐8, flow cytometry and TUNEL assays. We found that BMSCs was induced into islet‐like cells and that miR‐124a could promote the BMSCs to differentiate into islet‐like cells. BMSCs in combination with miR‐124a regulated islet cell‐specific transcription factors, apoptosis‐related genes, podocytes‐related genes as well as the activity of Notch signalling pathway. However, BMSCs in combination with miR‐124a relieved renal lesion caused by DN and decreased podocyte apoptosis caused by HG. The protective effect of BMSCs in combination with miR‐124a was closely related to the inactivation of Notch signalling pathway. MSCs in combination with miR‐124a protected kidney tissue from impairment and inhibited nephrocyte apoptosis in DN.

High-Throughput and Sensitive Fluorimetric Strategy for MicroRNAs in Blood Using Wettable Microwells Array and Silver Nanoclusters with Red Fluorescence Enhanced by Metal Organic Frameworks

A high-throughput and sensitive fluorimetric analysis method has been developed with wettable microwells array for probing short-chain microRNAs (miRNAs) in blood using silver nanoclusters (AgNCs) with red fluorescence amplified and stabilized by metal organic frameworks (MOFs). Glass slides were first spotted with polyacrylic acid to form hydrophilic microdots and then patterned with hydrophobic hexadecyltrimethoxysilane, followed by etching the microdots to yield the microwells array. Furthermore, the DNA capture probes with silver-binding G sequences were covalently bound onto the functionalized microwells to hybridize with targeting miRNAs. Exonuclease I catalytic digestion was then conducted to remove any single-strand DNA probes unhybridized. Eventually, AgNCs were applied to specifically recognize the G sequences of DNA probes survived to be further coated with MOFs of zeolitic imidazolate framework (ZIF-8). Unexpectedly, the red fluorescence of AgNCs probes could be dramatically enhanced due to the "electron-donor effect" of nitrogen-containing ligands of ZIF-8 coatings, together with improved sensing stability. High detection sensitivity and reproducibility could thereby be expected for detecting miRNAs in the blood with the concentrations linearly ranging from 0.175 to 500 pM. Markedly different from the common sandwiched DNA detection methods, the developed fluorimetric strategy using AgNCs coated with MOFs and DNA probes designed with silver-recognizing sequences would be tailored for quantifying various kinds of short-chain miRNAs with low levels in the complicated blood media.

miR-589 promotes gastric cancer aggressiveness by a LIFR-PI3K/AKT-c-Jun regulatory feedback loop

Background

As novel biomarkers for various cancers, microRNAs negatively regulate genes expression via promoting mRNA degradation and suppressing mRNA translation. miR-589 has been reported to be deregulated in several human cancer types. However, its biological role has not been functionally characterized in gastric cancer. Here, we aim to investigate the biological effect of miR-589 on gastric cancer and to reveal the possible mechanism.

Methods

Real-time PCR was performed to evaluate the expression of miR-589 in 34 paired normal and stomach tumor specimens, as well as gastric cell lines. Functional assays, such as wound healing, transwell assays and in vivo assays, were used to detect the biological effect of miR-589 and LIFR. We determined the role of miR-589 in gastric cancer tumorigenesis in vivo using xenograft nude models. Dual-luciferase report assays and Chromatin immunoprecipitation (ChIP) assay were performed for target evaluation, and the relationships were confirmed by western blot assay.

Result

MiR-589 expression was significantly higher in tumor tissues and gastric cancer cells than those in matched normal tissues and gastric epithelial cells, respectively. Clinically, overexpression of miR-589 is associated with tumor metastasis, invasion and poor prognosis of GC patients. Gain- and loss-of function experiments showed that miR-589 promoted cell migration, metastasis and invasion in vitro and lung metastasis in vivo. Mechanistically, we found that miR-589 directly targeted LIFR to activate PI3K/AKT/c-Jun signaling. Meanwhile, c-Jun bound to the promoter region of miR-589 and activated its transcription. Thus miR-589 regulated its expression in a feedback loop that promoted cell migration, metastasis and invasion.

Conclusion

Our study identified miR-589, as an oncogene, markedly induced cell metastasis and invasion via an atypical miR-589-LIFR-PI3K/AKT-c-Jun feedback loop, which suggested miR-589 as a potential biomarker and/or therapeutic target for the gastric cancer management.

Electronic supplementary material

The online version of this article (10.1186/s13046-018-0821-4) contains supplementary material, which is available to authorized users.

