Aptamer and Antisense-Mediated Two-Dimensional Isolation of Specific Cancer Cell Subpopulations

Apta FastZ: An Algorithm for the Rapid Identification of Aptamers with Defined Binding Affinities

Real-time biomolecular monitoring requires biosensors based on affinity reagents, such as aptamers, with moderate to low affinities for the best binding dynamics and signal gain. We recently reported Pro-SELEX, an approach that utilizes parallelized SELEX and high-content bioinformatics for the selection of aptamers with predefined binding affinities. The Pro-SELEX pipeline relies on an algorithm, termed AptaZ, that can predict the binding affinities of selected aptamers. The original AptaZ algorithm is computationally complex and slows the overall throughput of Pro-SELEX. Here, we present Apta FastZ, a rapid equivalent of AptaZ. The Apta FastZ algorithm considers the spare nature of the sequences from SELEX and is coded to avoid unnecessary comparison between sequences. As a result, Apta FastZ achieved a 10 to 40-fold faster computing speed compared to the original AptaZ algorithm while maintaining identical outcomes, allowing the bioinformatics to be completed within 1-10 h for large-scale data sets. We further validated the affinity of myeloperoxidase aptamers predicted by Apta FastZ by experiments and observed a high level of linear correlation between predicted scores and measured affinities. Taken together, the implementation of Apta FastZ could greatly accelerate the current Pro-SELEX workflow, allowing customized aptamers to be discovered within 3 days using preselected DNA libraries.

A magneto-activated nanoscale cytometry platform for molecular profiling of small extracellular vesicles

Exosomal PD-L1 (exoPD-L1) has recently received significant attention as a biomarker predicting immunotherapeutic responses involving the PD1/PD-L1 pathway. However, current technologies for exosomal analysis rely primarily on bulk measurements that do not consider the heterogeneity found within exosomal subpopulations. Here, we present a nanoscale cytometry platform NanoEPIC, enabling phenotypic sorting and exoPD-L1 profiling from blood plasma. We highlight the efficacy of NanoEPIC in monitoring anti-PD-1 immunotherapy through the interrogation of exoPD-L1. NanoEPIC generates signature exoPD-L1 patterns in responders and non-responders. In mice treated with PD1-targeted immunotherapy, exoPD-L1 is correlated with tumor growth, PD-L1 burden in tumors, and the immune suppression of CD8+ tumor-infiltrating lymphocytes. Small extracellular vesicles (sEVs) with different PD-L1 expression levels display distinctive inhibitory effects on CD8 + T cells. NanoEPIC offers robust, high-throughput profiling of exosomal markers, enabling sEV subpopulation analysis. This platform holds the potential for enhanced cancer screening, personalized treatment, and therapeutic response monitoring.

A Micropillar Array Based Microfluidic Device for Rare Cell Detection and Single-Cell Proteomics

Advancements in single-cell-related technologies have opened new possibilities for analyzing rare cells, such as circulating tumor cells (CTCs) and rare immune cells. Among these techniques, single-cell proteomics, particularly single-cell mass spectrometric analysis (scMS), has gained significant attention due to its ability to directly measure transcripts without the need for specific reagents. However, the success of single-cell proteomics relies heavily on efficient sample preparation, as protein loss in low-concentration samples can profoundly impact the analysis. To address this challenge, an effective handling system for rare cells is essential for single-cell proteomic analysis. Herein, we propose a microfluidics-based method that offers highly efficient isolation, detection, and collection of rare cells (e.g., CTCs). The detailed fabrication process of the micropillar array-based microfluidic device is presented, along with its application for CTC isolation, identification, and collection for subsequent proteomic analysis.

Aptamer-Mediated Enrichment of Rare Circulating Fetal Nucleated Red Blood Cells for Noninvasive Prenatal Diagnosis

Isolation of circulating fetal nucleated red blood cells (cfNRBCs) from maternal peripheral blood provides a superior strategy for noninvasive prenatal genetic diagnosis. Recent technical advances in single-cell isolation and genetic analyses have promoted the clinical application of circulating fetal cell-based noninvasive prenatal diagnosis. However, the lack of highly specific ligands for rare circulating fetal cell enrichment from massive maternal cells significantly impedes the clinical transformation progress. In this work, aptamers specific to NRBCs were developed through clinical sample-based cell-SELEX. Herein, the complex clinical system provides natural selection stringency through binding competition between target and background cells, and it empowers aptamers with high specificity. An aptamer-based strategy was also established to isolate cfNRBCs from maternal peripheral blood. Results show the remarkable selectivity and affinity of developed aptamers, enabling efficient enrichment of cfNRBCs from abundant maternal cells. Moreover, screening for fetal sex and trisomy syndrome achieved high accuracy through chromosome analysis of enriched cfNRBCs. To the best of our knowledge, this is the first report to develop aptamer ligands for cfNRBC enrichment, providing an efficient strategy to screen cfNRBC-specific ligands and demonstrating broad application potential for cfNRBC-based noninvasive prenatal diagnosis.

Double-Tetrahedral DNA Probe Functionalized Ag Nanorod Biointerface for Effective Capture, Highly Sensitive Detection, and Nondestructive Release of Circulating Tumor Cells

Circulating tumor cells (CTCs) are indicative of tumorigenesis, metastasis, and recurrence; however, it is still a great challenge to efficiently analyze the extremely rare CTCs in peripheral blood. Herein, a novel nanobiointerface integrating high affinities of arrayed silver nanorods (Ag NRs) and double-tetrahedral DNA (DTDN) probes by a clever strategy is proposed for the efficient capture, highly sensitive detection, and nondestructive release of CTCs. Under the optimal conditions, the DTDN-probe-functionalized Ag NRs nanobiointerface can capture 90.2% of SGC-7901 cells in PBS, and the capture efficiency is 2.8 times and 50 times those of a DTDN-probe-functionalized Ag film and unfunctionalized Ag NRs, respectively, benefiting from the nanorough interface of the Ag NRs array and multivalent recognition of the DTDN probe. In addition, 93.4% of cells was released via Zn2+-assisted DNAzyme cleavage, and the viability of the postreleased CTCs is about 98.0%. The potential practicality of the nanobiointerface for testing CTCs in blood was further characterized by spiking SGC-7901 cells in leukocytes collected from human blood, and the results show that 83.8% capture efficiency, 91.2% release efficiency, and single-cell detection limit were achieved, which indicates that the nanobiointerface has great potential in clinical applications for reliable CTC analyses.

