Combination of Immunomagnetic Separation with Aptamer-Mediated Double Rolling Circle Amplification for Highly Sensitive Circulating Tumor Cell Detection

Photoelectrochemical aptasensing and fluorescence imaging co-joint detecting MCF-7 cells in whole blood via an inertial separation microfluidic chip

The mortality rate of tumor is still very high till now. Circulating tumor cells (CTCs) are the major culprit of high cancer mortality. To improve survival rate of cancer patients, real-time monitoring and quantitative detection of CTCs are of indescribable value. However, due to the extremely small content and heterogeneous characteristics of CTCs, to accurately detect CTCs is still a tremendous challenge in clinical trials. Herein, the photoelectrochemical aptasensing and fluorescence imaging were co-joint to detect MCF-7 cells in whole blood via an inertial separation microfluidic chip. A portable inertial microfluidic chip with a height of 150 μm was designed to separate MCF-7 cells from whole blood samples. Niblue-C6-IMC was used to label and image MCF-7 cells through specifically reacting with COX-2 enzyme from the over-expression on the cellular surface. Subsequently, MCF-7 cells were detected with a Bi2O2S nanoflower based photoelectrochemical sensing system. Parameters including the channel height and length, flow rate, focusing position, fluorescence probe concentration, and flow length of the microfluidic chip were optimized. The separation efficiency and purity of MCF-7 cells were 85 % and 80 %, respectively. For 1 mL of blood sample (100 cells mL-1), 85 cells and 90 cells could be calculated based on the signals from fluorescence imaging and photoelectrochemical response, respectively. Nevertheless, for assaying 1 mL of blood samples containing 50 MCF-7 cells, 40 cells and 39 cells were obtained from fluorescence imaging and photoelectrochemical responses, respectively.

Point-of-need species identification using non-PCR DNA-based approaches to combat wildlife crime

Wildlife crime, defined as any unlawful exploitation and trade of wildlife, is a lucrative illegal global industry, along with narcotics and weapons trafficking. It encompasses the harvest, transport, exchange, and end use of wildlife or wildlife-derived products. Regulated internationally by the Convention on the International Trade in Endangered Species of Flora and Fauna (CITES, 1973), wildlife crime is primarily detected using morphological or DNA sequencing methods. However, there is a growing demand for rapid, portable, and cost-effective screening tools to bypass time-consuming workflows and specialist laboratory equipment. Point-of-need testing, particularly at wildlife hotspots like international borders, offers a promising solution for the swift detection of illegal activities. Isothermal amplification methods such as loop mediated isothermal amplification (LAMP), rolling circle amplification (RCA), and recombinase polymerase amplification (RPA), are favoured for their low resource needs compared to traditional PCR. These methods can be combined with target detection methods such as clustered regularly interspaced short palindromic repeats (CRISPR) and aptamers to enhance sensitivity. Integrating these methods with others, such as lateral flow assays (LFA) and microfluidic devices, simplifies sample preparation and visualisation. Already established in disease diagnosis and food safety, these innovations in genetic testing provide rapid, on-site detection. When applied to wildlife crime, they can serve as tools to complement traditional PCR and sequencing methods. This review explores how non-PCR based approaches could offer faster, simpler, and more cost-effective solutions to combat wildlife crime.

Design and Optimization of Isothermal Gene Amplification for Generation of High-Gain Oligonucleotide Products by MicroRNAs

