Ultrasensitive Exosomal MicroRNA Detection with a Supercharged DNA Framework Nanolabel

Paper-based degradable, label-free microRNA sensing platform based on oxide thin-film transistor arrays

MicroRNAs have started being used as an effective marker in early diagnosis and preoperative monitoring of cancers in recent years. Traditional microRNA testing technology, such as quantitative reverse transcription polymerase chain reaction (qRT-PCR) and various fluorescent and colorimetric assays, often suffer from complicated operations and limited sensitivity. They also produce significant electronic waste posing threats to human health and environment. Here, we propose a degradable biosensor using indium-gallium-zinc oxide (IGZO) thin-film transistor (TFT) arrays for rapid and highly sensitive detection of microRNAs from glioma exosome extracts (g-miRNAs). The IGZO transistor arrays fabricated on nanofibrillated cellulose paper exhibit high electronic performance with a current on/off ratio >1.5 × 106, a mobility of 9.6 cm2 V-1·s-1, a subthreshold swing <0.5 V·dec-1, and excellent bias stress stability. Specific DNA probes in the IGZO channel bind selectively with g-miRNA targets to form DNA-RNA double strands, offering high specificity even when coexisting with high concentrations of nonspecific microRNAs. The inherent negative charges in DNA and g-miRNA molecules sensitively modulate the IGZO channel conductivity, leading to a positive shift of threshold voltage and decrease of source-drain current. These changes are linearly correlated with microRNA concentrations from 1 fM to 100 pM, with a detection limitation of 350 aM. Furthermore, the paper-based IGZO transistor array nearly completely dissolves in a NaOH solution after 300 min. The proposed approach combines easy-to-operate, point-of-care microRNA testing with lightweight, low-cost, biocompatible, and degradable devices, showing great promise for early diagnosis of glioma and most likely also other tumors.

Magnetically controlled all-in-one sensing platform for triple-mode detection of organophosphorus pesticides using DNA tetrahedrons-polydopamine reporters

Accurate and on-site detection of organophosphorus pesticides (OPs) in complex matrixes is important for environmental monitoring and food safety. Herein, a colorimetric (CL), photothermal (PT) and fluorescence (FL) triple-mode sensor was constructed for OPs detection based on magnetically controlled all-in-one platform, which was featured of specific recognition unit, abundant loading of DNA tetrahedrons-Fe3+-polydopamine (TDN-Fe3+-PDA) with peroxidase-like activity, and verifiable triple-mode signal output. Based on the aptamer-target recognition and efficient separation of MBs, large amount of TDN-Fe3+-PDA reporters was released. Taking full advantages of the supernatant and precipitation, OPs was sensitively detected with the TDN-Fe3+-PDA catalyzed 3,3',5,5'-tetramethylbenzidine (TMB)-H2O2 system (CL mode), photothermal effect of TDN-Fe3+-PDA and oxidized TMB (oxTMB) (PT mode), and fluorescent signal of TDN-templated copper nanoclusters on MBs (FL mode). Using profenofos (Pro) as the model target, the triple-mode sensing platform realized sensitive detection of Pro with the detection limits 0.23 ng/mL, 0.40 ng/mL and 0.14 ng/mL for CL, PT and FL mode, respectively. The proposed strategy provided a simple and accurate method for on-site detection of OPs, holding promising application in environmental and food contamination monitoring.

S9.6 Antibody-Mediated Wireless Portable Biosensor with Multiple Affinity Enhancements for Comprehensive Detection of Nucleic Acid in Serum

Creating biosensors capable of facilely and entirely excluding the influence of interfering biomolecules in complex samples holds profound significance for advancing detection technology and diagnostics. Here, we develop a wireless portable biosensor (WPB) that prevents interference from abundant biomolecules in serum through homogeneous hybridization and S9.6 antibody-mediated multivalent capture. By transferring the hybridization environment from a heterogeneous chip surface to a homogeneous solution, the biosensor maintains consistent hybridization efficiency in serum as in buffer. Additionally, the use of S9.6 antibody-mediated multivalent capture ensures nearly unchanged binding affinity in serum compared to buffer. On the basis of the multiple affinity enhancements, S9.6 antibody-mediated WPB can achieve ultrasensitive detection of nucleic acid in 50% human serum. Specifically, a subtle blocker is designed to eliminate the competitive monovalent S9.6 antibody-heteroduplex binding, ensuring the efficiency of multivalent S9.6 antibody-heteroduplex interactions. The blocker also enables single-step detection. Moreover, the sensing platform utilizes interferents in serum as in situ antifouling biomolecules to prevent nonspecific adsorption. As a result, the proposed WPB achieves a similar limit of detection for nucleic acids in human serum (95 aM) and in buffer (86 aM). This approach inspires a new idea for complex interference elimination and usage and exhibits comprehensive detection performance in complex samples with potential future diagnostic applications.

A rapid, specific, and simple-to-use biosensor for amplification-free determination of microRNA based on electrical potential-assisted and ternary hybridization

An ultra-fast, easy-to-use and non-amplification electrochemical detection platform was constructed for microRNA (miRNA) detection. A set of label-free hairpin probes and capture probes were introduced to form a ternary complex, which could enhance the selectivity and stability of miRNA detection due to the ability of reducing non-specific bind with non-target and enhancing accessibility of target to probes. Moreover, the capture probe immobilization and hybridization process were accelerated by the external electric field, shortening the detection time from 2 h to 5 min. The platform showed a detection limit of 1.28 fM under ideal experimental control conditions and had ability to identify 1- or 2-nucleotide (nt) difference. In addition, the designed sensor achieved the sensitive determination of miRNA-21 in serum samples. The excellent anti-interference capability of this detection method indicated its potential for clinical application. Its simplicity and high specificity made this method a promising tool for detecting different miRNA to assist the diagnosis of diverse cancers.

