Recent Advances in Aptamer-Based Liquid Biopsy

Electrochemical Sensor for the Detection and Accurate Early Diagnosis of Ovarian Cancer

Ovarian cancer (OC) has the highest mortality rate among malignant tumors, primarily because it is difficult to diagnose early. Exosomes, a type of extracellular vesicle rich in parental information, have garnered significant attention in the field of cancer diagnosis and treatment. They play an important regulatory role in the occurrence, development, and metastasis of OC. Consequently, exosomes have emerged as noninvasive biomarkers for early cancer detection. Therefore, identifying cancer-derived exosomes may offer a novel biomarker for the early detection of OC. In this study, we developed a metal-organic frameworks assembled "double hook"-type aptamer electrochemical sensor, which enables accurate early diagnosis of OC. Under optimal experimental conditions, electrochemical impedance spectroscopy technology demonstrated a good linear relationship within the concentration range of 31-3.1 × 106 particles per microliter, with a detection limit as low as 12 particles per microliter. The universal exosome detection platform is constructed, and this platform can not only differentiate between high-grade serous ovarian cancer (HGSOC) patients and healthy individuals but also distinguish between HGSOC patients and nonhigh-grade serous OC (non-HGSOC). Consequently, it provides a novel strategy for the early diagnosis of OC and holds great significance in clinical differential diagnosis.

Immunomagnetic capture and traceless release of native tumor-derived exosomes from human plasma for exploring interaction with recipient cells by aptamer-functionalized nanoflowers

BACKGROUND

Tumor-derived exosomes (TEXs) play an important role in the development process of cancer, which can transport a large number of carcinogenic molecules to normal cells, and subsequently promote tumor metastasis. However, TEXs that were utilized in most of previous researches were obtained from the cell medium of tumor cell lines, which cannot reflect the physiological state of primary cells in vivo. Isolation of native TEXs from human plasma with intact function is contributed to exploring the interaction between TEXs and recipient cells for understanding their true biological functions.

RESULTS

We developed a strategy that involves both capture and release processes to obtain native TEXs from plasma of cancer patients. An MoS2-based immunomagnetic probe (Fe3O4@MoS2-Au-Aptamer, named as FMAA) with the advantages of high surface area, magnetic response and abundant affinity sites was designed and synthesized to capture TEXs through recognizing high-expression tumor-associated antigens of EpCAM. With the assistance of complementary sequences of EpCAM, TEXs were released with non-destruction and no residual labels. According to NTA analysis, 107-108 TEXs were recovered from per mL plasma of breast cancer patients. The interaction between native TEXs and normal epithelial cells confirms TEXs could induce significant activation of autophagy of recipient cells with co-culture for 12 h. Proteomics analysis demonstrated a total of 637 proteins inside epithelial cells had dynamic expression with the stimulation of TEXs and 5 proteins in the pathway of autophagy had elevated expression level.

SIGNIFICANCE

This work not only obtains native TEXs from human plasma with non-destruction and no residual labels, but also explores the interaction between TEXs and recipient cells for understanding their true biological functions, which will accelerate the application of TEXs in the field of biomarkers and therapeutic drugs.

Spatial Control of Receptor Dimerization Using Programmable DNA Nanobridge

Receptor dimerization is an essential mechanism for the activation of most receptor tyrosine kinases by ligands. Thus, regulating the nanoscale spatial distribution of cell surface receptors is significant for studying both intracellular signaling pathways and cellular behavior. However, there are currently very limited methods for exploring the effects of modulating the spatial distribution of receptors on their function by using simple tools. Herein, we developed an aptamer-based double-stranded DNA bridge acting as "DNA nanobridge", which regulates receptor dimerization by changing the number of bases. On this basis, we confirmed that the different nanoscale arrangements of the receptor can influence receptor function and its downstream signals. Among them, the effect gradually changed from helping to activate to inhibiting as the length of DNA nanobridge increased. Hence, it can not only effectively inhibit receptor function and thus affect cellular behavior but also serve as a fine-tuning tool to get the desired signal activity. Our strategy is promising to provide insight into the action of receptors in cell biology from the perspective of spatial distribution.

