In-particle stem-loop RT-qPCR for specific and multiplex microRNA profiling

Enhancing early breast cancer detection with APE1-triggered oligonucleotide probes and graphene oxide: The impact of variable AP site modification on sensitivity and specificity

There is a critical need for inclusive diagnostic platforms to enhance the accuracy of early breast cancer detection. Dysregulated microRNA-1246 (miR-1246), closely linked to the disease progression and recurrence, has emerged as a promising diagnostic and prognostic biomarker for BC. However, achieving simple, rapid, and ultrasensitive quantification of serum miRNAs remains significant challenge. In this study, we present an innovative detection platform triggered by endogenous DNA repair enzyme apurinic/apyrimidinic endonuclease 1 (APE1). This platform utilizes an oligonucleotide probe with variable modified AP sites (denoted as AOP) coupled with graphene oxide (GO) for quantifying miR-1246. Our in vitro experiments reveal that the proposed method employing the AOP2 probe with two AP sites exhibits exceptional selectivity and sensitivity. The method achieves a detection limit as low as 2.3 pM towards miR-1246, which is approximately 260-fold more sensitive than the enzyme-free system. RT-qPCR experiments further validate the accuracy and practicability of the AOP2-based platform. In clinical trials, our platform has successfully differentiated between BC patients and normal healthy controls. In conclusion, we have established an integrated biosensing technology for PCR-free, non-invasive liquid biopsies of miR-1246, offering a promising approach for BC diagnosis.

Dual DNAzyme amplification-based colorimetric sensing assay for the identification and quantification of tumor-associated miRNAs

Herein, we present a colorimetric sensing strategy for the identification and quantification of tumor-associated miRNAs based on dual DNAzyme amplification. In this sensing ensemble, the substrate portion of the Pb2+-dependent 8-17 DNAzyme combines with the G-quadruplex portion to form a hairpin substrate strand. The two split 8-17 DNAzyme strands are partially complementary to the substrate strand and serve as a recognition unit for binding the target miRNA. In the presence of the target miRNA, the activated DNAzyme cleaves the substrate strand, releasing the G-quadruplex. This G-quadruplex binds to hemin to form a G-quadruplex/hemin complex with horseradish peroxidase (HRP)-like properties, which catalyzes the oxidation of ABTS2- by H2O2. This oxidation reaction produces a colorimetric signal output, enabling the detection of the target miRNA. Under the optimal reaction conditions explored in this study, the constructed sensing ensembles tailored for each of the specific target miRNAs successfully identified and quantified the four target miRNAs-miR-122, miR-21, miR-335, and miR-155-in both buffer solutions and cell extracts. This colorimetric sensing strategy offers significant advantages in terms of simplicity, cost, and versatility and holds great potential for wide application in biomedical research and clinical diagnostics.

RNA biosensors for detection of pancreatic cancer

Pancreatic cancer is recognized as one of the most lethal types of cancer globally, characterized by a high mortality rate and a bleak prognosis, which greatly contributes to cancer-related deaths. Forecasts suggest that by 2030, pancreatic cancer will exceed other cancer types in prevalence. The disease presents considerable difficulties owing to the lack of prominent symptoms in its early stages, restricted options for early detection, rapid progression, and unfavorable outcomes. Presently, traditional methods for diagnosing pancreatic cancer primarily rely on imaging techniques. However, these methods often entail significant costs, require considerable time, and necessitate specialized skills for both operating the equipment and interpreting the resulting images. To overcome these obstacles, the use of biosensors has been proposed as a potentially valuable tool for the early detection of pancreatic cancer. MicroRNAs (miRs), a type of small non-coding RNA molecules, have emerged as highly sensitive molecular diagnostic tools that have the potential to function as precise indicators for a range of diseases, including cancer. Biosensors have been suggested as a potential solution for tackling these challenges, offering a promising approach for the early detection of pancreatic cancer. Small non-coding RNA molecules known as MicroRNAs (miRs) have become recognized as extremely sensitive molecular diagnostic tools and can act as precise biomarkers for different diseases, such as cancer. Moreover, this manuscript presents a thorough summary of the latest innovations in nano-biosensors that have been specifically developed for the identification of non-coding RNAs related to pancreatic cancer.

Urease-Driven Janus Nanomotors for Dynamic Enrichment and Multiplexed Detection of Bladder Cancer MicroRNAs in Urine

Bladder cancer diagnosis typically involves approaches such as cystoscopy, biopsy, urine cytology, and medical imaging. However, these invasive procedures carry a risk of complications, and direct in vitro detection on clinical samples often results in low sensitivity. Therefore, this study proposed urease-driven magnetic nanomotors for the simultaneous detection of bladder cancer biomarkers miRNA-21 and miRNA-182 in urine samples, aiming for noninvasive diagnosis. The nanomotor was constructed from gold nanorods, mesoporous organo-silica, Fe3O4, and hairpin DNA (hDNA), functioning as a recognition probe for the target miRNAs. In the urea solution, urease catalyzed urea into ammonia and carbon dioxide, propelling the nanomotor for about 60 min, which enhanced the capacity of the probes to capture the target miRNAs. Subsequently, magnetic enrichment enabled highly sensitive dual-miRNA analysis, allowing quantification of miRNA-21 and miRNA-182 with detection limits of 29 and 362 fM, respectively. The nanoprobes also effectively detected miRNAs in spiked urine samples. This simultaneous detection of multiple miRNAs increased the reliability of cancer diagnosis, presenting a novel noninvasive strategy for bladder cancer detection through precise in vitro analysis of actual urine samples.