Nanoparticles-based electrochemical sensing platform for high-through immunoassay with redox-activity CaCO3 nanotags on a magnetic microfluidic device

A new nanoparticles-based sensing platform was designed for high-through electrochemical immunoassay of ferritin (FET) biomarker on a magneto-controlled microfluidic device by using anti-FET capture antibody-conjugated magnetic sensing probes. Thionine-doped calcium carbonate (CaCO3) nanoparticles labeled with anti-FET detection antibodies were utilized as the recognition elements. Introduction of target FET caused the sandwich-type immunoreaction between two antibodies. The formed immunocomplexes were attached onto magnetic microfluidic sensing interface through an external magnet. Subsequently, the carried CaCO3 nanoparticles were dissolved under acidic conditions to release the doped thionine molecules with redox activity. The thionine-based voltammetric signals increased with the increment of target FET levels within the linear range 0.01-100 ng mL-1. The limit of detection was 7.9 pg mL-1 FET. Good analytical properties such as selectivity, reproducibility, and accuracy were achieved with the nanoparticles-based magnetic electrochemical immunoassay. More significantly, the magnetic microfluidic electrochemical immunoassay provides new opportunities for rapid, simple, and cost-effective serum sample analysis.

Advancements in functional tetrahedral DNA nanostructures for multi-biomarker biosensing: Applications in disease diagnosis, food safety, and environmental monitoring

Deoxyribonucleic acid (DNA) offers the fundamental building blocks for the precisely controlled assemblies due to its inherent self-assembly and programmability. The tetrahedral DNA nanostructure (TDN) stands out as a widely utilized nanostructure, attracting attention for its high biostability, excellent biocompatibility, and versatile modification sites. The capability of DNA tetrahedron to interact with various signal outputs makes it ideal for developing functional DNA nanostructures in biosensing platforms. This review highlights recent advancements in functional tetrahedral DNA nanostructures (FTDN) for various biomarkers monitoring, including nucleic acid, protein, mycotoxin, agent, and metal ion. Additionally, it discusses the potential of FTDN in the fields of disease diagnosis, food safety, and environmental monitoring. The review also introduces the application of FTDN-based biosensors for simultaneous identification of multiple biomarkers. Finally, challenges and prospects are addressed to provide guidance for the continued development of FTDN-based biosensing platforms.

A microfluidic-based chemiluminescence biosensor for sensitive multiplex detection of exosomal microRNAs based on hybridization chain reaction

The analysis of microRNAs (miRNAs) in exosomes is of great importance for noninvasive early disease diagnosis. However, current techniques to detect exosomal miRNAs is hampered either by laborious exosome isolation or low abundance of miRNAs in exosomes. Here, we developed a microfluidic chemiluminescence (CL) analysis method for the multiplexed detection of exosomal miR-21 and miR-155. The microfluidic device contained three parts: a snake-shaped channel for fully mixing chemiluminescent reagents, a ship-shaped channel modified with CD63 protein aptamer for capturing exosomes, and another two parallel ship-shaped channels for hybridization chain reaction (HCR) amplification and CL detection. The multiple signal amplification was realized by Y-shaped arrays, HCR amplification, and poly-HRP catalyzed CL reaction. Using this multiple signal amplification method, our microfluidic CL biosensor achieves a limit of detection of miRNAs of 0.49 fM, with a linear range of 1 fM-10 pM, which is better or comparable to previously reported biosensors. What's more, the proposed microfluidic biosensor exhibits great specificity and selectivity to the target miRNA. Moreover, the microfluidic CL strategy exhibited excellent accuracy and could significantly distinguish different cancer subtypes as well as cancer patients and healthy people. These results suggest that this simple, high sensitive, and more accurate analytical strategy by analyzing different types of exosomal miRNAs has the potential applications in cancer diagnosis and stage monitoring.

MicroRNA Triggered Dimerization of DNA Tetrahedron for Enhanced Biosensing Performance of Solid-State Nanochannels Functionalized with MoS2 Nanosheets

Solid-state nanochannels (SSN) have great development potential as a biosensing interface. The integration of two-dimensional nanomaterials with nanochannels endows SSN with diverse properties, including distinguishing DNA nanostructures. In this study, by modifying MoS2 nanosheets, the outer surface of SSN could be endowed with robust adsorption properties for single-stranded DNA. Therefore, DNA tetrahedrons connected with single-stranded DNA could remain on the SSN surface, whereas DNA tetrahedron dimers with full double-stranded structures formed by the presence of target microRNA cannot be retained on the surface of nanochannels. The change in the DNA nanostructure generated by the target recognition process could cause variations of steric hindrance and electrostatic repulsion on the surface of the SSN. The variations were reflected by the free diffusion flux of [Fe(CN)6]3-. Then, the sensitive electrochemical detection method for microRNA was established, and the detection limit of the method for microRNA-31 was as low as 0.5 fM. The study provided a promising approach for the ultrasensitive detection of biomarkers, thereby offering potential means for early diagnosis of the related diseases.