Selection of DNA aptamer recognizing CD44 for high-efficiency capture of circulating tumor cells

Cancer stem cells play critical roles in cancer progression, cancer invasion and metastasis, and cancer recurrence. CD44 is known as a specific surface marker of cancer stem cells, which has been well-studied in cancer invasion and metastasis. Herein, we successfully selected the DNA aptamers for recognizing CD44⁺ cells using Cell-SELEX strategy, in which the engineered CD44 overexpression cells were used as target cells for selection. The optimized aptamer candidate C24S showed high binding affinity with the K_d value of 14.54 nM and good specificity. Then, the aptamer C24S was employed to prepare the functional aptamer-magnetic nanoparticles (C24S-MNPs) for CTC capture. To investigate the capture efficiency and sensitivity of C24S-MNPs, series of cell capture tests were performed using artificial samples with 10-200 of HeLa cells spiked into 1 mL PBS or PBMCs isolated from 1 mL peripheral blood, obtaining an efficiency of 95% and 90%, respectively. More importantly, we finally explored the facility of C24S-MNPs for CTC detection in blood samples from clinical cancer patients, indicating a potential and feasible strategy for cancer diagnostic technology in clinical applications.

Aptamer-based technology for gastric cancer theranostics

Gastric cancer is one of the most common causes of cancer death worldwide. This cancer exhibits high molecular and phenotype heterogeneity. The overall survival rate for gastric cancer is very low because it is always diagnosed in the advanced stages. Therefore, early detection and treatment are of great significance. Currently, biomedical studies have tapped the potential clinical applicability of aptamer-based technology for gastric cancer diagnosis and targeted therapy. Herein, we summarize the enrichment and evolution of relevant aptamers, followed by documentation of the recent developments in aptamer-based techniques for early diagnosis and precision therapy for gastric cancers.

Recent advances of fluorescent sensors for bacteria detection-A review

Bacterial infections have become a global public health problem. Rapid and sensitive bacterial detection is of great importance for human health. Among various sensor systems, fluorescence sensor is rapid, portable, multiplexed, and cost-efficient. Herein, we reviewed the current trends of fluorescent sensors for bacterial detection from three aspects (response materials, target and recognition way). The fluorescent materials have the advantages of high fluorescent strength, high stability, and good biocompatibility. They provide a new path for bacterial detection. Several recent fluorescent nanomaterials for bacterial detection, including semiconductor quantum dots (QDs), carbon dots (CDs), up-conversion nanoparticles (UCNPs) and metal organic frameworks (MOFs), were introduced. Their optical properties and detection mechanisms were analyzed and compared. For different response targets in the detection process, we studied the fluorescence strategy using DNA, bacteria, and metabolites as the response target. In addition, we classified the recognition way between nanomaterial and target, including specific recognition methods based on aptamers, antibodies, bacteriophages, and non-specific recognition methods based on biological functional materials. The characteristics of different recognition methods were summarized. Finally, the weaknesses and future development of bacterial fluorescence sensor were discussed. This review provides new insights into the application of fluorescent sensing systems as an important tool for bacterial detection.

Recent progress in aptamer-based microfluidics for the detection of circulating tumor cells and extracellular vesicles

Liquid biopsy is a technology that exhibits potential to detect cancer early, monitor therapies, and predict cancer prognosis due to its unique characteristics, including noninvasive sampling and real-time analysis. Circulating tumor cells (CTCs) and extracellular vesicles (EVs) are two important components of circulating targets, carrying substantial disease-related molecular information and playing a key role in liquid biopsy. Aptamers are single-stranded oligonucleotides with superior affinity and specificity, and they can bind to targets by folding into unique tertiary structures. Aptamer-based microfluidic platforms offer new ways to enhance the purity and capture efficiency of CTCs and EVs by combining the advantages of microfluidic chips as isolation platforms and aptamers as recognition tools. In this review, we first briefly introduce some new strategies for aptamer discovery based on traditional and aptamer-based microfluidic approaches. Then, we subsequently summarize the progress of aptamer-based microfluidics for CTC and EV detection. Finally, we offer an outlook on the future directional challenges of aptamer-based microfluidics for circulating targets in clinical applications.

