Capturing cancer cells using aptamer-immobilized square capillary channels

Designer tetrahedral DNA framework-based microfluidic technology for multivalent capture and release of circulating tumor cells

Circulating tumor cells (CTCs) have been recognized as a general biomarker for the early detection, diagnosis and therapy monitoring of cancer. Due to their extreme rarity in peripheral blood, the isolation and analysis of CTCs with high efficiency, high purity and high viability remains a tremendous technological challenge. Herein, we combined tetrahedral DNA framework (TDFs), herringbone channel (HB) chip, together with aptamer-triggered hybridization chain reaction (apt-HCR) to develop an efficient microfluidic system (T-μFS) for capture and release of simulated CTCs. The capture efficiency of MCF-7 ​cells was from 83.3% to 94.2% when the cell numbers ranged from 10 to 10³ using our T-μFS in the whole blood. The release efficiency of the MCF-7 ​cells was 96.2% and the MCF-7 ​cell viability after release was 94.6% using our T-μFS in PBS buffer. Reculture and RT-qPCR studies showed that there was almost no damage by the capture and release treatment for the MCF-7 ​cells viability. These results revealed that our T-μFS could be developed as an integrated and automatic technical platform with great performance for multivalent capture and release of CTCs and have a wide application prospect for tumor liquid biopsy.

•

Three-dimensional amine modified tetrahedral DNA frameworks (TDFs) as rigid scaffolds were anchored on the aldehyde modified substrate of HB-chip, which provided the better spatial orientation compared with single-stranded DNA.

•

Aptamer partially hybridized to an initiator was employed to trigger HCR reaction, and HCR produced modified long products with multi-branched arms for multivalent binding on TDFs to improve the capture efficiency of CTCs.

•

This is the first time that only employed DNA nanostructures in a microfluidic device system to capture CTCs, and all DNA nanostructures could be efficiently removed by enzymes without harming cells.

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.

Affinity chromatography: A review of trends and developments over the past 50 years

The field of affinity chromatography, which employs a biologically-related agent as the stationary phase, has seen significant growth since the modern era of this method began in 1968. This review examines the major developments and trends that have occurred in this technique over the past five decades. The basic principles and history of this area are first discussed. This is followed by an overview of the various supports, immobilization strategies, and types of binding agents that have been used in this field. The general types of applications and fields of use that have appeared for affinity chromatography are also considered. A survey of the literature is used to identify major trends in these topics and important areas of use for affinity chromatography in the separation, analysis, or characterization of chemicals and biochemicals.

Aptamer-Based Affinity Chromatography for Protein Extraction and Purification

Aptamers are oligonucleotide molecules able to recognize very specifically proteins. Among the possible applications, aptamers have been used for affinity chromatography with effective results and advantages over most advanced protein separation technologies. This chapter first discusses the context of the affinity chromatography with aptamer ligands. With the adaptation of SELEX, the chemical modifications of aptamers to comply with the covalent coupling and the separation process are then extensively presented. A focus is then made about the most important applications for protein separation with real-life examples and the comparison with immunoaffinity chromatography. In spite of well-advanced demonstrations and the extraordinary potential developments, a significant optimization work is still due to deserve large-scale applications with all necessary validations. Graphical Abstract Aptamer-protein complexes by X-ray crystallography.

TOD-CUP: a gene expression rank-based majority vote algorithm for tissue origin diagnosis of cancers of unknown primary

Gene expression profiling holds great potential as a new approach to histological diagnosis and precision medicine of cancers of unknown primary (CUP). Batch effects and different data types greatly decrease the predictive performance of biomarker-based algorithms, and few methods have been widely applied to identify tissue origin of CUP up to now. To address this problem and assist in more precise diagnosis, we have developed a gene expression rank-based majority vote algorithm for tissue origin diagnosis of CUP (TOD-CUP) of most common cancer types. Based on massive tissue-specific RNA-seq data sets (10 553) found in The Cancer Genome Atlas (TCGA), 538 feature genes (biomarkers) were selected based on their gene expression ranks and used to predict tissue types. The top scoring pairs (TSPs) classifier of the tumor type was optimized by the TCGA training samples. To test the prediction accuracy of our TOD-CUP algorithm, we analyzed (1) two microarray data sets (1029 Agilent and 2277 Affymetrix/Illumina chips) and found 91% and 94% prediction accuracy, respectively, (2) RNA-seq data from five cancer types derived from 141 public metastatic cancer tumor samples and achieved 94% accuracy and (3) a total of 25 clinical cancer samples (including 14 metastatic cancer samples) were able to classify 24/25 samples correctly (96.0% accuracy). Taken together, the TOD-CUP algorithm provides a powerful and robust means to accurately identify the tissue origin of 24 cancer types across different data platforms. To make the TOD-CUP algorithm easily accessible for clinical application, we established a Web-based server for tumor tissue origin diagnosis (http://ibi. zju.edu.cn/todcup/).