Small Molecule Inhibition of MicroRNA miR-21 Rescues Chemosensitivity of Renal-Cell Carcinoma to Topotecan

Chemical probes of microRNA (miRNA) function are potential tools for understanding miRNA biology that also provide new approaches for discovering therapeutics for miRNA-associated diseases. MicroRNA-21 (miR-21) is an oncogenic miRNA that is overexpressed in most cancers and has been strongly associated with driving chemoresistance in cancers such as renal cell carcinoma (RCC). Using a cell-based luciferase reporter assay to screen small molecules, we identified a novel inhibitor of miR-21 function. Following structure-activity relationship studies, an optimized lead compound demonstrated cytotoxicity in several cancer cell lines. In a chemoresistant-RCC cell line, inhibition of miR-21 via small molecule treatment rescued the expression of tumor-suppressor proteins and sensitized cells to topotecan-induced apoptosis. This resulted in a >10-fold improvement in topotecan activity in cell viability and clonogenic assays. Overall, this work reports a novel small molecule inhibitor for perturbing miR-21 function and demonstrates an approach to enhancing the potency of chemotherapeutics specifically for cancers derived from oncomir addiction.

A Review on Graphene-Based Nanomaterials in Biomedical Applications and Risks in Environment and Health

Graphene-based nanomaterials (GBNs) have attracted increasing interests of the scientific community due to their unique physicochemical properties and their applications in biotechnology, biomedicine, bioengineering, disease diagnosis and therapy. Although a large amount of researches have been conducted on these novel nanomaterials, limited comprehensive reviews are published on their biomedical applications and potential environmental and human health effects. The present research aimed at addressing this knowledge gap by examining and discussing: (1) the history, synthesis, structural properties and recent developments of GBNs for biomedical applications; (2) GBNs uses as therapeutics, drug/gene delivery and antibacterial materials; (3) GBNs applications in tissue engineering and in research as biosensors and bioimaging materials; and (4) GBNs potential environmental effects and human health risks. It also discussed the perspectives and challenges associated with the biomedical applications of GBNs.

Inferring potential small molecule-miRNA association based on triple layer heterogeneous network

Recently, many biological experiments have indicated that microRNAs (miRNAs) are a newly discovered small molecule (SM) drug targets that play an important role in the development and progression of human complex diseases. More and more computational models have been developed to identify potential associations between SMs and target miRNAs, which would be a great help for disease therapy and clinical applications for known drugs in the field of medical research. In this study, we proposed a computational model of triple layer heterogeneous network based small molecule–MiRNA association prediction (TLHNSMMA) to uncover potential SM–miRNA associations by integrating integrated SM similarity, integrated miRNA similarity, integrated disease similarity, experimentally verified SM–miRNA associations and miRNA–disease associations into a heterogeneous graph. To evaluate the performance of TLHNSMMA, we implemented global and two types of local leave-one-out cross validation as well as fivefold cross validation to compare TLHNSMMA with one previous classical computational model (SMiR-NBI). As a result, for Dataset 1, TLHNSMMA obtained the AUCs of 0.9859, 0.9845, 0.7645 and 0.9851 ± 0.0012, respectively; for Dataset 2, the AUCs are in turn 0.8149, 0.8244, 0.6057 and 0.8168 ± 0.0022. As the result of case studies shown, among the top 10, 20 and 50 potential SM-related miRNAs, there were 2, 7 and 14 SM–miRNA associations confirmed by experiments, respectively. Therefore, TLHNSMMA could be effectively applied to the prediction of SM–miRNA associations.

Improving the Signal-to-Background Ratio during Catalytic Hairpin Assembly through Both-End-Blocked DNAzyme

Catalyzed hairpin assembly (CHA) is an important DNA engineering tool for a variety of applications such as DNA nanotechnology and biosensing. Here we report a hairpin-type of both-end-blocked DNAzyme to improve the signal-to-background ratio during the CHA process. In the design, the DNAzyme activity can be blocked efficiently via locking both ends of the G-rich DNAzyme sequence in the loop and stem (blocking efficiency = 96%) and can be easily recovered during the CHA process (activation efficiency = 94%). The both-end-blocked DNAzyme is by far the most sensitive optical detection mode for monitoring the CHA process that can be used for determination of 0.05 fmol miRNA-21. The fabricated CHA-DNAzyme sensing system was also able to discriminate miRNA-21 from single-/three-base mismatch miRNA-21. The feasibility of real application was also tested via detection of miRNA-21 levels in tumor cell samples. Therefore, the sensing system with the advantages of convenience, high sensitivity, and selectivity is an appealing strategy for miRNA detection.