Thermal cycling-based quantitative polymerase chain reaction (qPCR) represents the gold standard method for accurate and sensitive nucleic acid quantification in laboratory settings. However, its reliance on costly thermal cyclers limits the implementation of this technique for rapid point-of-care (POC) diagnostics. To address this, isothermal amplification techniques such as rolling circle amplification (RCA) have been developed, offering a simpler alternative that can operate without the need for sophisticated instrumentation. This study focuses on the development and optimization of toehold-mediated RCA (TRCA), which employs a conformationally switchable dumbbell DNA template for the sensitive and selective detection of cancer-associated miRNAs, specifically miR-21. In addition, we developed variants of hyperbranched TRCA (HTRCA), nicking-assisted TRCA (NTRCA), and hyperbranched NTRCA (HNTRCA) to facilitate exponential amplification by enhancing TRCA through the sequential incorporation of reverse primer (Pr) and nicking endonuclease (nE). By conducting a systematic kinetic analysis of the initial rate and end point signals for varying concentrations of key reaction components, we could identify optimal conditions that markedly enhanced the sensitivity and specificity of the TRCA variants. In particular, HNTRCA, which exploits the synergistic effect of Pr and nE, demonstrated an approximately 3000-fold improvement in the detection limit (260 fM) and a wider dynamic range of more than 4 log orders of magnitude compared to TRCA, thereby evidencing its superior performance. Also, we established a mechanistic model for TRCA that includes the roles of Pr and nE in different amplification processes. Model parameters were fitted to the experimental data, and additional simulations were conducted to compare the four amplification methods. Further tests with real biological samples revealed that this technique showed a good correlation with qPCR in quantifying miR-21 expression in various cell lines (0.9510 of Pearson's r), confirming its potential as a robust and rapid tool for nucleic acid detection. Therefore, the simplicity, high sensitivity, and potential for integration with POC diagnostic platforms make the HNTRCA system suitable for field deployment in resource-limited environments.

Immuno-Rolling Circle Amplification (Immuno-RCA): Biosensing Strategies, Practical Applications, and Future Perspectives

In the rapidly evolving field of life sciences and biomedicine, detecting low-abundance biomolecules, and ultraweak biosignals presents significant challenges. This has spurred a rapid development of analytical techniques aiming for increased sensitivity and specificity. These advancements, including signal amplification strategies and the integration of biorecognition events, mark a transformative era in bioanalytical precision and accuracy. A prominent method among these innovations is immuno-rolling circle amplification (immuno-RCA) technology, which effectively combines immunoassays with signal amplification via RCA. This process starts when a targeted biomolecule, such as a protein or cell, binds to an immobilized antibody or probe on a substrate. The introduction of a circular DNA template triggers RCA, leading to exponential amplification and significantly enhanced signal intensity, thus the target molecule is detectable and quantifiable even at the single-molecule level. This review provides an overview of the biosensing strategy and extensive practical applications of immuno-RCA in detecting biomarkers. Furthermore, it scrutinizes the limitations inherent to these sensors and sets forth expectations for their future trajectory. This review serves as a valuable reference for advancing immuno-RCA in various domains, such as diagnostics, biomarker discovery, and molecular imaging.

Immunomagnetic particles exhibiting programmable hierarchical flower-like nanostructures for enhanced separation of tumor cells

Immunomagnetic particles are extensively used for the separation of biological molecules and particles, and have exhibited great potential in many fields including biosensors, disease diagnosis and biomedical engineering. However, most immunomagnetic particles exhibit a smooth surface, resulting in a limited separation efficiency for biological particles featuring enormous surface nanostructures, such as tumor cells. Here we report flower-like immunomagnetic particles (FIMPs) prepared by streptavidin (SA)-assisted biomineralization and one-step antibody modification, and demonstrate their superior capability for highly efficient and selective separation of circulating tumor cells (CTCs). SA can link inorganic nanosheets and magnetic nanoparticles together to obtain FIMPs with programmable hierarchical flower-like nanostructures and provide enormous binding sites for post-antibody modification. The synergetic effect of nano-sized petals and micro-sized particles in the hierarchical nanostructure enhances the interaction between the cells and the matrix, thus enabling FIMPs to separate CTCs with high selectivity and high efficiency. Our study provides a promising platform for the selective separation of trace biological molecules and particles from complex samples and shows great potential for downstream detection and diagnosis.