Unraveling Cancer Metastatic Cascade Using Microfluidics-based Technologies

Cancer has long been a leading cause of death. The primary tumor, however, is not the main cause of death in more than 90% of cases. It is the complex process of metastasis that makes cancer deadly. The invasion metastasis cascade is the multi-step biological process of cancer cell dissemination to distant organ sites and adaptation to the new microenvironment site. Unraveling the metastasis process can provide great insight into cancer death prevention or even treatment. Microfluidics is a promising platform, that provides a wide range of applications in metastasis-related investigations. Cell culture microfluidic technologies for in vitro modeling of cancer tissues with fluid flow and the presence of mechanical factors have led to the organ-on-a-chip platforms. Moreover, microfluidic systems have also been exploited for capturing and characterization of circulating tumor cells (CTCs) that provide crucial information on the metastatic behavior of a tumor. We present a comprehensive review of the recent developments in the application of microfluidics-based systems for analysis and understanding of the metastasis cascade from a wider perspective.

Nanomaterial-Based Immunocapture Platforms for the Recognition, Isolation, and Detection of Circulating Tumor Cells

Circulating tumor cells (CTCs) are a type of cancer cells that circulate in the peripheral blood after breaking away from solid tumors and are essential for the establishment of distant metastasis. Up to 90% of cancer-related deaths are caused by metastatic cancer. As a new type of liquid biopsy, detecting and analyzing CTCs will provide insightful information for cancer diagnosis, especially the in-time disease status, which would avoid some flaws and limitations of invasive tissue biopsy. However, due to the extremely low levels of CTCs among a large number of hematologic cells, choosing immunocapture platforms for CTC detection and isolation will achieve good performance with high purity, selectivity, and viability. These properties are directly associated with precise downstream analysis of CTC profiling. Recently, inspired by the nanoscale interactions of cells in the tissue microenvironment, platforms based on nanomaterials have been widely explored to efficiently enrich and sensitively detect CTCs. In this review, various immunocapture platforms based on different nanomaterials for efficient isolation and sensitive detection of CTCs are outlined and discussed. First, the design principles of immunoaffinity nanomaterials are introduced in detail. Second, the immunocapture and release of platforms based on nanomaterials ranging from nanoparticles, nanostructured substrates, and immunoaffinity microfluidic chips are summarized. Third, recent advances in single-cell release and analysis of CTCs are introduced. Finally, some perspectives and challenges are provided in future trends of CTC studies.

Dual-Aptamer-Targeted Immunomagnetic Nanoparticles to Accurately Explore the Correlations between Circulating Tumor Cells and Gastric Cancer

It has been acknowledged that circulating tumor cells (CTCs) are promising biomarkers in liquid biopsy for cancer diagnosis and prognosis. However, the relationship between the CTC number and gastric cancer has scarcely been quantitatively investigated. Moreover, the single criterion of epithelial cell adhesion molecule (EpCAM) antibody/aptamer to specifically recognize epithelial CTCs cannot be universally applied for clinical applications, as it fails to recognize EpCAM-negative CTCs. Herein, we propose simple, low-cost, dual-aptamer (EpCAM and PTK7)-modified immunomagnetic Fe₃O₄ particles (IMNs) for efficient capture of heterogeneous CTCs and downstream analysis in gastric cancer patients. High PTK7 expression and a significant negative correlation between PTK7 and EpCAM expression were observed in primary gastric cancer tissues. Taking MGC-803 and BGC-823 cells as CTC models, the obtained dual-targeting IMNs could distinguishably recognize these cells with both high or low EpCAM and PTK7 expressions, which enhanced the accuracy of CTC recognition in gastric cancer. More than 95% of these two kinds of cells could be captured within 20 min of incubation, which was significantly more efficient than that of single EpCAM- or PTK7-modified IMNs. With this strategy, as low as five CTCs could be captured from phosphate-buffered saline (PBS), a cell mixture containing THP-1 cells, and lysed blood mediums. Moreover, the obtained CTCs can be used for subsequent gene analysis. Finally, the fabricated IMNs were successfully applied for CTC capture in 1.0 mL of peripheral blood samples from patients with gastric cancer. The detected CTC numbers in 72 participants were found to have close relationships with chemotherapy sensitivity, diagnosis, stage, and distant metastasis of patients. This work provides important references for further investigations on CTC-related diagnosis and individualized treatment.

Basic Principles and Recent Advances in Magnetic Cell Separation

Magnetic cell separation has become a key methodology for the isolation of target cell populations from biological suspensions, covering a wide spectrum of applications from diagnosis and therapy in biomedicine to environmental applications or fundamental research in biology. There now exists a great variety of commercially available separation instruments and reagents, which has permitted rapid dissemination of the technology. However, there is still an increasing demand for new tools and protocols which provide improved selectivity, yield and sensitivity of the separation process while reducing cost and providing a faster response. This review aims to introduce basic principles of magnetic cell separation for the neophyte, while giving an overview of recent research in the field, from the development of new cell labeling strategies to the design of integrated microfluidic cell sorters and of point-of-care platforms combining cell selection, capture, and downstream detection. Finally, we focus on clinical, industrial and environmental applications where magnetic cell separation strategies are amongst the most promising techniques to address the challenges of isolating rare cells.