Curcumin suppresses the progression of laryngeal squamous cell carcinoma through the upregulation of miR-145 and inhibition of the PI3K/Akt/mTOR pathway

Background

Curcumin is a polyphenol extracted from the rhizomes of Curcuma longa with extensive biological and pharmacological effects. The present study aimed to investigate the mechanisms of curcumin in laryngeal squamous cell carcinoma (LSCC).

Methods

Quantitative real-time reverse transcriptase-polymerase chain reaction was performed to detect the expressions of miR-145 in LSCC tissues and cells. The effects of miR-145 and curcumin on cell proliferation, apoptosis, cell cycle, migration and invasion were explored by MTT assay, flow cytometry analysis, Transwell migration and invasion assay, respectively. The effects of miR-145 combined with curcumin on the phosphoinositol 1,3 kinase (PI3K)/protein kinase B (Akt)/mammalian target of rapamycin (mTOR) pathway were detected by Western blot analysis.

Results

miR-145 was significantly downregulated in LSCC tissues and cells. Curcumin administration upregulated miR-145 expression in LSCC cells in a dose-dependent manner. miR-145 overexpression and curcumin treatment both markedly suppressed cell proliferation, migration and invasion and induced cell cycle arrest and apoptosis in LSCC cells. Moreover, curcumin treatment reversed the enhanced effects on cell viability, migration and invasion and the inhibitory effects on apoptosis conferred by anti-miR-145 in LSCC cells. Curcumin treatment dramatically aggravated miR-145-induced inhibition of the PI3K/Akt/mTOR pathway and reversed anti-miR-145-mediated activation of the PI3K/Akt/mTOR pathway in LSCC cells.

Conclusion

Curcumin suppressed LSCC progression through the upregulation of miR-145 and inhibition of the PI3K/Akt/mTOR pathway.

Advances in Tetrazine Bioorthogonal Chemistry Driven by the Synthesis of Novel Tetrazines and Dienophiles

Bioorthogonal chemistry has found increased application in living systems over the past decade. In particular, tetrazine bioorthogonal chemistry has become a powerful tool for imaging, detection, and diagnostic purposes, as reflected in the increased number of examples reported in the literature. The popularity of tetrazine ligations are likely due to rapid and tunable kinetics, the existence of high quality fluorogenic probes, and the selectivity of reaction. In this Account, we summarize our recent efforts to advance tetrazine bioorthogonal chemistry through improvements in synthetic methodology, with an emphasis on developing new routes to tetrazines and expanding the range of useful dienophiles. These efforts have removed specific barriers that previously limited tetrazine ligations and have broadened their potential applications. Among other advances, this Account describes how our group discovered new methodology for tetrazine synthesis by developing a Lewis acid-promoted, one-pot method for generating diverse symmetric and asymmetric alkyl tetrazines with functional substituents in satisfactory yields. We attached these tetrazines to microelectrodes and succeeded in controlling tetrazine ligation by changing the redox state of the reactants. Using this electrochemical control process, we were able to modify an electrode surface with redox probes and enzymes in a site-selective fashion. This Account also describes how our group improved the ability of tetrazines to act as fluorogenic probes by developing a novel elimination-Heck cascade reaction to synthesize alkenyl tetrazine derivatives. In this approach, tetrazine was conjugated to fluorophores to produce strongly quenched probes that, after bioorthogonal reaction, are "turned on" to enhance fluorescence, in many cases by >100-fold. These probes have allowed no-wash fluorescence imaging in living cells and intact animals. Finally, this Account reviews our efforts to expand the range of dienophile substrates to make tetrazine bioorthogonal chemistry compatible with specific biochemical and biomedical applications. We found that methylcyclopropene is sufficiently stable and reactive in the biological milieu to act as an efficient dienophile. The small size of the reactive tag minimizes steric hindrance, allowing cyclopropene to serve as a metabolic reporter group to reveal biological dynamics and function. We also used norbornadiene derivatives as strained dienophiles to undergo tetrazine-mediated transfer (TMT) reactions involving tetrazine ligation followed by a retro-Diels-Alder process. This TMT reaction generates a pair of nonligating products. Using nucleic acid-templated chemistry, we have combined the TMT reaction with our fluorogenic tetrazine probes to detect endogenous oncogenic microRNA at picomolar concentrations. In a further display of dienophile versatility, we used a novel vinyl ether to cage a near-infrared fluorophore in a nonfluorescent form. Then we opened the cage in a "click to release" tetrazine bioorthogonal reaction, restoring the fluorescent form of the fluorophore. Combining this label with a corresponding nucleic acid probe allowed fluorogenic detection of target mRNA. In summary, this Account describes improvements in tetrazine and dienophile synthesis and application to advance tetrazine bioorthogonal chemistry. These advances have further enabled application of tetrazine ligation chemistry, not only in fundamental research but also in diagnostic studies.