2D compounds with heterolayered architecture for infrared photodetectors

Compounds with heterolayered architecture, as a family of two-dimensional (2D) materials, are composed of alternating positive and negative layers. Their physical properties are determined not only by the charged constituents, but also by the interaction between the two layers. This kind of material has been widely used for superconductivity, thermoelectricity, energy storage, etc. In recent years, heterolayered compounds have been found as an encouraging choice for infrared photodetectors with high sensitivity, fast response, and remarkable reliability. In this review, we summarize the research progress of heterolayered materials for infrared photodetectors. A simple development history of the materials with three-dimensional (3D) or 2D structures, which are suitable for infrared photodetectors, is introduced firstly. Then, we compare the differences between van der Waals layered 2D materials and heterolayered 2D cousins and explain the advantages of heterolayered 2D compounds. Finally, we present our perspective on the future direction of heterolayered 2D materials as an emerging class of materials for infrared photodetectors.

Glowing Octopus-Inspired Nanomachine: A Versatile Aptasensor for Efficient Capture, Imaging, Separation, and NIR-Triggered Release of Cancer Cells

The separation and analysis of circulating tumor cells (CTCs) in liquid biopsy significantly facilitated clinical cancer diagnosis and personalized therapy. However, current methods face challenges in simultaneous efficient capturing, separation, and imaging of CTCs, and most of the devices cannot be reused/regenerated. We present here an innovative glowing octopus-inspired nanomachine (GOIN), capable of capturing, imaging, separating, and controlling the release of cancer cells from whole blood and normal cells. The GOIN comprises an aptamer-decorated magnetic fluorescent covalent organic framework (COF), which exhibits a strong affinity for nucleolin-overexpressed cancer cells through a multivalent binding effect. The captured cancer cells can be directly imaged using the intrinsic stable fluorescence of the COF layer in the GOIN. Employing magnet and NIR laser assistance enables easy separation and mild photothermal release of CTCs from the normal cells and the nanomachine without compromising cell viability. Moreover, the GOIN demonstrates a reusing capability, as the NIR-triggered CTC release is mild and nondestructive, allowing the GOIN to be reused at least three times.

A near-infrared photoelectrochemical aptasensing system based on Bi2O2S nanoflowers and gold nanoparticles for high-performance determination of MCF-7 cells

Circulating tumor cells (CTCs) are commonly considered as the major cause of tumor metastasis and can eventually lead to death. Therefore, developing a high-performance method for the determination of CTCs is very significant for promoting the cancer survival rate. Photoelectrochemical biosensing systems have been extensively investigated and applied for bioassays. Herein, Bi₂O₂S nanoflowers were successfully prepared through a simple one-step hydrothermal method. After being integrated with gold nanoparticles with a diameter of ∼45 nm, AuNPs/Bi₂O₂S nanocomposites were coated onto an ITO electrode surface to build a photoelectrochemical sensing platform which can be excited with near-infrared light to produce photocurrent response. Subsequently, mercapto-group functionalized aptamer (SH-Apt) was fixed onto the AuNPs/Bi₂O₂S/ITO surface. Due to the overexpress of MUC1 protein in the cell membrane, MCF-7 cells were specifically trapped on the SH-Apt/AuNPs/Bi₂O₂S/ITO surface. The introduce of MCF-7 cells lead to an obvious decrease on the photocurrent response. The photocurrent variation shows a satisfied linear relationship to the logarithm of MCF-7 cells concentration ranged from 50 to 6 × 10⁵ cell mL^-1. The detection limit obtained is 17 cell mL^-1. The PEC biosensor shows excellent sensitivity, selectivity and stability for sensing MCF-7 cells, even for determining MCF-7 cells in clinical serum samples.

Engineering Sandwiched Nanochannel Aptasensor for Efficiently Screening Cancer Cells

Cancer cells are a class of important tumor biomarkers and are closely related to tumorous progression. It is urgent to develop a sensitive and highly efficient method for the rapid and accurate detection of cancer cells. Herein, an aptamer sandwiched nanochannel electrochemical sensor was established for the highly selective determination of cancer cells. By virtue of the porous nanochannels as the filter platform and immobilized with DNA aptamers for specifically capturing the cancer cells, the nanochannel-based electrochemical sensor denotes excellent performance for MCF-7 screening, and allowing a low limit of detection of 36 cells mL^-1 . The nanochannels-based sandwich structure aptasensor not only presents an efficacious and reliable approach for cancer cell detection but also provides great advantage for preventing electrode passivation in the process of biomarkers analysis.