Recent Advances in Aptamer-Based Liquid Biopsy

Liquid biopsy capable of noninvasive and real-time molecular profiling is considered as a breakthrough technology, endowing an opportunity for precise diagnosis of individual patients. Extracellular vesicles (EVs) and circulating tumor cells (CTCs) consisting of substantial disease-related molecular information play an important role in liquid biopsy. Therefore, it is critically significant to exploit high-performance recognition ligands for efficient isolation and analysis of EVs and CTCs from complex body fluids. Aptamers exhibit extraordinary merits of high specificity and affinity, which are considered as superior recognition ligands for liquid biopsy. In this review, we first summarize recent advanced strategies for the evolution of high-performance aptamers and the construction of various aptamer-based recognition elements. Subsequently, we mainly discuss the isolation and analysis of EVs and CTCs based on the aptamer functioned biomaterials/biointerface. Ultimately, we envision major challenges and future direction of aptamer-based liquid biopsy for clinical utilities.

A pH-independent electrochemical aptamer-based biosensor supports quantitative, real-time measurement in vivo

An electrochemical aptamer-based sensor, enabling in vivo measurements of drug concentrations directly in the bladder of living rats under pH-variable conditions, was developed employing a π-extended tetrathiafulvalene (exTTF) as redox reported.

A new insight to deformability correlation of circulating tumor cells with metastatic behavior by application of a new deformability-based microfluidic chip

Isolation and characterization of circulating tumor cells (CTCs) found in blood samples of cancer patients have been considered as a reliable source for cancer prognosis and diagnosis. A new continuous microfluidic platform has been designed in this investigation for simultaneous capture and characterization of CTCs based on their deformability. The deformability-based chip (D-Chip) consists of two sections of separation and characterization where slanted weirs with a gap of 7 μm were considered. Although sometimes CTCs and leukocytes have the same size, the deformability differs in such a way that can be exploited for enrichment purposes. MCF7 and MDA-MB-231 cell lines were used for the initial evaluation of the D-Chip performance. In the separation section, cancer cells were isolated based on deformability differences with an efficiency of higher than 93% (∼average capturing capacity of 2085 out of 2200 cancer cells ml^-1) and with significantly high purity (15-40 WBCs ml^-1; ∼5 log depletion of WBCs). Cancer cells were categorized based on the deformability difference in the characterization section. Subsequently, 15 clinical blood samples from breast cancer patients were analyzed by the D-Chip. Suggest 'The chip detected CTCs in all patient samples, processed the blood sample at a high throughput of 5.3 ml/h, and properly categorized CTCs based on deformability differences. Further characterization showed that the highly deformable breast cancer CTCs in our patient samples also showed higher potential of metastasis in support of a broader correlation between deformability of CTCs and metastatic behavior.

Capture, Detection, and Simultaneous Identification of Rare Circulating Tumor Cells Based on a Rhodamine 6G-Loaded Metal-Organic Framework

Circulating tumor cells (CTCs) play a key role in the development of tumor metastasis. It will be a big step forward for CTC application as a reliable clinical liquid biopsy marker to be able to identify the captured CTCs while achieving a high capture efficiency within one analytical system. Herein, in this work, a stimuli-responsive and rhodamine 6G (Rho 6G)-entrapped fluorescent metal-organic framework (MOF) probe, named MOF-Rho 6G-DNA, was designed to capture, detect, and subsequently identify CTCs from blood samples of cancer patients. The probe was fabricated by modifying the epithelial cell adhesion molecule (EpCAM) hairpin DNA aptamer with Rho 6G enclosed and an Arm-DNA-attached UiO-66-NH2 MOF by sequence complementation. CTCs could be captured by the EpCAM hairpin DNA on the probe; as a result, Rho 6G loaded in the probe was released, and the number of CTCs was positively related to the concentration of released Rho 6G. An excellent correlation of fluorescence intensities with CTC numbers was obtained from 2 to 500 cells/mL. More importantly, the MOF-Rho 6G-DNA probe simultaneously realized rapid identification of the captured cells within 30 min by only relying on the residue Rho 6G in the MOF cavity. The captured target cells can be conveniently released from the probe using the complementary DNA sequence. These performance features of the probe were further verified by blood samples from patients of various types of tumor.

Simultaneous single-cell phenotype analysis of hepatocellular carcinoma CTCs using a SERS-aptamer based microfluidic chip

Hepatocellular carcinoma (HCC) is a harmful malady that truly debilitates human health, and hence it is of significance to isolate and on-line profile the phenotype of HCC cells for further diagnosis and therapy. We developed a novel strategy for efficient capture and in situ heterogeneous phenotype analysis of circulating tumor cells (CTCs) at the single-cell level based on surface-enhanced Raman scattering (SERS) fingerprint characteristics. Herein, a new microfluidic chip with lantern-like bypass structure was designed to capture CTCs by their large size from whole blood. Furthermore, two types of SERS-aptamer nanotags were fabricated, realizing spectral recognition of single CTCs in accordance with the surface membrane protein expression. Up to 84% of CTCs with a purity of 95% were captured from whole blood samples using the present SERS-aptamer based microfluidic chip at 20 μL min^-1. The results showed that the proposed strategy can successfully identify HCC cell subtypes by SERS measurements, which was related to the clinical surface biomarkers. This may open a new avenue for serving as a powerful tool of cancer diagnosis and prognosis evaluation.