Minute level ultra-rapid and thousand copies level high-sensitive pathogen nucleic acid identification based on contactless impedance detection microsensor

Early screening for pathogens is crucial during pandemic outbreaks. Nucleic acid testing (NAT) is a valuable method for keeping pathogens from spreading. However, the long detection time and large size of the instruments involved significantly limited the efficiency of detection. This work described an integrated NAT microsensor that facilitated rapid and extremely sensitive detection based on nucleic acid amplification (NAA) on a chip. The biochip consisted of two layers incorporating a heater, a thermometer, an interdigital electrode (IDE) and a reaction chamber. The Pt electrode based heater and thermometer were utilized to maintain a specific temperature for the sample in the chamber. The thermometer exhibited a good linear correlation with a sensitivity of 9.36 Ω/°C and the heater achieved a heating efficiency of approximately 6.5 °C/s. Multiple ions were released during NAA, resulting in a decrease in the impedance of the amplification system solution. A large signal of impedance was generated by the released ions due to its linear correlation with the logarithm of the ion concentration. With this detection principle, IDE was employed for real-time monitoring of the in-chip reaction system impedance and NAA process. Specific nucleic acids from two pathogens (SARS-CoV-2, Vibrio vulnificus) were detected with this microsensor. The samples were qualitatively analyzed on microchip within 3 min, with a limit of detection (LOD) of 103 copies/μL. The proposed sensor presented several advantages, including reduced NAT time and increased sensitivity. Consequently, it has shown significant potential in rapid and high-quality nucleic acid testing for the field of epidemic prevention.

Recent advances in the applications of DNA frameworks in liquid biopsy: A review

Cancer is one of the serious threats to public life and health. Early diagnosis, real-time monitoring, and individualized treatment are the keys to improve the survival rate and prolong the survival time of cancer patients. Liquid biopsy is a potential technique for cancer early diagnosis due to its non-invasive and continuous monitoring properties. However, most current liquid biopsy techniques lack the ability to detect cancers at the early stage. Therefore, effective detection of a variety of cancers is expected through the combination of various techniques. Recently, DNA frameworks with tailorable functionality and precise addressability have attracted wide spread attention in biomedical applications, especially in detecting cancer biomarkers such as circulating tumor cells (CTCs), exosomes and circulating tumor nucleic acid (ctNA). Encouragingly, DNA frameworks perform outstanding in detecting these cancer markers, but also face some challenges and opportunities. In this review, we first briefly introduced the development of DNA frameworks and its typical structural characteristics and advantages. Then, we mainly focus on the recent progress of DNA frameworks in detecting commonly used cancer markers in liquid-biopsy. We summarize the advantages and applications of DNA frameworks for detecting CTCs, exosomes and ctNA. Furthermore, we provide an outlook on the possible opportunities and challenges for exploiting the structural advantages of DNA frameworks in the field of cancer diagnosis. Finally, we envision the marriage of DNA frameworks with other emerging materials and technologies to develop the next generation of disease diagnostic biosensors.

Nanocluster/metal-organic framework nanosheet-based confined ECL enhancement biosensor for the extracellular vesicle detection

Gastric cancer (GC) was one of the most common cancers with high mortality. The detection of GC peritoneal metastasis had important significance. In this work, we have developed the novel electrochemiluminescence (ECL) biosensor to detect microRNA in GC extracellular vesicle (EV). Firstly, in situ growth of Cu nanocluster (Cu NC) on the metal-organic frameworks (MOFs) nanosheet was achieved successfully. Due to the confinement effect, Cu NCs in the porous structure of Zn MOF possessed the high quantum yield and good stability. Meanwhile, Zn MOF provided good electrochemical activity for the ECL reaction. Furthermore, the nanosized MOFs did not only act as sensing platform to load Cu NCs and link biomolecules, but also reduce steric hindrance effect for biomolecular recognition. Additionally, Au NPs/MXene and phospholipid layer were prepared and modified on the electrode, which can regulate electron transfer and improve the target recognition efficiency. The Cu NCs/Zn MOF nanosheet-based ECL sensor was employed to detect miRNA-421 from 1 fM to 1 nM with a detection limit of 0.5 fM. Finally, extracellular vesicles form clinic GC patient ascites were extracted and analyzed. The results showed that the constructed biosensor can be used for the GC peritoneal metastasis diagnosis.

DNA-Based Nanomaterials for Analysis of Extracellular Vesicles

Extracellular vesicles (EVs) are cell-derived nanovesicles comprising a myriad of molecular cargo such as proteins and nucleic acids, playing essential roles in intercellular communication and physiological and pathological processes. EVs have received substantial attention as noninvasive biomarkers for disease diagnosis and prognosis. Owing to their ability to recognize protein and nucleic acid targets, DNA-based nanomaterials with excellent programmability and modifiability provide a promising tool for the sensitive and accurate detection of molecular cargo carried by EVs. In this perspective, recent advancements in EV analysis using a variety of DNA-based nanomaterials are summarized, which can be broadly classified into three categories: linear DNA probes, DNA nanostructures, and hybrid DNA nanomaterials. The design, construction, advantages, and disadvantages of different types of DNA nanomaterials, as well as their performance for detecting EVs are reviewed. The challenges and opportunities in the field of EV analysis by DNA nanomaterials are also discussed.