Nondestructive separation/enrichment and rolling circle amplification-powered sensitive SERS enumeration of circulating tumor cells via aptamer recognition

Nondestructive separation/enrichment and reliable detection of extremely rare circulating tumor cells (CTCs) in peripheral blood are of considerable importance in tumor precision diagnosis and treatment, yet this remains a big challenge. Herein, a novel strategy for nondestructive separation/enrichment and ultra-sensitive surface-enhanced Raman scattering (SERS)-based enumeration of CTCs is proposed via aptamer recognition and rolling circle amplification (RCA). In this work the magnetic beads modified with "Aptamer (Apt)-Primer" (AP) probes were utilized to specifically capture CTCs, and then after magnetic separation/enrichment, the RCA-powered SERS counting and benzonase nuclease cleavage-assisted nondestructive release of CTCs were realized, respectively. The AP was assembled by hybridizing the EpCAM-specific aptamer with a primer, and the optimal AP contains 4 mismatched bases. The RCA enhanced SERS signal nearly 4.5-fold, and the SERS strategy has good specificity, uniformity and reproducibility. The proposed SERS detection possesses a good linear relationship with the concentration of MCF-7 cells spiked in PBS with the limit of detection (LOD) of 2 cells/mL, which shows good potential practicality for detecting CTCs in blood with recoveries ranging from 100.56% to 116.78%. Besides, the released CTCs remained good cellular activity with the normal proliferation after re-culture for 48 h and normal growth for at least three generations. The proposed strategy of nondestructive separation/enrichment and SERS-based sensitive enumeration is promising for reliable analysis of EpCAM-positive CTCs in blood, which is expected to provide a powerful tool for analysis of extremely rare circulating tumor cells in complex peripheral blood for liquid biopsy.

Nucleic acid and nanomaterial-assisted signal-amplified strategies in fluorescent analysis of circulating tumor cells and small extracellular vesicles

As two main types of liquid biopsy markers, both circulating tumor cells (CTCs) and small extracellular vesicles (sEVs) play important roles in the diagnosis and prognosis of cancers. CTCs are malignant cells that detach from the original tumor tissue and enter the circulation of body fluids. sEVs are nanoscale vesicles secreted by normal cells or pathological cells. However, CTCs and sEVs in body fluids are scarce, leading to great difficulties in the accurate analysis of related diseases. For the sensitive detection of CTCs and sEVs in body fluids, various types of nucleic acid and nanomaterial-assisted signal amplification strategies have been developed. In this review, we summarize the recent advances in fluorescent detection of CTCs and sEVs in liquid biopsy based on nucleic acid and nanomaterial-assisted signal amplification strategies. We also discuss their advantages, challenges, and future prospects.

Redox-labelled electrochemical aptasensors with nanosupported cancer cells

The transfer of redox-labelled bioelectrochemical sensors from proteins to cells is not straightforward because of the cell downward force issue on the surface of the sensors. In this paper, 20-nm-thick nanopillars are introduced to overcome this issue, in a well-controlled manner. We show on both molecular dynamics simulations and experiments that suspending cells a few nanometers above an electrode surface enables redox-labelled tethered DNA aptamer probes to move freely, while remaining at an interaction distance from a target membrane protein, i. e. epithelial cell adhesion molecule (EpCAM), which is typically overexpressed in cancer cells. By this nanopillar configuration, the interaction of aptamer with cancer cells is clearly observable, with 13 cells as the lower limit of detection. Nanoconfinement induced by the gap between the electrode surface and the cell membrane appears to improve the limit of detection and to lower the melting temperature of DNA aptamer hairpins, offering an additional degree of freedom to optimize molecular recognition mechanisms. This novel nanosupported electrochemical DNA cell sensor scheme including Brownian-fluctuating redox species opens new opportunities for the design of all-electrical sensors using redox-labelled probes.