Immunomagnetic separation in a novel cavity-added serpentine microchannel structure for the selective isolation of lung adenocarcinoma cells

The manipulation and separation of circulating tumor cells (CTCs) in continuous fluidic flows play an essential role in various biomedical applications, particularly the early diagnosis and treatment of diseases. Recent advances in magnetic bead development have provided promising solutions to the challenges encountered in CTC manipulation and isolation. In this study, we proposed a biomicrofluidic platform for specifically isolating human lung carcinoma A549 cells in microfluidic channels. The principle of separation was based on the effect of the magnetic field on aptamer-conjugated magnetic beads, also known as immunomagnetic beads, in a serpentine microchannel with added cavities (SMAC). The magnetic cell separation performance of the proposed structure was modeled and simulated by using COMSOL Multiphysics. The experimental procedures for aptamer molecular conjugation on 1.36 µm-diameter magnetic beads and magnetic bead immobilization on A549 cells were also reported. The lung carcinoma cell-bead complexes were then experimentally separated by an external magnetic field. Separation performance was also confirmed by optical microscopic observations and fluorescence analysis, which showed the high selectivity and efficiency of the proposed system in the isolation and capture of A549 cells in our proposed SMAC. At the flow rate of 5 µL/s, the capture rate of human lung carcinoma cells exceeded 70% in less than 15 min, whereas that of the nontarget cells was approximately 4%. The proposed platform demonstrated its potential for high selectivity, portability, and facile operation, which are suitable considerations for developing point-of-care applications for various biological and clinical purposes.

Rapid Naked-Eye Tracking of On-Cell Phenotype Based on Dual-Aptamer-Weaved Cascade Assembly of Nanostructures

Phenotypic plasticity is an emerging paradigm for providing biological and clinical insights into cancer initiation, progression, and resistance to therapy. However, it is a great challenge to track phenotypic information on live cells with high levels of sensitivity, specificity, and simplicity, when a specific cancer-cell subset is being targeted. In this work, we have successfully achieved cascade assembly of nanoparticles on the surface of specific cancer cells by designing a dual-aptamer-weaved molecular AND logic system. Taking advantage of spatial addressability, precise controllability, and targeting recognition of the nanostructure assemblies, we can precisely label the target-cell subset in a large population of similar cells and rapidly obtain phenotypic information in response to the surface changes of captured cancer cells. Without sophisticated instruments, we can know the phenotypic information on HepG2 cells in whole blood with a high level of sensitivity and rapid naked-eye tracking of on-cell phenotype changes of HepG2 cells undergoing epithelial-mesenchymal transition.

Circulating tumor cell profiling for precision oncology

Analysis of circulating tumor cells (CTCs) collected from patient's blood offers a broad range of opportunities in the field of precision oncology. With new advances in profiling technology, it is now possible to demonstrate an association between the molecular profiles of CTCs and tumor response to therapy. In this Review, we discuss mechanisms of tumor resistance to therapy and their link to phenotypic and genotypic properties of CTCs. We summarize key technologies used to isolate and analyze CTCs and discuss recent clinical studies that examined CTCs for genomic and proteomic predictors of responsiveness to therapy. We also point out current limitations that still hamper the implementation of CTCs into clinical practice. We finally reflect on how these shortcomings can be addressed with the likely contribution of multiparametric approaches and advanced data analytics.

pH-Sensitive Dye-Based Nanobioplatform for Colorimetric Detection of Heterogeneous Circulating Tumor Cells

The efficient capture and sensitive detection of circulating tumor cells (CTCs) play a vital role in cancer diagnosis and prognosis. However, CTCs in the peripheral blood are very rare and heterogeneous, which make them difficult to isolate and detect. Herein, a novel colorimetric nanobioplatform was successfully developed for the highly efficient capture and highly sensitive detection of heterogeneous CTCs, which consisted of two parts: the multivalent aptamer-modified gold nanoparticles as the capture unit and two kinds of aptamer-functionalized pH-sensitive allochroic dyes (thymolphthalein and curcumin) @ molybdenum disulfide nanoflakes (MoS₂ NFs) acting as the visual simultaneous detection of heterogeneous CTCs. Using MCF-7 and HeLa cells as the CTC models, the capture unit can effectively isolate the CTCs due to the multivalent probe with improved affinity. The two allochroic dyes can display obvious color changes under alkaline conditions (pH 12.5) in the presence of MCF-7 and HeLa cells, which provided a rapid and sensitive strategy for visualizing simultaneous detection of heterogeneous CTCs as low as 5 cells mL^-1. This nanoplatform possessed a high sensitivity toward CTC detection owing to high dye loading capacity of MoS₂ NFs and allochroic dyes with excellent pH sensitivity. It can successfully distinguish and quantitatively detect the targeted heterogeneous CTCs from numerous interfering cells in diluted whole blood. It can also be used to detect CTCs from lysed blood samples from cancer patients, indicating promising application for cancer diagnosis.

The Potential of Aptamer-Mediated Liquid Biopsy for Early Detection of Cancer

The early detection of cancer favors a greater chance of curative treatment and long-term survival. Exciting new technologies have been developed that can help to catch the disease early. Liquid biopsy is a promising non-invasive tool to detect cancer, even at an early stage, as well as to continuously monitor disease progression and treatment efficacy. Various methods have been implemented to isolate and purify bio-analytes in liquid biopsy specimens. Aptamers are short oligonucleotides consisting of either DNA or RNA that are capable of binding to target molecules with high specificity. Due to their unique properties, they are considered promising recognition ligands for the early detection of cancer by liquid biopsy. A variety of circulating targets have been isolated with high affinity and specificity by facile modification and affinity regulation of the aptamers. In this review, we discuss recent progress in aptamer-mediated liquid biopsy for cancer detection, its associated challenges, and its future potential for clinical applications.