MicroRNA-146a-5p induces cell cycle arrest and enhances apoptosis in gastric cancer via targeting CDC14A

Objective: The present study was designed to investigate the expression of miRNA-146a-5p in gastric cancer (GC) tissues and the paired nonmalignant counterparts, to explore the influences of miRNA-146a-5p on the cell biological behavior of MKN-28 cells (highly metastatic human gastric cancer cells), and to identify the function of abnormal expression of its target gene cell division cycle 14 homolog A (CDC14A) in GC. Methods: We detected the expression of miRNA-146a-5p in formalin-fixed and paraffin-embedded (FFPE) GC tissues through microarray and quantitative real-time polymerase chain reaction (qRT-PCR). Then, we employed cell counting kit-8 (CCK-8) assays, cell cycle assays, and apoptosis analysis to uncover the latent function of miRNA-146a-5p in MKN-28 human GC cells. We also validated the target of miRNA-146a-5p via luciferase reporter assays. Results: miRNA-146a-5p levels were examined in the majority of primary GC tissues and several GC cell lines. As a result, miRNA-146a-5p levels were significantly declined in the GC tissues and cells. In addition, miRNA-146a-5p demonstrated a straight act on its 3'-untranslated region (3'-UTR) of CDC14A mRNA, accordingly decreasing the contents of CDC14A mRNA as well as its protein expression. An inverse correlation between CDC14A and miRNA-146a-5p was observed. Conclusion: The data suggest miRNA-146a-5p may contribute to inducing cell cycle arrest as well as prompting GC cell apoptosis via directly targeting CDC14A. Therefore, miRNA-146a-5p may be a potential indicator of the occurrence and development of GC.

Polychromatic Quantum Dot Array to Compose a Community Signal Ensemble for Multiplexed miRNA Detection

We herein describe a polychromatic quantum dot array (PQDA) to compose a community signal ensemble enabling accurate and precise quantification of miRNAs in a multiplexed manner. Advanced multicomponent ultrahigh-resolution patterning technique achieved by capsulation-assisted transfer printing following self-assembly-based poly(methyl methacrylate) (PMMA) patterning is utilized to manufacture the PQDA, which is designed to discharge a target miRNAs-specific set of fluorescent quantum dots (QDs) through the activity of duplex-specific nuclease (DSN). On the basis of the community signal ensemble produced by the discharged QD profiles, target miRNAs are very specifically identified down to a femtomolar level (1.27 fM) in a multiplexed manner over a wide dynamic range of up to 6 orders of magnitude. The practical diagnostic capability of this strategy is also demonstrated by reliably identifying breast cancer-specific miRNAs from heterogeneous cancer cell lysates.

A wheel-like DNA nanosensor with background correction for analysis of miRNA-21 in living cells

A silica ring-based ratiometric fluorescence nanosensing and imaging platform was established for the quantification of miRNA-21 with carbon dots and nucleic-functionalized gold nanoparticles inside and outside the ring, respectively. In the presence of miRNA-21, on one hand, the fluorescence emission signal of the originally quenched 6-carboxyfluorescein (FAM), which was labeled on the nucleic acid molecules that modified on the gold nanoparticles, was re-emitted. On the other hand, the fluorescence intensity of the carbon dots inside the ring remained essentially unchanged, which served to eliminate background interference. The ring rather than the shell well maintained the fluorescence of the carbon dots. The ratio of the recovered fluorescence intensity of FAM to the fluorescence intensity of the carbon dots was linearly correlated with the logarithm of miRNA-21 concentration. The linear range of the probe for miRNA detection was more than 3 orders of magnitude, and the detection limit was as low as 2.5 aM. The feasibility of the method for clinical application was verified by the quantitative analysis of intracellular miRNA.

Non-Coding RNA-Based Biosensors for Early Detection of Liver Cancer

Primary liver cancer is an aggressive, lethal malignancy that ranks as the fourth leading cause of cancer-related death worldwide. Its 5-year mortality rate is estimated to be more than 95%. This significant low survival rate is due to poor diagnosis, which can be referred to as the lack of sufficient and early-stage detection methods. Many liver cancer-associated non-coding RNAs (ncRNAs) have been extensively examined to serve as promising biomarkers for precise diagnostics, prognostics, and the evaluation of the therapeutic progress. For the simple, rapid, and selective ncRNA detection, various nanomaterial-enhanced biosensors have been developed based on electrochemical, optical, and electromechanical detection methods. This review presents ncRNAs as the potential biomarkers for the early-stage diagnosis of liver cancer. Moreover, a comprehensive overview of recent developments in nanobiosensors for liver cancer-related ncRNA detection is provided.

Advances in multiplexed techniques for the detection and quantification of microRNAs

MicroRNA detection is currently a crucial analytical chemistry challenge: almost 2000 papers were referenced in PubMed in 2018 and 2019 for the keywords "miRNA detection method". MicroRNAs are potential biomarkers for multiple diseases including cancers, neurodegenerative and cardiovascular diseases. Since miRNAs are stably released in bodily fluids, they are of prime interest for the development of non-invasive diagnosis methods, such as liquid biopsies. Their detection is however challenging, as high levels of sensitivity, specificity and robustness are required. The analysis also needs to be quantitative, since the aim is to detect miRNA concentration changes. Moreover, a high multiplexing capability is also of crucial importance, since the clinical potential of miRNAs probably lays in our ability to perform parallel mapping of multiple miRNA concentrations and recognize typical disease signature from this profile. A plethora of biochemical innovative detection methods have been reported recently and some of them provide new solutions to the problem of sensitive multiplex detection. In this review, we propose to analyze in particular the new developments in multiplexed approaches to miRNA detection. The main aspects of these methods (including sensitivity and specificity) will be analyzed, with a particular focus on the demonstrated multiplexing capability and potential of each of these methods.