Simultaneous detection of circulating tumor DNAs using a SERS-based lateral flow assay biosensor for point-of-care diagnostics of head and neck cancer

Circulating tumor DNA (ctDNA) has recently emerged as an ideal target for biomarker analytes. Thus, the development of rapid and ultrasensitive ctDNA detection methods is essential. In this study, a high-throughput surface-enhanced Raman scattering (SERS)-based lateral flow assay (LFA) strip is proposed. The aim of this method is to achieve accurate quantification of TP53 and PIK3CA E545K, two types of ctDNAs associated with head and neck squamous cell carcinoma (HNSCC), particularly for point-of-care testing (POCT). Raman reporters and hairpin DNAs are used to functionalize the Pd-Au core-shell nanorods (Pd-AuNRs), which serve as the SERS probes. During the detection process, the existence of targets could open the hairpins on the surface of Pd-AuNRs and trigger the first step of catalytic hairpin assembly (CHA) amplification. The next stage of CHA amplification is initiated by the hairpins prefixed on the test lines, generating numerous "hot spots" to enhance the SERS signal significantly. By the combination of high-performing SERS probes and a target-specific signal amplification strategy, TP53 and PIK3CA E545K are directly quantified in the range of 100 aM-1 nM, with the respective limits of detection (LOD) calculated as 33.1 aM and 20.0 aM in the PBS buffer and 37.8 aM and 23.1 aM in human serum, which are significantly lower than for traditional colorimetric LFA methods. The entire detection process is completed within 45 min, and the multichannel design realizes the parallel detection of multiple groups of samples. Moreover, the analytical performance is validated, including reproducibility, uniformity, and specificity. Finally, the SERS-LFA biosensor is employed to analyze the expression levels of TP53 and PIK3CA E545K in the serum of patients with HNSCC. The results are verified as consistent with those of qRT-PCR. Thus, the SERS-LFA biosensor can be considered as a noninvasive liquid biopsy assay for clinical cancer diagnosis.

Design and application of DNA nanostructures for organelle-targeted delivery of anticancer drugs

INTRODUCTION

DNA nanostructures targeting organelles are of great significance for the early diagnosis and precise therapy of human cancers. This review is expected to promote the development of DNA nanostructure-based cancer treatment with organelle-level precision in the future.

AREAS COVERED

In this review, we introduce the different principles for targeting organelles, summarize the progresses in the development of organelle-targeting DNA nanostructures, highlight their advantages and applications in disease treatment, and discuss current challenges and future prospects.

EXPERT OPINION

Accurate targeting is a basic problem for effective cancer treatment. However, current DNA nanostructures cannot meet the actual needs. Targeting specific organelles is expected to further improve the therapeutic effect and overcome tumor cell resistance, thereby holding great practical significance for tumor treatment in the clinic. With the deepening of the research on the molecular mechanism of disease development, especially on tumorigenesis and tumor progression, and increasing understanding of the behavior of biological materials in living cells, more versatile DNA nanostructures will be constructed to target subcellular organelles for drug delivery, essentially promoting the early diagnosis of cancers, classification, precise therapy and the estimation of prognosis in the future.

High sensitivity detection of tumor cells in biological samples using a multivalent aptamer strand displacement strategy

Monitoring the cell surface-expressed nucleolin facilitates early cancer diagnosis. Herein, we developed a multivalent aptamer displacement strand duplex strategy on cell membranes using a multi-receptor co-recognition design for improving the sensitivity and specificity of cancer cell recognition with an ultra-low background. The AS1411 aptamer labeled with the FAM fluorophore can be quenched using a partial complementary sequence modified with a BHQ1 tag which is partially hybridized with the AS1411 aptamer to create a receptor-activating aptamer. The multi-AS1411 activable probe based on the strand displacement strategy was constructed using multiple copies of the structure-switching AS1411 aptamer (bearing a short poly-A tail) linked together using the poly-T long chain (as a scaffold) which was synthesized by Terminal Deoxynucleotidyl Transferase (TDT)-mediated extension. We demonstrated the promising efficacy and sensitivity of our method in recognizing tumor cells in both cell mixtures and clinical cytology specimens. Due to its simple and fast operation with excellent cell recognition sensitivity and accuracy, it is expected to achieve the detection of low abundance target cells. Our approach will have broad application in clinical rapid detection and personalized medicine.