Fine synthesis of Prussian-blue analogue coated gold nanoparticles (Au@PBA NPs) for sorting specific cancer cell subtypes

Multiplex surface-enhanced Raman scattering (SERS) detection of markers without background in tumor biosystems has its superiority over other optical methods. Herein, we reported a strategy of quantitative discrimination of two breast cancer cell subtypes. Based on our previous studies, two kinds of Prussian blue analogue coated gold nanoparticles (Au@PBA NPs) were designed and synthesized by the replacement of Fe²⁺ with Pb²⁺ or Cu²⁺. Therefore, two distinct SERS emissions of C≡N bonds at 2122 cm^-1 and 2176 cm^-1 have been acquired. When modified with aptamers of epithelial cell adhesion molecule (EpCAM) and epidermal growth factor receptor (EGFR), which are both expressed in MCF-7 and MDA-MB-231 cell lines but in different levels, the SERS nanoprobes simultaneously identified the relative expression of these biomarkers on the cell surface, providing a good example for ratiometric detection in biosystems without any interference. Each surface marker of tumor cells corresponds to a single SERS emission. Thus, each subtype could be described in a molecular profiling way through duplex C≡N bonds-based SERS emission, which is more advanced than traditional flow cytometry method.

Recent Advances in Aptamer-Based Biosensors for Global Health Applications

Since aptamers were first reported in the early 2000s, research on their use for the detection of health-relevant analytical targets has exploded. This review article provides a brief overview of the most recent developments in the field of aptamer-based biosensors for global health applications. The review provides a description of general aptasensing principles and follows up with examples of recent reports of diagnostics-related applications. These applications include detection of proteins and small molecules, circulating cancer cells, whole-cell pathogens, extracellular vesicles, and tissue diagnostics. The review also discusses the main challenges that this growing technology faces in the quest of bringing these new devices from the laboratory to the market.

Microtechnology-enabled filtration-based liquid biopsy: challenges and practical considerations

Liquid biopsy, an important enabling technology for early diagnosis and dynamic monitoring of cancer, has drawn extensive attention in the past decade. With the rapid developments of microtechnology, it has been possible to manipulate cells at the single-cell level, which dramatically improves the liquid biopsy capability. As the microtechnology-enabled liquid biopsy matures from proof-of-concept demonstrations towards practical applications, a main challenge it is facing now is to process clinical samples which are usually of a large volume while containing very rare targeted cells in complex backgrounds. Therefore, a high-throughput liquid biopsy which is capable of processing liquid samples with a large volume in a reasonable time along with a high recovery rate of rare targeted cells from complex clinical liquids is in high demand. Moreover, the purity, viability and release feasibility of recovered targeted cells are the other three key impact factors requiring careful considerations. To date, among the developed techniques, micropore-type filtration has been acknowledged as the most promising solution to address the aforementioned challenges in practical applications. However, the presently reported studies about micropore-type filtration are mostly based on trial and error for device designs aiming at different cancer types, which requires lots of efforts. Therefore, there is an urgent need to investigate and elaborate the fundamental theories of micropore-type filtration and key features that influence the working performances in the liquid biopsy of real clinical samples to promote the application efficacy in practical applications. In this review, the state of the art of microtechnology-enabled filtration is systematically and comprehensively summarized. Four key features of the filtration, including throughput, purity, viability and release feasibility of the captured targeted cells, are elaborated to provide the guidelines for filter designs. The recent progress in the filtration mode modulation and sample standardization to improve the filtration performance of real clinical samples is also discussed. Finally, this review concludes with prospective views for future developments of filtration-based liquid biopsy to promote its application efficacy in clinical practice.

Aptamer-based nanostructured interfaces for the detection and release of circulating tumor cells

Analysis of circulating tumor cells (CTCs) can provide significant clinical information for tumors, which has proven to be helpful for cancer diagnosis, prognosis monitoring, treatment efficacy, and personalized therapy. However, CTCs are an extremely rare cell population, which challenges the isolation of CTCs from patient blood. Over the last few decades, many strategies for CTC detection have been developed based on the physical and biological properties of CTCs. Among them, nanostructured interfaces have been widely applied as CTC detection platforms to overcome the current limitations associated with CTC capture. Furthermore, aptamers have attracted significant attention in the detection of CTCs due to their advantages, including good affinity, low cost, easy modification, excellent stability, and low immunogenicity. In addition, effective and nondestructive release of CTCs can be achieved by aptamer-mediated methods that are used under mild conditions. Herein, we review some progress in the detection and release of CTCs through aptamer-functionalized nanostructured interfaces.

Aptamer-Based Detection of Circulating Targets for Precision Medicine

The past decade has witnessed ongoing progress in precision medicine to improve human health. As an emerging diagnostic technique, liquid biopsy can provide real-time, comprehensive, dynamic physiological and pathological information in a noninvasive manner, opening a new window for precision medicine. Liquid biopsy depends on the sensitive and reliable detection of circulating targets (e.g., cells, extracellular vesicles, proteins, microRNAs) from body fluids, the performance of which is largely governed by recognition ligands. Aptamers are single-stranded functional oligonucleotides, capable of folding into unique tertiary structures to bind to their targets with superior specificity and affinity. Their mature evolution procedure, facile modification, and affinity regulation, as well as versatile structural design and engineering, make aptamers ideal recognition ligands for liquid biopsy. In this review, we present a broad overview of aptamer-based liquid biopsy techniques for precision medicine. We begin with recent advances in aptamer selection, followed by a summary of state-of-the-art strategies for multivalent aptamer assembly and aptamer interface modification. We will further describe aptamer-based micro-/nanoisolation platforms, aptamer-enabled release methods, and aptamer-assisted signal amplification and detection strategies. Finally, we present our perspectives regarding the opportunities and challenges of aptamer-based liquid biopsy for precision medicine.