Research Progress on Rolling Circle Amplification (RCA)-Based Biomedical Sensing

Enhancing the limit of detection (LOD) is significant for crucial diseases. Cancer development could take more than 10 years, from one mutant cell to a visible tumor. Early diagnosis facilitates more effective treatment and leads to higher survival rate for cancer patients. Rolling circle amplification (RCA) is a simple and efficient isothermal enzymatic process that utilizes nuclease to generate long single stranded DNA (ssDNA) or RNA. The functional nucleic acid unit (aptamer, DNAzyme) could be replicated hundreds of times in a short period, and a lower LOD could be achieved if those units are combined with an enzymatic reaction, Surface Plasmon Resonance, electrochemical, or fluorescence detection, and other different kinds of biosensor. Multifarious RCA-based platforms have been developed to detect a variety of targets including DNA, RNA, SNP, proteins, pathogens, cytokines, micromolecules, and diseased cells. In this review, improvements in using the RCA technique for medical biosensors and biomedical applications were summarized and future trends in related research fields described.

miR-483-5p promotes prostate cancer cell proliferation and invasion by targeting RBM5

OBJECTIVE

miR-483-5p has been identified as a miRNA oncogene in certain cancers. However, its role in prostate cancer has not been sufficiently investigated. In this study, we investigated the role of miR-483-5p in prostate cancer and examined RBM5 regulation by miR-483-5p.

MATERIAL AND METHODS

Expression levels of miR-483-5p were determined by quantitative real-time PCR. The effect of miR-483-5p on proliferation was evaluated by MTT assay, cell invasion was evaluated by trans-well invasion assays, and target protein expression was determined by western blotting in LNCaP, DU-145, and PC-3 cells. Luciferase reporter plasmids were constructed to confirm the action of miR-483-5p on downstream target gene RBM5 in HEK-293T cells.

RESULTS

we observed that miR-483-5p was upregulated in prostate cancer cell lines and tissues. A miR-483-5p inhibitor inhibited prostate cancer cell growth and invasion in DU-145 and PC-3 cells. miR-483-5p directly bound to the 3' untranslated region (3'UTR) of RBM5 in HEK-293T cells. RBM5 overexpression inhibited prostate cancer cell growth and invasion in LNCaP cells. Enforced RBM5 expression alleviated miR- 483-5p promotion of prostate cancer cell growth and invasion in LNCaP cells.

CONCLUSION

The present study describes a potential mechanism underlying a miR-483- 5p/RBM5 link that contributes to prostate cancer development.

A photo-degradable supramolecular hydrogel for selective delivery of microRNA into 3D-cultured cells

Multi-functional supramolecular hydrogels have emerged as smart biomaterials for diverse biomedical applications. Here we report a multi-functional supramolecular hydrogel formed by the conjugate of the bioactive GRGDS peptide with biaryltetrazole that is the substrate of photo-click reaction. The hydrogel was used as a biocompatible matrix to encapsulate live cells for 3D culture. The presence of the RGD epitope in the hydrogelator enhanced the interaction of the nanofiber with integrin over-expressing cells, which resulted in the selective enhancement in the miRNA delivery into the encapsulated U87 cells. The intramolecular photo-click reaction of the biaryltetrazole moiety in the hydrogelator leads to a sensitive photo-response of the hydrogel, which allowed photo-degradation of the hydrogel for release of the encapsulated live cells for further bio-assay of the intracellular species.

MicroRNAs as novel endogenous targets for regulation and therapeutic treatments

MicroRNAs (miRNAs) are small non-coding RNAs that have been identified as key endogenous biomolecules that are able to regulate gene expression at the post-transcriptional level. The abnormal expression or function of miRNAs has been demonstrated to be closely related to the occurrence or development of various human diseases, including cancers. Regulation of these abnormal miRNAs thus holds great promise for therapeutic treatments. In this review, we summarize exogenous molecules that are able to regulate endogenous miRNAs, including small molecule regulators of miRNAs and synthetic oligonucleotides. Strategies for screening small molecule regulators of miRNAs and recently reported small molecules are introduced and summarized. Synthetic oligonucleotides including antisense miRNA oligonucleotides and miRNA mimics, as well as delivery systems for these synthetic oligonucleotides to enter cells, that regulate endogenous miRNAs are also summarized. In addition, we discuss recent applications of these small molecules and synthetic oligonucleotides in therapeutic treatments. Overall, this review aims to provide a brief synopsis of recent achievements of using both small molecule regulators and synthetic oligonucleotides to regulate endogenous miRNAs and achieve therapeutic outcomes. We envision that these regulators of endogenous miRNAs will ultimately contribute to the development of new therapies in the future.