Biosupramolecular networks: Taking inspiration from nature to create powerful synthetic platforms

Nature is predicated on the ability to process large number of parallel signals to produce specific downstream outputs. Biosupramolecular networks are beginning to allow such processing power in synthetic systems, particularly through harnessing the recognition power of biomolecules. Such systems can be summarised through the reductionist view of containing inputs, circuitry motifs and functional outputs, with each of these elements able to be readily combined in a modular approach. Through the inherent 'plug and play' nature of these systems the field continues to rapidly expand, providing a wealth of new smart diagnostic and therapeutic systems.

Rolling Circle Amplification as a Universal Method for the Analysis of a Wide Range of Biological Targets

Detection and quantification of biotargets are important analytical tasks, which are solved using a wide range of various methods. In recent years, methods based on the isothermal amplification of nucleic acids (NAs) have been extensively developed. Among them, a special place is occupied by rolling circle amplification (RCA), which is used not only for the detection of a specific NA but also for the analysis of other biomolecules, and is also a versatile platform for the development of highly sensitive methods and convenient diagnostic devices. The present review reveals a number of methodical aspects of RCA-mediated analysis; in particular, the data on its key molecular participants are presented, the methods for increasing the efficiency and productivity of RCA are described, and different variants of reporter systems are briefly characterized. Differences in the techniques of RCA-mediated analysis of biotargets of various types are shown. Some examples of using different RCA variants for the solution of specific diagnostic problems are given.

Inertial microfluidics for high-throughput cell analysis and detection: a review

Since it was first proposed in 2007, inertial microfluidics has been extensively studied in terms of theory, design, fabrication, and application. In recent years, with the rapid development of microfabrication technologies, a variety of channel structures that can focus, concentrate, separate, and capture bioparticles or fluids have been designed and manufactured to extend the range of potential biomedical applications of inertial microfluidics. Due to the advantages of high throughput, simplicity, and low device cost, inertial microfluidics is a promising candidate for rapid sample processing, especially for large-volume samples with low-abundance targets. As an approach to cellular sample pretreatment, inertial microfluidics has been widely employed to ensure downstream cell analysis and detection. In this review, a comprehensive summary of the application of inertial microfluidics for high-throughput cell analysis and detection is presented. According to application areas, the recent advances can be sorted into label-free cell mechanical phenotyping, sheathless flow cytometric counting, electrical impedance cytometer, high-throughput cellular image analysis, and other methods. Finally, the challenges and prospects of inertial microfluidics for cell analysis and detection are summarized.

A 'smart' aptamer-functionalized continuous label-free cell catch-transport-release system

Label-free cell sorting devices are of great significance for biomedical research and clinical therapeutics. However, current platforms for label-free cell sorting cannot achieve continuity and selectivity simultaneously, resulting in complex steps and limited reliability. Here, an immunoaffinity-based cell catch-transport-release thermo-chemo-mechanical coupling hydrogel (iCatch) device is reported. It contains a temperature-responsive hydrogel that can generate spatial movement synergically with the reversible binding of affinity handle modified. The functionalized hydrogel is embedded inside a biphasic microfluidic platform to enable cell transportation between the flows. The cell sorting capability and biocompatibility of the iCatch device were validated with CCRF-CEM cells as a proof-of-concept, and CCRF-CEM-specific aptamers with thermo-responsive affinity as well as a hydrogel with temperature-dependent volume were employed accordingly. A cell catching efficiency of ∼40% and a recovery rate of ∼70% were achieved. The iCatch device provides a high-throughput (∼900 cells mm-1 s-1) platform for cell sorting and is ultimately valuable for downstream biomedical applications.