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

Breast cancer is the most frequently diagnosed cancer among women, and the circulating tumor cell (CTC)-meditated distant metastasis is the leading cause of death. Thus, the detection of CTCs is of great importance for the early diagnosis of breast cancer and the prevention of metastasis. In this study, using human breast carcinoma BT474 cells as the model CTCs, a powerful assay platform is demonstrated by fluorescence spectrometry for the highly sensitive CTC detection by combining the dual-recognizing elements receptor-binding antibody and aptamer-mediated separation with double rolling circle amplification reactions (d-RCA, including RCA1 and RCA2). The aptamer-inserted RCA1 product (RCA1-p) exhibits the considerably improved affinity towards target cells originating from the multivalent binding effect. The immunomagnetic separation removes nontarget cells coexisting in complex biological milieu, while the centrifugal separation of cells/DNAs mixture eliminates the excess probes, thereby circumventing the unwanted interferences. The fluorescence spectrometric results show that a 34-fold enhanced fluorescence signal is achieved upon BT474 cells, and the target cells can be quantitatively detected down to 9 cells/200 μL with the linear range of five orders of magnitude, indicating a significantly enhanced detection performance. Even if BT474 cells are spiked in the fresh whole blood, no obvious fluctuation in the fluorescence signal is detected, demonstrating that the newly developed d-RCA assay system is suitable for screening CTCs in complex environments and is expected to be a promising tool for estimating distant metastasis and predicting the recurrence of tumors.

Ex vivo identification of circulating tumor cells in peripheral blood by fluorometric "turn on" aptamer nanoparticles

The detection of the circulating tumor cells (CTCs) detached from solid tumors has emerged as a burgeoning topic for cancer diagnosis and treatment. The conventional CTC enrichment and identification mainly rely on the specific binding of the antibodies on the capture interface of the magnetic nanoparticles with the corresponding biomarkers on the cell membranes. However, these methods could easily generate false-negative results due to the extremely low concentration of CTCs and the internal heterogeneity of the tumor cells. Herein, with the aim of selectively identifying CTCs and improving the detection accuracy in peripheral blood, we designed the fluorometric "turn on" Au nanoparticles (DHANs) with the modification of a tumor-targeted moiety, dehydroascorbic acid (DHA) and a fluorometric aptamer, which could be "switched-on" by an over-expressed intracellular protein, namely hypoxia-inducible factor-1α (HIF 1α). This novel nanoformulated detection platform demonstrated the great capacity for visualizing various CTCs in peripheral blood with significantly improved detection efficiency and sensitivity. As a result, the nanoplatform has a great potential to be further applied for CTC detection in vitro or in vivo, which holds promise for extensive CTC studies.

Recent advances in microfluidic technologies for circulating tumor cells: enrichment, single-cell analysis, and liquid biopsy for clinical applications

Circulating tumor cells (CTCs) detach from primary or metastatic lesions and circulate in the peripheral blood, which is considered to be the cause of distant metastases. CTC analysis in the form of liquid biopsy, enumeration and molecular analysis provide significant clinical information for cancer diagnosis, prognosis and therapeutic strategies. Despite the great clinical value, CTC analysis has not yet entered routine clinical practice due to lack of efficient technologies to perform CTC isolation and single-cell analysis. Taking the rarity and inherent heterogeneity of CTCs into account, reliable methods for CTC isolation and detection are in urgent demand for obtaining valuable information on cancer metastasis and progression from CTCs. Microfluidic technology, featuring microfabricated structures, can precisely control fluids and cells at the micrometer scale, thus making itself a particularly suitable method for rare CTC manipulation. Besides the enrichment function, microfluidic chips can also realize the analysis function by integrating multiple detection technologies. In this review, we have summarized the recent progress in CTC isolation and detection using microfluidic technologies, with special attention to emerging direct enrichment and enumeration in vivo. Further, few insights into single CTC molecular analysis are also demonstrated. We have provided a review of potential clinical applications of CTCs, ranging from early screening and diagnosis, tumor progression and prognosis, treatment and resistance monitoring, to therapeutic evaluation. Through this review, we conclude that the clinical utility of CTCs will be expanded as the isolation and analysis techniques are constantly improving.

A liquid biopsy for detecting circulating mesothelial precursor cells: A new biomarker for diagnosis and prognosis in mesothelioma

BACKGROUND

Malignant pleural mesothelioma (MPM) is an aggressive cancer related to asbestos exposure. Early diagnosis is challenging due to generic symptoms and a lack of biomarkers. We previously demonstrated that mesothelial precursor cells (MPC) characterized by mesothelin (MSLN)+CD90+CD34+ could be implicated in the development of mesothelioma after asbestos exposure. Here, we aimed to determine the clinical significance of detecting MPC in blood for early-stage diagnosis and prognosis of mesothelioma.

METHODS

Due to the rarity of MPC in blood, it is challenging to identify this cell population using conventional techniques. Hence, we have developed a microfluidic liquid biopsy platform called MesoFind that utilizes an immunomagnetic, mesothelin capture strategy coupled with immunofluorescence to identify rare populations of cells at high sensitivity and precision. To validate our technique, we compared this approach to flow cytometry for the detection of MPC in murine blood and lavage samples. Upon successful validation of the murine samples, we then proceeded to examine circulating MPC in 23 patients with MPM, 23 asbestos-exposed individuals (ASB), and 10 healthy donors (HD) to evaluate their prognostic and diagnostic value.

FINDING

MPC were successfully detected in the blood of murine samples using MesoFind but were undetectable with flow cytometry. Circulating MPC were significantly higher in patients with epithelioid MPM compared to HD and ASB. The MPC subpopulation, MSLN+ and CD90+, were upregulated in ASB compared to HD suggesting an early role in pleural damage from asbestos. The MPC subpopulation, MSLN+ and CD34+, in contrast, were detected in advanced MPM and associated with markers of poor prognosis, suggesting a predominant role during cancer progression.

INTERPRETATION

The identification of circulating MPC presents an attractive solution for screening and early diagnosis of epithelioid mesothelioma. The presence of different subtypes of MPC have a prognostic value that could be of assistance with clinical decisions in patients with MPM.

FUNDING

Princess Margaret Hospital Foundation Mesothelioma Research Fund, Toronto General & Western Hospital Foundation.