Multi-parameter Inputted Logic-Gating on Aptamer-Encoded Extracellular Vesicles for Colorectal Cancer Diagnosis

Extracellular vesicles (EVs) have emerged as a potential biomarker in liquid biopsy. However, cancer heterogeneity poses significant challenge to precise molecular diagnosis based on single-parameter input. Hence, strategies for analyzing multiple inputs with molecular computing were developed with the aim of improving diagnostic accuracy in liquid biopsy. In the present study, based on the surface of aptamer-encoded EVs, three toe-hold extended DNA aptamers served as specific inputs to perform AND-logic-gating to distinguish between healthy and cancerous EVs. In addition, this strategy has been successfully employed to analyze circulating EVs in clinical samples from colorectal cancer patients and healthy donors. The developed method has a promising future in the analysis of multiplex EV membrane proteins and the identification of early cancer.

Novel Molecular Aptamer Beacon for the Specific Simultaneous Analysis of Circulating Tumor Cells and Exosomes of Colorectal Cancer Patients

Liquid biopsy provides non-invasive and real-time detection for cancer diagnosis, but the lack of specific markers targeted to liquid biopsy components, such as circulating tumor cells (CTCs) and exosomes, has impeded its effective utilization in clinical settings. W3 is an aptamer, and its target has been previously demonstrated to be a predictor of colorectal cancer (CRC) metastasis. Herein, we developed a W3-based molecular beacon (MAB-W3-3G) to specifically detect CTCs and exosomes derived from CRC patients by modifying the W3 sequence and adding a fluorescent group FAM at the 5' end and a quencher group BHQ1 at the 3' end, resulting in a detectable green fluorescence only in the presence of the target. MAB-W3-3G retained features similar to those of the original W3, including high specificity and affinity for metastatic CRC cells, as well as excellent plasma stability. Notably, W3 target-positive CTCs were visualized, positive exosomes were quantified in CRC patients' whole blood without any sample pretreatment, and both detections could be finished in one step without any routine washing procedures. For CRC, the W3 target-positive CTC enumeration in metastasis was higher than that in non-metastasis (p < 0.01), and the quantitation of positive exosomes was correlated with CRC patients (p < 0.0001). Moreover, the MAB-W3-3G-based simultaneous detection of CTCs and exosomes was proven to have the potential for more precise clinical diagnosis. In conclusion, MAB-W3-3G could detect CTCs and exosomes in the blood samples of tumor patients with simple manipulation, rapid analysis, and high specificity, providing an effective liquid biopsy tool for the prediction of CRC.

Ultrasensitive thrombin sensing platform based on three-way junction initiated dual signal amplification

The sensitive and precise quantitative determination of thrombin is important for both fundamental research and clinical diagnostics of hypoxic ischemic encephalopathy because it is a key biological molecule in hemostasis and hemolysis. Herein, we depict a sensitive and label-free thrombin detection approach by taking the advantages of aptamer’s superior capability to bind with thrombin and the high efficiency of three-way junction initiated dual signal recycle. In this method, a capture probe which is inserted with an aptamer sequence is designed to specifically identify thrombin molecule and facilitate the signal amplification. Based on the DNA polymerase and endonuclease Nb.BbvCI-assisted chain extension, a large amount of single-strand DNA sequences that can fold into G-quadruplex are produced to specifically recognize commercial fluorescent dye thioflavin T for signal generation. Consequently, the approach exhibits a high detection sensitivity with the limit of detection as low as 768 fM, holding a great promise for detection of thrombin and disease diagnosis in the clinic.