Proximity-Enhanced Electrochemiluminescence Sensing Platform for Effective Capturing of Exosomes and Probing Internal MicroRNAs Involved in Cancer Cell Apoptosis

Exosomal microRNAs (miRNAs) play critical regulatory roles in many cellular processes, and so how to probe them has attracted increasing interest. Here we propose an aptamer-functionalized dimeric framework nucleic acid (FNA) nanoplatform for effective capture of exosomes and directly probing internal miRNAs with electrochemiluminescence (ECL) detection, not requiring RNA extraction in conventional counterparts. A CD63 protein-binding aptamer is tethered to one of the FNA structures, allowing exosomes to be immobilized there and release internal miRNAs after lysis. The target miRNA induces the formation of a Y-shaped junction on another FNA structure in a close proximity state, which benefits the loading of covalently hemin-modified spherical nucleic acid enzymes for enhanced ECL readout in the luminol-H2O2 system. In this facile way, the ultrasensitive detection of exosomal miR-21 from cancer cells is accomplished and then used for cell apoptosis analysis, indicating that the oncogene miR-21 negatively participates in the regulation of the apoptotic process; namely, downregulating the miR-21 level is unbeneficial for cancer cell growth.

CRISPR/dCas9-Mediated Specific Molecular Assembly Facilitates Genotyping of Mutant Circulating Tumor DNA

Breakthroughs in circulating tumor DNA (ctDNA) analysis are critical in tumor liquid biopsies but remain a technical challenge due to the double-stranded structure, extremely low abundance, and short half-life of ctDNA. Here, we report an electrochemical CRISPR/dCas9 sensor (E-dCas9) for sensitive and specific detection of ctDNA at a single-nucleotide resolution. The E-dCas9 design harnesses the specific capture and unzipping of target ctDNA by dCas9 to introduce a complementary reporter probe for specific molecular assembly and signal amplification. By efficient homogeneous assembly and interfacial click reaction, the assay demonstrates superior sensitivity (up to 2.86 fM) in detecting single-base mutant ctDNA and a broad dynamic range spanning 6 orders of magnitude. The sensor is also capable of measuring 10 fg/μL of a mutated target in excess of wild-type ones (1 ng/μL), equivalent to probing 0.001% of the mutation relative to the wild type. In addition, our sensor can monitor the dynamic expression of cellular genomic DNA and allows accurate analysis of blood samples from patients with nonsmall cell lung cancer, suggesting the potential of E-dCas9 as a promising tool in ctDNA-based cancer diagnosis.

Dual amplified electrochemical sensing coupling of ternary hybridization-based exosomal microRNA recognition and perchlorate-assisted electrocatalytic cycle

Exosomal microRNA (miRNA) are important biomarkers for liquid biopsy, and display clinical molecular signatures for cancer diagnosis. Although advanced detection methods have been established to detect exosomal miRNAs, they are faced with certain challenges. Therefore, we aimed to establish a dual amplification-based electrochemical method for detecting exosomal miRNA. This method combined a two-hairpins-based ternary hybridization structure (thTHS)-initiated single-stranded DNA (ssDNA) amplification reaction (ssDAR) and sodium perchlorate (NaClO4)-assisted electrocatalytic cycle. Two DNA hairpins were designed to hybridize with target miRNA, forming thTHS. Next, ssDAR was triggered by thTHS to produce long ssDNA on magnetic beads. The long ssDNA, complementary to the signal probes, was subsequently released onto a methylene blue (MB)-labeled double-stranded DNA-modified electrode for strand displacement reaction. This led to a quantitative change in MB and a change in electrocatalytic reduction current from the electrocatalytic cycle of MB-ferricyanide. An amplified electrocatalytic reduction current was produced by adding NaClO4 to the electrocatalytic system, which substantially improved the signal response range and detection sensitivity. Ultimately, exosomal miRNA detection was achieved by recording changes in the electrocatalytic reduction current before and after miRNA addition. This electrochemical method exhibited a sensitive concentration response with a detection limit of 45 aM and selective miRNA recognition, and successfully used to detect exosomal miRNA derived from cells and serum. Additionally, this method exhibited better discrimination ability between patients with breast cancer (BC) and those people without BC (patients with benign breast disease and healthy people), providing a promising strategy for detecting and monitoring cancer biomarkers.

On-Site-Activated Transmembrane Logic DNA Nanodevice Enables Highly Specific Imaging of Cancer Cells by Targeting Tumor-Related Nucleolin and Intracellular MicroRNA

The ability to specifically image cancer cells is essential for cancer diagnosis; however, this ability is limited by the false positive associated with single-biomarker sensors and off-site activation of "always active" nucleic acid probes. Herein, we propose an on-site, activatable, transmembrane logic DNA (TLD) nanodevice that enables dual-biomarker sensing of tumor-related nucleolin and intracellular microRNA for highly specific cancer cell imaging. The TLD nanodevice is constructed by assembling a tetrahedral DNA nanostructure containing a linker (L)-blocker (B)-DNAzyme (D)-substrate (S) unit. AS-apt, a DNA strand containing an elongated segment and the AS1411 aptamer, is pre-anchored to nucleolin protein, which is specifically expressed on the membrane of cancer cells. Initially, the TLD nanodevice is firmly sealed by the blocker containing an AS-apt recognition zone, which prevents off-site activation. When the nanodevice encounters a target cancer cell, AS-apt (input 1) binds to the blocker and unlocks the sensing ability of the nanodevice for miR-21 (input 2). The TLD nanodevice achieves dual-biomarker sensing from the cell membrane to the cytoplasm, thereby ensuring cancer cell-specific imaging. This TLD nanodevice represents a promising strategy for the highly reliable analysis of intracellular biomarkers and a promising platform for cancer diagnosis and related biomedical applications.