miR-23a acts as an oncogene in pancreatic carcinoma by targeting FOXP2

MicroRNAs have been reported to play an important role in tumor development and progression by targeting oncogenes and tumor suppressors. miR-23a has been described as significantly upregulated in multiple cancers and involved in tumorigenesis. The aim of this study was to evaluate the potential roles of miR-23a in pancreatic ductal adenocarcinoma (PDAC). We found that miR-23a level was significantly increased in tissues of PDAC compared with that in the control by real-time PCR. FOXP2 expression was downregulated and inversely correlated with miR-23a. miR-23a directly targeted the 3'-untranslated region of FOXP2 mRNA and repressed its expression. Mechanistically, enhancement of miR-23a by transfection with mimics in Aspc-1 cells significantly promoted cell proliferation and invasion, while miR-23a inhibitors transfection in SW1990 cells induced an inhibitory effect. Moreover, restoration of FOXP2 impaired the pro-proliferation and proinvasion effects of miR-23a, indicating FOXP2 is a direct mediator of miR-23a functions. In conclusion, our findings suggest a novel miR-23a/FOXP2 link contributing to PDAC development and invasion. It may be a potential diagnostic and therapeutic target for PDAC.

miR-211 promotes lens epithelial cells apoptosis by targeting silent mating-type information regulation 2 homolog 1 in age-related cataracts

AIM

To detect the expression of miR-211 in age-related cataract tissue, explore the effects of miR-211 on lens epithelial cell proliferation and apoptosis, and identify its target gene.

METHODS

This study used real-time quantitative polymerase chain reaction (RT-qPCR) to measure the expression of miR-211 and its predicted target gene [silent mating-type information regulation 2 homolog 1 (SIRT1)] in 46 anterior lens capsules collected from age-related cataract patients. Human lens epithelial cell line (SRA01/04) cells were transfected with either miR-211 mimics, mimic controls, miR-211 inhibitors or inhibitor controls, 72h after transfection, miRNA and protein expression of SIRT1 were measured using RT-qPCR and Western blotting; then cells were exposed to 200 µmol/L H₂O₂ for 1h, whereupon cell viability was measured by MTS assay, caspase-3 assay was performed. Dual luciferase reporter assay was performed to verify the relationship between miR-211 of SIRT1.

RESULTS

Compared to the control group, expression of miR-211 was significantly increased (P<0.001), the miRNA and protein expression of SIRT1 were significantly decreased (P<0.001) in the anterior lens capsules of patients with age-related cataracts. Relative to the control group, SIRT1 miRNA and protein levels in the miR-211 mimic group were significantly reduced, cell proliferation activity significantly decreased, and caspase-3 activity was significantly increased (P<0.001). In the miR-211 inhibitor group, SIRT1 miRNA and protein expression were significantly increased, cell proliferation activity significantly increased, and caspase-3 activity was significantly decreased (P<0.001). A dual luciferase reporter assay confirmed that SIRT1 is a direct target of miR-211.

CONCLUSION

miR-211 is highly expressed in the anterior lens capsules of patients with age-related cataracts. By negatively regulating the expression of SIRT1, miR-211 promotes lens epithelial cell apoptosis and inhibits lens epithelial cell proliferation.

Multi-Functional Peptide-MicroRNA Nanocomplex for Targeted MicroRNA Delivery and Function Imaging

Targeted delivery of microRNA (miRNA) mimics into specific cells/tissues and real-time monitoring on the biological function of delivered miRNA mimics at molecular level represent two major challenges in the development of miRNA-based therapeutics. Here we report a highly efficient method to address these two challenges simultaneously by using the self-assembled nanocomplex formed by miRNA mimics with a multi-functional peptide conjugate. Using the nanocomplex formed by tumor-suppressive miR-34a and the multi-functional peptide conjugate FA-R9-FP_cas3 , we demonstrated the highly efficient and target-selective delivery of miR-34a into HeLa cells and tumors. With the activatable fluorescence probe integrated in the peptide conjugate FA-R9-FP_cas3 , the intracellular function of miR-34a delivered by the nanocomplex to upregulate active Caspase-3 was imaged in real-time. The nanocomplex also showed significant therapeutic effects to induce apoptosis in HeLa cells and to suppress tumor growth upon tail vein injection into living mice bearing subcutaneous HeLa tumors.