Bioinspired DNA Nanointerface with Anisotropic Aptamers for Accurate Capture of Circulating Tumor Cells

The capture and analysis of circulating tumor cells (CTCs) have provided a non-invasive entry for cancer diagnosis and disease monitoring. Despite recent development in affinity-based CTCs isolation, it remains challenging to achieve efficient capture toward CTCs with dynamic surface expression. Enlightened by the synergistic effect insideimmune synapses, the development of a nanointerface engineered with topology-defined anisotropic aptamers programmed by DNA scaffold (DNA nanosynapse), for accurate CTCs isolation, is herein reported. As compared to isotropic aptamers, the DNA nanosynapse exhibits enhanced anchoring on the cell membrane with both high and low epithelial cell adhesion molecule (EpCAM) expression. This nanointerface enables accurate capture toward CTCs of heterogeneous EpCAM, without dramatically proportional change inside the mixture of diverse phenotypes. By applying this nanoplatform, CTCs detection as well as downstream analysis for measuring disease status can be achieved in clinical samples from breast cancer patients.

Magnetic Ranking Cytometry: Profiling Rare Cells at the Single-Cell Level

Cellular heterogeneity in biological systems presents major challenges in the diagnosis and treatment of disease and also complicates the deconvolution of complex cellular phenomena. Single-cell analysis methods provide information that is not masked by the intrinsic heterogeneity of the bulk population and can therefore be applied to gain insights into heterogeneity among different cell subpopulations with fine resolution. Over the last 5 years, an explosion in the number of single-cell measurement methods has occurred. However, most of these methods are applicable to pure populations of cultured cells and are not able to handle high levels of phenotypic heterogeneity or a large background of nontarget cells. Microfluidics is an attractive tool for single cell manipulation as it enables individual encasing of single cells, allowing for high-throughput analysis with precise control of the local environment. Our laboratory has developed a new microfluidics-based analytical strategy to meet this unmet need referred to as magnetic ranking cytometry (MagRC). Cells expressing a biomarker of interest are labeled with receptor-coated magnetic nanoparticles and isolated from nontarget cells using a microfluidic device. The device ranks the cells according to the level of bound magnetic nanoparticles, which corresponds to the expression level of a target biomarker. Over the last several years, two generations of MagRC devices have been developed for different applications. The first-generation MagRC devices are powerful tools for the quantitation and analysis of rare cells present in heterogeneous samples, such as circulating tumor cells, stem cells, and pathogenic bacteria. The second-generation MagRC devices are compatible with the efficient recovery of cells sorted on the basis of protein expression and can be used to analyze large populations of cells and perform phenotypic CRISPR screens. To improve analytical precision, newer iterations of the first-generation and second-generation MagRC devices have been integrated with electrochemical sensors and Hall effect sensors, respectively. Both generations of MagRC devices permit the isolation of viable cells, which sets the stage for a wide range of applications, such as generating cell lines from rare cells and in vitro screening for effective therapeutic interventions in cancer patients to realize the promise of personalized medicine. This Account summarizes the development and application of the MagRC and describes a suite of advances that have enabled single-cell tumor cell analysis and monitoring tumor response to therapy, stem cell analysis, and detection of pathogens.

Highly Sensitive Minimal Residual Disease Detection by Biomimetic Multivalent Aptamer Nanoclimber Functionalized Microfluidic Chip

Minimal residual disease (MRD) offers a highly independent prognostic factor for leukemia patients. However, challenges confronting conventional MRD assays are high invasiveness, as well as limited detection sensitivity and clinical applicability. Inspired by the self-adaptive skeleton and multiple suckers or tendrils of climbing plants, a biomimetic Multivalent Aptamer Nanoclimber (MANC)-functionalized microfluidic chip (MANC-Chip) is reported for minimally invasive, highly sensitive and clinically applicable MRD detection in the peripheral blood of T-cell acute lymphoblastic leukemia patients. The MANCs are synthesized by a simple co-polymerization reaction. Due to their flexible structure and cooperative multivalent effect, MANCs dramatically enhance the binding affinity of aptamers targeting leukemia cells. A deterministic lateral displacement-patterned microfluidic chip is designed to further increase the collision probability between MANCs and leukemia cells. Benefiting from the synergistic effect of multivalent binding and enhanced collision, a high capture efficiency of 92.2% for leukemia cells is achieved. Moreover, the captured leukemia cells can be released with high efficiency of 88.9% and high viability of 93.8% via nuclease treatment prior to downstream analysis. Overall, the excellent features of MANC-Chip make it very useful for precise detection of MRD and better understanding of leukemia.

Flexible Three-Dimensional Net for Intravascular Fishing of Circulating Tumor Cells

Current strategies for in vitro isolation of circulating tumor cells (CTCs) fail to detect extremely rare CTCs heterogeneously distributed in blood. It is possible to devise methods for in vivo capture of CTCs based on processing almost all of the blood in the human body to improve detection sensitivity, but the complicated manipulation, biosafety concerns, and limited capture efficiency of conventional detection strategies prohibit their implementation in the clinic. Herein, we present a flexible three-dimensional (3-D) CTC-Net probe for intravascular collection of CTCs. The CTC-Net, consisting of a 3-D elastic scaffold with an interconnected, spatially distributed network accommodates a large quantity of immobilized antibodies and provides an enhanced substrate-cell contact frequency, which results in an enhanced capture efficiency and effective detection of heterogeneous CTCs. The as-prepared CTC-Net can be readily compressed and injected into blood vessels and fully unfolded to form a 3-D "fishing-net" structure for capture of the CTCs, and then retracted for imaging and downstream gene analysis of the captured CTCs. Significant advantages for the CTC-Net over currently available in vitro and in vivo procedures are demonstrated for detection of extremely rare CTCs from wild-type rats and successful capture of CTCs and CTC clusters before metastasis in the case of tumor-bearing rats. Our research demonstrates for the first time the use of a 3-D scaffold CTC-Net probe for in vivo capture of CTCs. The method shows exceptional performance for cell capture, which is readily implemented and holds great potential in the clinic for early diagnosis of cancer.