Tetrahedral DNA Nanostructure-Engineered Paper-Based Sensor with an Enhanced Antifouling Ability for Photoelectrochemical Sensing

Herein, a newly designed two-in-one tetrahedral DNA (TDN) nanostructure with an antifouling surface and backbone-rigidified interfacial tracks was developed for highly sensitive and selective detection of miRNA-182-5p. The well-regulated TDN tracks were assembled onto the surface of the TiO₂/MIL-125-NH₂-functionalized paper electrode, which efficiently avoided the obstacle of DNA strand tangling and decreased the probability of suspension during the walking process, thus greatly promoting the moving efficiency of DNA walkers. More interestingly, the TDN-modified sensing interfaces demonstrated incomparable antifouling ability against protein samples and interfering miRNAs due to the strong hydrophilic capacity and special molecular conformations, which addressed the dilemma of low sensitivity from traditional antifouling coating strategies. As a proof of concept, the designed bifunctional tetrahedron-modified paper-based photoelectrochemical sensor was successfully used to quantify miRNA-182-5p with a low detection limit of 0.09 fM and high specificity and was validated for monitoring of miRNA-182-5p in real samples. This TDN-engineered biointerface could be used as a universal platform for tracking various targets by substituting the biorecognition events, providing great promise for bioanalysis and clinical diagnosis.

Tetrahedral DNA framework assisted rotational paper-based analytical device for differential detection of SARS-CoV-2 and influenza A H1N1 virus

Coronavirus disease 2019 (COVID-19) and influenza A are two respiratory infectious diseases with similar clinical manifestations. Because of the complex global epidemic situation of COVID-19, the distinction and diagnosis of COVID-19 and influenza A infected persons is crucial for epidemic prevention and control. In this study, tetrahedral DNA framework (TDF) was combined with a rotational paper-based analytical device, and the color change generated by the reaction between horseradish peroxidase (HRP) and 3,3'5,5'-tetramethylbenzidine (TMB)-H₂O₂ was used for grayscale signal analysis by ImageJ software. The quantitative detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and influenza A H1N1 virus were realized simultaneously. Under the optimal conditions, the paper-based analytical device showed a good linear relationship between the two viruses in the range of 10^-14-10^-8g/mL, and the two viruses were not affected by cross reaction. This sensor provides a convenient and reliable method for clinical rapid differentiation and diagnosis of COVID-19 and influenza A.

Practical tips and new trends in electrochemical biosensing of cancer-related extracellular vesicles

To tackle cancer and provide prompt diagnoses and prognoses, the constantly evolving biosensing field is continuously on the lookout for novel markers that can be non-invasively analysed. Extracellular vesicles (EVs) may represent a promising biomarker that also works as a source of biomarkers. The augmented cellular activity of cancerous cells leads to the production of higher numbers of EVs, which can give direct information on the disease due to the presence of general and cancer-specific surface-tethered molecules. Moreover, the intravesicular space is enriched with other molecules that can considerably help in the early detection of neoplasia. Even though EV-targeted research has indubitably received broad attention lately, there still is a wide lack of practical and effective quantitative procedures due to difficulties in pre-analytical and analytical phases. This review aims at providing an exhaustive outline of the recent progress in EV detection using electrochemical and photoelectrochemical biosensors, with a focus on handling approaches and trends in the selection of bioreceptors and molecular targets related to EVs that might guide researchers that are approaching such an unstandardised field.

Recent Advances in Exosomal miRNA Biosensing for Liquid Biopsy

As a noninvasive detection technique, liquid biopsy plays a valuable role in cancer diagnosis, disease monitoring, and prognostic assessment. In liquid biopsies, exosomes are considered among the potential biomarkers because they are important bioinformation carriers for intercellular communication. Exosomes transport miRNAs and, thus, play an important role in the regulation of cell growth and function; therefore, detection of cancer cell-derived exosomal miRNAs (exo-miRNAs) gives effective information in liquid biopsy. The development of sensitive, convenient, and reliable exo-miRNA assays will provide new perspectives for medical diagnosis. This review presents different designs and detection strategies of recent exo-miRNA assays in terms of signal transduction and amplification, as well as signal detection. In addition, this review outlines the current attempts at bioassay methods in liquid biopsies. Lastly, the challenges and prospects of exosome bioassays are also considered.

Recent Advances in Detection for Breast-Cancer-Derived Exosomes

Breast cancer is the most common malignant tumor in women, its incidence is secret, and more than half of the patients are diagnosed in the middle and advanced stages, so it is necessary to develop simple and efficient detection methods for breast cancer diagnosis to improve the survival rate and quality of life of breast cancer patients. Exosomes are extracellular vesicles secreted by all kinds of living cells, and play an important role in the occurrence and development of breast cancer and the formation of the tumor microenvironment. Exosomes, as biomarkers, are an important part of breast cancer fluid biopsy and have become ideal targets for the early diagnosis, curative effect evaluation, and clinical treatment of breast cancer. In this paper, several traditional exosome detection methods, including differential centrifugation and immunoaffinity capture, were summarized, focusing on the latest research progress in breast cancer exosome detection. It was summarized from the aspects of optics, electrochemistry, electrochemiluminescence and other aspects. This review is expected to provide valuable guidance for exosome detection of clinical breast cancer and the establishment of more reliable, efficient, simple and innovative methods for exosome detection of breast cancer in the future.

Exosomal MicroRNAs as Novel Cell-Free Therapeutics in Tissue Engineering and Regenerative Medicine

Extracellular vesicles (EVs) are membrane-bound vesicles (50-1000 nm) that can be secreted by all cell types. Microvesicles and exosomes are the major subsets of EVs that exhibit the cell-cell communications and pathological functions of human tissues, and their therapeutic potentials. To further understand and engineer EVs for cell-free therapy, current developments in EV biogenesis and secretion pathways are discussed to illustrate the remaining gaps in EV biology. Specifically, microRNAs (miRs), as a major EV cargo that exert promising therapeutic results, are discussed in the context of biological origins, sorting and packing, and preclinical applications in disease progression and treatments. Moreover, advanced detection and engineering strategies for exosomal miRs are also reviewed. This article provides sufficient information and knowledge for the future design of EVs with specific miRs or protein cargos in tissue repair and regeneration.