Polydopamine-assisted versatile modification of a nucleic acid probe for intracellular microRNA imaging and enhanced photothermal therapy

MicroRNAs play an important role in various biological processes, and their aberrant expression is closely associated with various human diseases, especially cancer. Real-time monitoring of microRNAs in living cells may help us to understand their role in cellular processes, which can further provide a basis for diagnosis and treatment. In this study, polydopamine was used to assist the versatile modification of a nucleic acid probe for intracellular microRNA imaging and enhanced photothermal therapy. Polydopamine can be covalently linked with a thiol-terminated nucleic acid probe through the Michael addition reaction under slightly alkaline conditions. This modification is mild and can be performed directly in an aqueous solution, which can better resist hydrolysis than the traditional modification processes, resulting in a nanoprobe with better stability and higher loading of nucleic acids. This prepared nanoprobe can easily enter cells without transfection agents and then realize the imaging of intracellular miRNA through fluorescence restoration. Moreover, the coating of PDA can enhance the photothermal conversion efficiency of the nanoprobe, making it suitable for photothermal therapy of cancer. It is expected that the PDA-based versatile modification can help to construct a promising platform for tumor imaging and treatment.

Polydopamine can assist the versatile modification of a nucleic acid probe for intracellular miRNA responsed fluorescence imaging and enhanced photothermal therapy.

Paperfluidic Chip Device for Small RNA Extraction, Amplification, and Multiplexed Analysis

Small RNAs have been considered as potential biomarkers of various human diseases. Sensitive and multiplexed determination of small RNAs with point-of-care (POC) assay would be of great significance. Herein, an integrated paperfluidic chip device for multiplexed small RNA analysis was developed for the first time. In this system, the extraction and purification of small RNA was completed through a poly(ether sulfone) (PES) paper chip without the need for centrifugation. Subsequently, a newly designed hairpin probe-exponential amplification reaction (HP-EXPAR) was directly performed within the extraction paper chip. For the simultaneous realization of multiple detection, a multilayer paper chip was designed in a foldable manner with more portability and usability. Quantum dots (QDs) were employed as signal labels, which endowed this assay with high optical detection efficiency. Moreover, magnetic sheets were introduced as an alternative method for layer stacking, not only guaranteeing adjacent layers are in contact but also facilitating the sample dispersion. With these outstanding characteristics, our platform obtained a satisfactory sensitivity range from 3 × 10⁵ to 3 × 10⁸ copies with a limit of 3 × 10⁶ copies. Additionally, the multiplex small RNA analyses from various cancer cells were in good agreement with the results of the real-time polymerase chain reaction (qRT-PCR). More importantly, simultaneous analysis of two types of miRNAs from clinical tumor samples demonstrated the clinical applicability of the system. Therefore, the proposed paper-based device shows great promise for POC applications in the future.

Both plasma and tumor tissue miR-146a high expression correlates with prolonged overall survival of surgical patients with intrahepatic cholangiocarcinoma

The purpose of this study was to investigate the association of tumor tissue and plasma miR-146a/b expressions with the clinicopathological properties and overall survival (OS) in surgical patients with intrahepatic cholangiocarcinomas (ICC).Eighty-seven patients with ICC were enrolled. Tumor tissue and plasma sample were collected and miR-146a/b expressions were assessed by quantitative polymerase chain reaction (qPCR). The median follow-up duration was 31 months, and the last follow-up date was January 2017.miR-146a (P < .001) and miR-146b (P = .006) expressions in tumor tissue were positively associated with that in plasma. Tissue miR-146a was negatively correlated with age (P = .036), poor differentiation (P = .020), N stage (P = .020), and TNM stage (P = .007), as well as ECOG performance (P = .008), whereas plasma miR-146a was inversely associated with N stage (P = .003), TNM stage (P = .003), and ECOG performance (P = .011). Moreover, tissue miR-146b was negatively correlated with gender (P = .043) and T stage (P = .047). Kaplan-Meier curves suggested that high expression of tissue miR-146a (P < .001) and plasma miR-146a (P = .029) were correlated with prolonged OS. Nevertheless, no association of miR-146b expression in tumor tissue (P = .187) and plasma (P = .336) with OS was discovered. Univariate analysis indicated that both tissue miR-146a (P < .001) and plasma miR-146a (P = .035) could predict better OS, whereas multivariate analysis revealed that only tissue miR-146a (P = .001) high expression was an independent factor for prolonged OS.Both plasma and tissue miR-146a expression correlated with favorable OS, whereas only tissue miR-146a was an independent prognostic biomarker in surgical patients with ICC.