Selection of Aptamers Against Vimentin for Isolation and Release of Circulating Tumor Cells Undergoing Epithelial Mesenchymal Transition

Circulating tumor cells (CTCs) undergoing epithelial mesenchymal transition (EMT) play an essential role in metastasis and have a better correlation with poor disease outcomes, but the most current affinity-based enrichment methods rely on targeting epithelial markers, which are less effective in capturing CTCs undergoing EMT. Herein, we identified and optimized an aptamer (ZY5C) sequence with high binding affinity and specificity against cell surface vimentin (CSV), which is overexpressed on the post-EMT CTCs. Not only can the hairpin-structured ZY5C aptamer specifically recognize a number of cancer cells with native CSV expression, but it can also bind to CSV expressed on EMT-cells. The K_d value of the ZY5C aptamer against CSV-positive T24 cells was found to be 38 ± 4 nM. Using the evolved ZY5C aptamer and multivalent ZY5C aptamer-functionalized chip, we were able to isolate CTCs from the blood of adenocarcinoma, sarcoma, and carcinosarcoma patients. Overall, this ZY5C aptamer and isolation method bring a fresh approach to CTCs analysis, which not only detects CTCs from nonepithelial origin, but also provides an efficient way to in-depth study the role of post-EMT CTCs in clinical application and metastasis mechanisms.

Nanostructured Substrates for Detection and Characterization of Circulating Rare Cells: From Materials Research to Clinical Applications

Circulating rare cells in the blood are of great significance for both materials research and clinical applications. For example, circulating tumor cells (CTCs) have been demonstrated as useful biomarkers for "liquid biopsy" of the tumor. Circulating fetal nucleated cells (CFNCs) have shown potential in noninvasive prenatal diagnostics. However, it is technically challenging to detect and isolate circulating rare cells due to their extremely low abundance compared to hematologic cells. Nanostructured substrates offer a unique solution to address these challenges by providing local topographic interactions to strengthen cell adhesion and large surface areas for grafting capture agents, resulting in improved cell capture efficiency, purity, sensitivity, and reproducibility. In addition, rare-cell retrieval strategies, including stimulus-responsiveness and additive reagent-triggered release on different nanostructured substrates, allow for on-demand retrieval of the captured CTCs/CFNCs with high cell viability and molecular integrity. Several nanostructured substrate-enabled CTC/CFNC assays are observed maturing from enumeration and subclassification to molecular analyses. These can one day become powerful tools in disease diagnosis, prognostic prediction, and dynamic monitoring of therapeutic response-paving the way for personalized medical care.

Circulating Tumor Cell Enrichment Technologies

Circulating tumor cells (CTCs) are responsible for the metastatic spread of cancer and therefore are extremely valuable not only for basic research on cancer metastasis but also as potential biomarkers in diagnosing and managing cancer in the clinic. While relatively non-invasive access to the blood tissue presents an opportunity, CTCs are mixed with approximately billion-times more-populated blood cells in circulation. Therefore, the accuracy of technologies for reliable enrichment of the rare CTC population from blood samples is critical to the success of downstream analyses. The focus of this chapter is to provide the reader an overview of significant advances made in the development of diverse CTC enrichment technologies by presenting the strengths of individual techniques in addition to specific challenges remaining to be addressed.

Detection of pathogenic bacteria via nanomaterials-modified aptasensors

Detection and identification of special cells via aptamer-based nano-conjugates sensors have been revolutionized over the past few years. These sensing platforms rely on selecting aptamers using systematic evolution of ligands by exponential enrichment (SELEX) in vitro, which allows for sensitive detection of cells. Integration of the aptamer-based sensors (aptasensors) with nanomaterials offers enhanced specificity and sensitivity, which in turn, offers great promise for numerous applications, spanning from bioanalysis to biomedical applications. Accordingly, the demand for using aptamer-conjugated nanomaterials for various applications has progressively increased over the past years. In light of this, this Review seeks to highlight the recent advances in the development of aptamer-conjugated nanomaterials and their utilization for the detection of various pathogens involved in infectious diseases and food contamination.

Proteasome-Independent Protein Knockdown by Small-Molecule Inhibitor for the Undruggable Lung Adenocarcinoma

Therapeutic target identification and corresponding drug development is a demanding task for the treatment of lung adenocarcinoma, especially the most malignant proximal-proliferative subtype without druggable protein kinase mutations. Using a cell-SELEX-generated aptamer, we discovered a new tumor driver protein, leucine-rich pentatricopeptide repeat-containing protein (LRPPRC), which is specifically overexpressed in the most lethal subtype of lung adenocarcinoma. Targeted LRPPRC protein knockdown is a promising therapeutic strategy for the undruggable LUAD (lung adenocarcinoma). Nevertheless, LRPPRC is mainly located in mitochondria and degraded by protease. Current protein knockdown approaches, such as proteolysis-targeting chimeras (PROTACs), have limitations in their applications to the proteins degraded through proteasome-independent ways. Here, we designed an aptamer-assisted high-throughput method to screen small molecules that could bind to LRPPRC directly, disrupt the interaction of LRPPRC with its stabilizing chaperon protein, and lead to LRPPRC degradation by mitochondrial protease. The screened compound, gossypolacetic acid (GAA), is an old medicine that can accomplish the new function for targeted LRPPRC knockdown. It showed significant antitumor effects even with the LRPPRC-positive patient-derived tumor xenograft (PDX) model. This work not only extended the application of aptamers to screen small-molecule inhibitors for the undruggable lung cancers, but more importantly provided a new strategy to develop protein knockdown methods beyond the proteasome system.