Piezotronic Effect-Assisted Photoelectrochemical Exosomal MicroRNA Monitoring Based on an Electron Donor Self-Supplying Strategy

Exosomal microRNAs (miRNAs) as newly emerging reliable and noninvasive biomarkers have demonstrated a significant function in early cancer diagnosis. Photoelectrochemical (PEC) biosensing has attracted unprecedented attention in exosomal miRNA monitoring due to its inherent advantages of both electrochemical and optical techniques; however, the severe charge carrier recombination greatly restricts the PEC assay performance. Herein, a high-sensitive PEC strategy assisted by the piezoelectric effect is designed based on Bi₂WO₆/Cu₂S heterojunctions and implemented for the monitoring of exosomal miRNAs. The introduction of the piezoelectric effect enables promoted electron-hole transfer and separation, thereby improving the analytical sensitivity. In addition, a target reprogramming metal-organic framework-capped CaO₂ (MOF@CaO₂) hybrids is prepared, in which MOF@CaO₂ being responsive to exosomal miRNAs induces exposure of the capped CaO₂ to H₂O and then triggers self-supplying of H₂O₂, which effectively suppresses the electron-hole recombination, giving rise to an amplified photocurrent and a decrease in the cost of the reaction. Benefiting from the coupled sensitization strategy, the as-fabricated PEC strategy exhibits high sensitivity, specificity, low cost, and ease of use for real-time analysis of exosomal miRNAs within the effectiveness linear range of 0.1 fM-1 μM. The present work demonstrates promising external field coupling-enhanced PEC bioassay and offers innovative thoughts for applying this strategy in other fields.

Simultaneous detection of cancerous exosomal miRNA-21 and PD-L1 with a sensitive dual-cycling nanoprobe

Simultaneous detection of specific exosomal surface proteins and inner microRNAs are hampered by their heterogeneity, low abundance and spatial segregation in nanovesicles. Here, we design a dual-cycling nanoprobe (DCNP) to enable single-step simultaneous quantitation of cancerous exosomal surface programmed death-ligand 1 (PD-L1) (ExoPD-L1) and miRNA-21 (ExomiR-21) directly in exosome lysates, without resorting to either RNA extraction or time-consuming transmembrane penetration. In this design, DNA molecular machine-based dual-recognition probes co-assemble onto gold nanoparticle surface for engineering 'silent' DCNPs, which enable signal-amplified synchronous response to dual-targets as activated by ExomiR-21 and ExoPD-L1 within 20 min. Benefiting from cycling amplification of the molecular machine, DCNPs sensor achieves detection limits of tumor exosomes, ExoPD-L1 and ExomiR-21 down to 10 particles/μL, 0.17 pg/mL and 66 fM, respectively. Such a sensitive dual-response strategy allows simultaneous tracking the dynamic changes of ExoPD-L1 and ExomiR-21 expression regulated by signaling molecules or therapeutics. This approach further detects circulating ExoPD-L1 and ExomiR-21 in human plasma to differentiate breast cancer patients from healthy individuals with high accuracy, showing great potential of DCNPs for simultaneous profiling exosomal surface and inside biomarkers, and for clinical precision diagnosis.

Interfacial DNA Framework-Enhanced Background-to-Signal Transition for Ultrasensitive and Specific Micro-RNA Detection

Interfacial DNA self-assembly is fundamental to solid nucleic acid biosensors, whereas how to improve the signal-to-noise ratio has always been a challenge, especially in the charge-based electrochemical DNA sensors because of the large noise from the negatively charged DNA capture probes. Here, we report a DNA framework-reversed signal-gain strategy through background-to-signal transition for ultrasensitive and highly specific electrical detection of microRNAs (miRNAs) in blood. By using a model of enzyme-catalyzed deposition of conductive molecules (polyaniline) targeting to DNA, we observed the highest signal contribution per unit area by the highly charged three-dimensional (3D) tetrahedral DNA framework probe, relative to the modest of two-dimensional (2D) polyA probe and the lowest of one-dimensional (1D) single-stranded (ss)DNA probe, suggesting the positive correlation of background DNA charge with signal enhancement. Using such an effective signal-transition design, the DNA framework-based electrochemical sensor achieves ultrasensitive miRNAs detection with sensitivity up to 0.29 fM (at least 10-fold higher than that with 1D ssDNA or 2D polyA probes) and high specificity with single-base resolution. More importantly, this high-performance sensor allows for a generalized sandwich detection of tumor-associated miRNAs in the complex matrices (multiple cell lysates and blood serum) and further distinguishes the tumor patients (e.g., breast, lung, and liver cancer) from the normal individuals. These advantages signify the promise of this miRNA sensor as a versatile tool in precision diagnosis.