A Chiral-Nanoassemblies-Enabled Strategy for Simultaneously Profiling Surface Glycoprotein and MicroRNA in Living Cells

Assemblies of nanomaterials for biological applications in living cells have attracted much attention. Herein, graphene oxide (GO)-gold nanoparticle (Au NP) assemblies are driven by a splint DNA strand, which is designed with two regions at both ends that are complementary with the DNA sequence anchored on the surface of the GO and the Au NPs. In the presence of microRNA (miR)-21 and epithelial cell-adhesion molecule (EpCAM), the hybridization of miR-21 with a molecular probe leads to the separation of 6-fluorescein-phosphoramidite-modified Au NPs from GO, resulting in a decrease in the Raman signal, while EpCAM recognition reduces circular dichroism (CD) signals. The CD signals reverse from negative in original assemblies into positive when reacted with cells, which correlates with two enantiomer geometries. The EpCAM detection has a good linear range of 8.47-74.78 pg mL^-1 and a limit of detection (LOD) of 3.63 pg mL^-1 , whereas miR-21 detection displays an outstanding linear range of 0.07-13.68 amol ng^-1_RNA and LOD of 0.03 amol ng^-1_RNA . All the results are in good agreement with those of the Raman and confocal bioimaging. The strategy opens up an avenue to allow the highly accurate and reliable diagnosis (dual targets) of clinic diseases.

Lateral flow nucleic acid biosensor for sensitive detection of microRNAs based on the dual amplification strategy of duplex-specific nuclease and hybridization chain reaction

MicroRNAs (miRNAs) constitute novel biomarkers for various diseases. Accurate and quantitative analysis of miRNA expression is critical for biomedical research and clinical theranostics. In this study, a method was developed for sensitive and specific detection of miRNAs via dual signal amplification based on duplex specific nuclease (DSN) and hybridization chain reaction (HCR). A reporter probe (RP), comprising recognition sequence (3’ end modified with biotin) for a target miRNA of miR-21 and capture sequence (5’ end modified with Fam) for HCR product, was designed and synthesized. HCR was initiated by partial sequence of initiator probe (IP), the other part of which can hybridize with capture sequence of RP, and was assembled by hairpin probes modified with biotin (H1-bio and H2-bio). A miR-21 triggered cyclical DSN cleavage of RP, which was immobilized to a streptavidin (SA) coated magnetic bead (MB). The released Fam labeled capture sequence then hybridized with the HCR product to generate a detectable dsDNA. This polymer was then dropped on lateral flow strip and positive result was observed. The proposed method allowed quantitative sequence-specific detection of miR-21 (with a detection limit of 2.1 fM, S/N = 3) in a dynamic range from 100 fM to 100 pM, with an excellent ability to discriminate differences in miRNAs. The method showed acceptable testing recoveries for the determination of miRNAs in serum.

Production of a fluorescence resonance energy transfer (FRET) biosensor membrane for microRNA detection

MicroRNAs (miRNAs) play a key role in regulating gene expression but can be associated with abnormalities linked to carcinogenesis and tumor progression. Hence there is increasing interest in developing methods to detect these non-coding RNA molecules in the human circulation system. Here, a novel FRET miRNA-195 targeting biosensor, based on silica nanofibers incorporated with rare earth-doped calcium fluoride particles (CaF₂:Yb,Ho@SiO₂) and gold nanoparticles (AuNPs), is reported. The formation of a sandwich structure, as a result of co-hybridization of the target miRNA which is captured by oligonucleotides conjugated at the surface of CaF₂:Yb,Ho@SiO₂ fibers and AuNPs, brings the nanofibers and AuNPs in close proximity and triggers the FRET effect. The intensity ratio of green to red emission, I₅₄₁/I₆₅₀, was found to decrease linearly upon increasing the concentration of the target miRNA and this can be utilized as a standard curve for quantitative determination of miRNA concentration. This assay offers a simple and convenient method for miRNA quantification, with the potential for rapid and early clinical diagnosis of diseases such as breast cancer.

Identification of microRNA differentially expressed in three subtypes of non-small cell lung cancer and in silico functional analysis