Sensitive, Highly Stable, and Anti-Fouling Electrode with Hexanethiol and Poly-A Modification for Exosomal microRNA Detection

It remains a huge challenge to integrate the sensitivity, stability, reproducibility, and anti-fouling ability of electrochemical biosensors for practical applications. Herein, we propose a self-assembled electrode combining hexanethiol (HT), poly-adenine (poly-A), and cholesteryl-modified DNA to meet this challenge. HT can tightly pack at the electrode interface to form a hydrophobic self-assembled monolayer (SAM), effectively improving the stability and signal-to-noise ratio (SNR) of electrochemical detection. Cholesteryl-modified DNA was immobilized at the electrode through the hydrophobic interaction with HT to avoid the competition between the SAM and the DNA probe on the gold site. Thus, the assembly efficiency and uniformity of the DNA probe as well as the detection reproducibility were increased remarkedly. Poly-A was added on the HT assembled electrode to occupy the unreacted sites of gold to further enhance the anti-fouling ability. The combination of HT and poly-A allows the electrode to ensure favorable anti-fouling ability without sacrificing the detection performance. On this basis, we proposed a dual-signal amplification electrochemical biosensor for the detection of exosomal microRNAs, which showed excellent sensitivity with a detection limit down to 1.46 aM. Importantly, this method has been successfully applied to detect exosomal microRNA-21 in cells and human serum samples, proving its potential utility in cancer diagnosis.

Photoelectrochemical Detection of Exosomal miRNAs by Combining Target-Programmed Controllable Signal Quenching Engineering

MicroRNAs extracted from exosomes (exosomal miRNAs) have recently emerged as promising biomarkers for early prognosis and diagnosis. Thus, the development of an effective approach for exosomal miRNA monitoring has triggered extensive attention. Herein, a sensitive photoelectrochemical (PEC) biosensing platform is demonstrated for exosomal miRNA assay via the target miRNA-powered λ-exonuclease for the amplification strategy. The metal-organic framework (MOF)-decorated WO₃ nanoflakes heterostructure is constructed and implemented as the photoelectrode. Also, a target exosomal miRNA-activatable programmed release nanocarrier was fabricated, which is responsible for signal control. Hemin that acted as the electron acceptor was prior entrapped into the programmed control release nanocarriers. Once the target exosomal miRNAs-21 was introduced, the as-prepared programmed release nanocarriers were initiated to trigger the release of hemin, which enabled the quenching of the photocurrent. Under the optimized conditions, the level of exosomal miRNAs-21 could be accurately tracked ranging from 1 fM to 0.1 μM with a low detection limit of 0.5 fM. The discoveries illustrate the possibility for the rapid and efficient diagnosis and prognosis prediction of diseases based on the detection of exosomal miRNAs-21 and would provide feasible approaches for the fabrication of an efficient platform for clinical applications.

Advances in quantifying circulatory microRNA for early disease detection

Precision preventive healthcare aims to improve patient health by integrating preventive measures with early disease detection for timely intervention with precision medicine. Key to the delivery of preventive healthcare is the clinical adoption of novel assays that enable early disease detection. Such assays, typically based on biomarkers such as microRNAs (miRNAs) from liquid biopsy or excreta, are entering clinical practice after years of clinical development and validation. In this review, we discuss the clinical utility and validation of miRNA-based molecular diagnostics for early disease detection through large-cohort studies and key considerations for developing multi-analyte clinical assays. We also highlight recent advances in the ongoing development of integrated PCR-free miRNA detection systems for point-of-care testing.

Advances in the DNA Nanotechnology for the Cancer Biomarkers Analysis: Attributes and Applications

The most commonly used clinical methods are enzyme-linked immunosorbent assay (ELISA) and quantitative PCR (qPCR) in which ELISA was applied for the detection of protein biomarkers and qPCR was especially applied for nucleic acid biomarker analysis. Although these constructed methods have been applied in wide range, they also showed some inherent shortcomings such as low sensitivity, large sample volume and complex operations. At present, many methods have been successfully constructed on the basis of DNA nanotechnology with the merits of high accuracy, rapid and simple operation for cancer biomarkers assay. In this review, we summarized the bioassay strategies based on DNA nanotechnology from the perspective of the analytical attributes for the first time and discussed and the feasibility of the reported strategies for clinical application in the future.

Exosomes: Breast cancer-derived extracellular vesicles; recent key findings and technologies in disease progression, diagnostics, and cancer targeting

Breast cancer is one of the most frequently diagnosed types of cancer in women. Metastasis, particularly to the lungs and brain, increases mortality in breast cancer patients. Recently, breast cancer-related exosomes have received significant attention because of their key role in breast cancer progression. As a result, numerous exosome-based therapeutic tools for diagnosis and treatment have been developed, and their biological and chemical mechanisms have been explored. This review summarizes up-to-date advanced key findings and technologies in breast cancer progression, diagnostics, and targeting. We focused on recent research on the basic biology of exosomes and disease-related exosomal genes and proteins, as well as their signal transduction in cell-to-cell communications, diagnostic markers, and exosome-based antibreast cancer technologies. We also paid special attention to technologies employing exosomes modified with functional peptides for the targeted delivery of therapeutic and diagnostic agents.

Two-Step Competitive Hybridization Assay: A Method for Analyzing Cancer-Related microRNA Embedded in Extracellular Vesicles

With an increased understanding of the role of microRNAs (miRNAs) in cancer evolution, there is a growing interest in the use of these non-coding nucleic acids in cancer diagnosis, prognosis, and treatment monitoring. miRNAs embedded in extracellular vesicles (EVs) are of particular interest given that circulating EVs carry cargo that are strongly correlated to their cells of origin such as tumor cells while protecting them from degradation. As such, there is a tremendous interest in new simple-to-operate vesicular microRNA analysis tools for widespread use in performing liquid biopsies. Herein, we present a two-step competitive hybridization assay that is rationally designed to translate low microRNA concentrations to large electrochemical signals as the measured signal is inversely proportional to the microRNA concentration. Using this assay, with a limit-of-detection of 122 aM, we successfully analyzed vesicular miRNA 200b from prostate cancer cell lines and human urine samples, demonstrating the expected lower expression levels of miRNA 200b in the EVs from prostate cancer cells and in the prostate cancer patient's urine samples compared to healthy patients and non-tumorigenic cell lines, validating the suitability of our approach for clinical analysis.

A novel microfluidic RNA chip for direct, single-nucleotide specific, rapid and partially-degraded RNA detection

Direct RNA detection is critical for providing the RNA insights into gene expression profiling, noncoding RNAs, RNA-associated diseases and pathogens, without reverse transcription. However, classical RNA analysis usually requires RT-PCR, which can cause bias amplification and quantitation errors. To address this challenge, herein we report a microfluidic RNA chip (the microchip prototype) for direct RNA detection, which is primarily based on RNA extension and labeling with DNA polymerase. This detection strategy is of high specificity (discriminating against single-nucleotide differences), rapidity, accuracy, nuclease resistance, and reusability. Further, we have successfully detected disease-associated RNAs in clinical samples, demonstrating its great potentials in biomedical research and clinical diagnosis.

DNA Structure-Stabilized Liquid-Liquid Self-Assembled Ordered Au Nanoparticle Interface for Sensitive Detection of MiRNA 155

Au nanoparticles (Au NPs) can be self-assembled in a bottom-up orderly manner at the oil-water interface, which is widely used as SERS platforms, but the stability of the Au NP interface needs to be improved due to shaking or shifting and the Brownian motion. The DNA structure with unique sequence specificity, excellent programmability, and flexible end-group modification capability owns good potential to precisely control the plasmonic structure's distance. In this study, a large area of the SERS substrate is obtained from the DNA structure-stabilized self-assembled ordered Au NPs on the cyclohexane-water interface. Combining with the exonuclease III (exo III)-assisted DNA recycling amplification strategy, we construct a liquid-phase SERS biosensor for efficient detection of microRNA 155 (miRNA 155). Compared with the traditional randomly assembled Au NPs on the two-phase interface, the SERS signal is significantly enhanced and more stable. The detection limit of the SERS biosensor for miRNA 155 reached 1.45 fmol/L, which has a very wide linear range (100 fmol/L-5 nmol/L). This work gives an efficient approach to stabilize the self-assembly Au NPs on the liquid-liquid interface, which can broaden the application of SERS analysis.

Peptide Nucleic Acid-Functionalized Nanochannel Biosensor for the Highly Sensitive Detection of Tumor Exosomal MicroRNA

Compared with free miRNAs in blood, miRNAs in exosomes have higher abundance and stability. Therefore, miRNAs in exosomes can be regarded as an ideal tumor marker for early cancer diagnosis. Here, a peptide nucleic acid (PNA)-functionalized nanochannel biosensor for the ultrasensitive and specific detection of tumor exosomal miRNAs is proposed. After PNA was covalently bound to the inner surface of the nanochannels, the detection of tumor exosomal miRNAs was achieved by the charge changes on the surface of nanochannels before and after hybridization (PNA-miRNA). Due to the neutral characteristics of PNA, the efficiency of PNA-miRNA hybridization was improved by significantly reducing the background signal. This biosensor could not only specifically distinguish target miRNA-10b from single-base mismatched miRNA but also achieve a detection limit as low as 75 aM. Moreover, the biosensor was further used to detect exosomal miRNA-10b derived from pancreatic cancer cells and normal pancreatic cells. The results indicate that this biosensor could effectively distinguish pancreatic cancer tumor-derived exosomes from the normal control group, and the detection results show good consistency with those of the quantitative reverse-transcription polymerase chain reaction method. In addition, the biosensor was used to detect exosomal miRNA-10b in clinical plasma samples, and it was found that the content of exosomal miRNA-10b in cancer patients was generally higher than that of healthy individuals, proving that the method is expected to be applied for the early diagnosis of cancer.

High-throughput immunosensor chip coupled with a fluorescent DNA dendrimer for ultrasensitive detection of cardiac troponin T

A novel fluorescence (FL) imaging platform was established for ultrasensitive and rapid detection of cardiac troponin T (cTnT), based on a high-throughput immunosensor chip and a DNA dendrimer capped with a large number of fluorescent dyes (FDD@Cy5). Through an enzyme-free and step-by-step strategy, FDD@Cy5 was self-assembled facilely. After the formation of a sandwich immunocomplex and biotin–streptavidin conjugation, FDD@Cy5 could be captured on the chip. FL signals emerged from Cy5 under external light and the enrichment of Cy5 on the dendrimer led to signal amplification. A FL image containing 90 spots could be collected instantaneously by laser confocal scanning microscopy and the brightness of all the spots corresponded to the concentrations of target cTnT. Under optimal conditions, the immunosensor chip coupled with FDD@Cy5 exhibited an excellent detection limit of 0.10 pg L⁻¹, a wide linear range from 0.20 pg L⁻¹ to 2.0 ng L⁻¹, a sample consumption down to 3.0 μL and a maximum throughput of 45 tests per h. The proposed approach was also applied to cTnT quantitation in serum samples with acceptable accuracy, providing a new avenue for early diagnosis and the prognosis evaluation of acute myocardial infarction.

A novel fluorescence imaging platform based on a high-throughput immunosensor chip and a DNA dendrimer capped with plenty of fluorescent dyes was proposed for ultrasensitive quantitation of cardiac troponin T.