Emerging studies demonstrated that miRNAs played fundamental roles in lung cancer. In this study, we attempted to explore the clinical significance of the miRNA signature in different histological subtypes of non-small cell lung cancer (NSCLC). Three miRNome profiling datasets (GSE19945, GSE25508 and GSE51853) containing lung squamous cell carcinoma (SCC), lung adenocarcinoma (ADC) and large cell lung cancer (LCLC) samples were obtained for bioinformatics and survival analysis. Moreover, pathway enrichment and coexpression network were performed to explore underlying molecular mechanism. MicroRNA-375 (miR-375), miR-203 and miR-205 were identified as differentially expressed miRNAs (DEmiRNAs) which distinguished SCC from other NSCLC subtypes. Pathway enrichment analysis suggested that Hippo signaling pathway was combinatorically affected by above mentioned three miRNAs. Coexpression analysis of three miRNAs and the Hippo signaling pathway related genes were conducted based on another dataset, GSE51852. Four hub genes (TP63, RERE, TJP1 and YWHAE) were identified as the candidate targets of three miRNAs, and three of them (TP63, TJP1 and YWHAE) were validated to be downregulated by miR-203 and miR-375, respectively. Finally, survival analysis further suggested the prognostic value of three-miRNA signature in SCC patients. Taken together, our study compared the miRNA profiles among three histological subtypes of NSCLC, and suggested that a three-miRNA signature might be potential diagnostic and prognostic biomarkers for SCC patients.

miR-204 Regulates Cell Proliferation and Invasion by Targeting EphB2 in Human Cervical Cancer

MicroRNAs (miRNAs) are small noncoding RNAs that are involved in human carcinogenesis and progression. miR-204 has been reported to be a tumor suppressor in several cancer types. However, the function and underlying molecular mechanism of miR-204 in cervical cancer (CC) are still unclear. In the present study, the expression level of miR-204 was measured using the qRT-PCR method in 30 paired CC clinical samples and in 6 CC cell lines. We found that the expression of miR-204 was significantly downregulated in CC tissues and cell lines compared to normal cervical tissues and cell line. miR-204 was overexpressed by transfection with the miR-204 mimic in HeLa and C33A cell lines in the following experiments. The results showed that overexpression of miR-204 dramatically suppressed cell proliferation, migration, and invasion, caused cell cycle arrest at the G0/G1 phase, promoted cell apoptosis in vitro, and inhibited tumor growth in vivo. Western blot results indicated that overexpressing miR-204 decreased the expressions of CDK2, cyclin E, MMP2, MMP9, Bcl2, whereas it enhanced Bax expression and suppressed the activation of the PI3K/AKT signaling pathways in CC cells. Ephrin type B receptor 2 (EphB2) was identified as a direct target of miR-204 in CC cells according to bioinformatics analysis and luciferase reporter assay. Furthermore, knockdown of EphB2 mimicked the inhibitory effect of miR-204 on the proliferation, invasion, and migration of CC cells. These findings suggested that miR-204 might serve as a tumor suppressor in the development of CC by directly targeting EphB2.

Simultaneous Imaging of Endogenous Survivin mRNA and On-Demand Drug Release in Live Cells by Using a Mesoporous Silica Nanoquencher

The design of multifunctional drug delivery systems capable of simultaneous target detection, imaging, and therapeutics in live mammalian cells is critical for biomedical research. In this study, by using mesoporous silica nanoparticles (MSNs) chemically modified with a small-molecule dark quencher, followed by sequential drug encapsulation, MSN capping with a dye-labeled antisense oligonucleotide, and bioorthogonal surface modification with cell-penetrating poly(disulfide)s, the authors have successfully developed the first mesoporous silica nanoquencher (qMSN), characterized by high drug-loading and endocytosis-independent cell uptake, which is able to quantitatively image endogenous survivin mRNA and release the loaded drug in a manner that depends on the survivin expression level in tumor cells. The authors further show that this novel drug delivery system may be used to minimize potential cytotoxicity encountered by many existing small-molecule drugs in cancer therapy.

An Exonuclease I-Based Quencher-Free Fluorescent Method Using DNA Hairpin Probes for Rapid Detection of MicroRNA

MicroRNAs (miRNAs) act as biomarkers for the diagnosis of a variety of cancers. Since the currently used methods for miRNA detection have limitations, simple, sensitive, and cost-effective methods for the detection of miRNA are required. This work demonstrates a facile, quencher-free, fluorescence-based analytical method for cost-effective and sensitive detection of miRNA using a super 2-aminopurine (2-AP)-labeled hairpin probe (HP) and exonuclease I activity. Specifically, the fluorescence of 2-AP is strongly quenched when it is incorporated within DNA. In the presence of a target miRNA, HP attains an open conformation by hybridizing with the target miRNA to form a double-stranded structure with a protruding 3′-terminus. Next, the digestion of the protruding 3′-terminus is triggered by exonuclease I, during which 2-AP is released free in solution from the DNA, thereby increasing fluorescence. This method is highly sensitive, with a detection limit of 0.5 nM—10 times lower than a previously reported quencher-free fluorescence method. Furthermore, this method has potential applications in clinical diagnosis and biomedical research.