Nucleic acid aptamers in diagnosis of colorectal cancer

Nucleic acid aptamers are promising recognition ligands for diagnostic applications. They are short DNA or RNA molecules isolated from large random libraries through the Systematic Evolution of Ligands by EXponential enrichment (SELEX) procedure. These molecules, with a particular three-dimensional shape, bind to a wide range of targets from small molecules to whole cells with high affinity and specificity. The unique properties of nucleic acid aptamers including high binding affinity and specificity, thermostability, ease of chemical production, ease of chemical modification, target adaptability, simple storage, resistance to denaturation, low immunogenicity, and low cost make them potential diagnostic tools for clinical use. Colorectal cancer is one of the most common types of cancer in humans and the third leading cause of cancer deaths in the world. Due to low response rate to current therapies in advanced stages of the disease, early detection of CRC can be useful in disease management. This review highlights recent advances in the development of nucleic acid aptamer-based methods for diagnosis, prognosis, and theranosis of colorectal cancer.

Bio-hybrid inorganic microparticles derived from CO2 for highly efficient and selective removal of antibiotics

BACKGROUND

Antibiotics, which are the most important medication in human history, have brought global concerns due to their potential risk to human health and environment by accelerating the development of drug-resistant bacteria, and accumulating in the food chain system. Among antibiotics, oxytetracycline (OTC) is widely used in aquaculture, and its potential risk of toxicity to human by bioaccumulation has been reported. Therefore, the effective removal of OTC is highly needed.

RESULTS

In this study, we report bio-hybrid inorganic microparticles (apt-mag-SiCC) for efficient capturing and facile magnet-based separation of oxytetracycline (OTC). These bio-hybrid inorganic microparticles are composed of magnetic separable silica coated calcium carbonate microparticles (mag-SiCC) derived from CO2, conjugated with oxytetracycline binding aptamers (OBA). These bio-hybrid inorganic microparticles were successfully synthesized, based on the characterization data obtained by SEM, FT-IR, EDAX, BET, and CLSM. About 6 μm sized bio-hybrid inorganic microparticles showed low non-specific adsorption to OTC and other molecules, and the selective capturing towards to the OTC in both buffer and tap water. Moreover, these bio-hybrid mineral microparticles were found to be stable, even after the repeated usages, maintaining the initial capturing efficiency.

CONCLUSION

Using the newly synthesized bio-hybrid inorganic microparticles, we could successfully capture OTC by facile magnet-based separation. With advantages of theses bio-hybrid inorganic microparticles such as easy fabrication, low-price, and environmental friendliness, this novel material could be utilized in the drinking water treatment, in vitro medicinal diagnostics, or in vitro removal of antibiotics lining out from the blood (blood purification).

The potential of aptamers for cancer research

Aptamers are promising alternatives to antibodies and can be used as high affinity agents for the cancer detection and the targeted drug transportation. In this manuscript, we highlight the advantages of aptamers, such as high affinities, specificity and excellent chemical stabilities, which are likely to benefit for the diagnosis of cancer in its early stages and then achieve molecular-level treatment. Also, we discuss the challenges and problems in the current application of aptamers.

Biomarkers in cancer therapy related cardiac dysfunction (CTRCD)

Biomarkers are at the cornerstone of preventive measures and contribute to the screening process. More recently, biomarkers have been used to gauge the biological response to the employed therapies. Since it is ubiquitously used to detect subclinical disease process, biomarkers also have found its place in cancer therapy related cardiac dysfunction (CTRCD). The aim of this review is to comprehensively present up-to-date knowledge of biomarkers in CTRCD and highlight some of the future biomedical technologies that may strengthen the screening process, and/or provide new insight in pathological mechanisms behind CTRCD.

Microfluidic Device for Aptamer-Based Cancer Cell Capture and Genetic Mutation Detection

We present a microfluidic device for specifically capturing cancer cells and isolating their genomic DNA (gDNA) for specific amplification and sequence analysis. To capture cancer cells within the device, nucleic acid aptamers that specifically bind to cancer cells were immobilized within a channel containing micropillars designed to increase capture efficiency. The captured cells were lysed in situ, and their gDNA was isolated by physical entanglement within a second smaller-dimensioned micropillar array. This type of isolation allows the gDNA to be retained and purified within the channel and enables amplification and analysis to be performed on the gDNA without the loss of the original template. We developed a technique for selectively amplifying genes from whole gDNA using multiple displacement amplification. The amplified gene samples were sequenced, and the resulting sequence information was compared against the known wild-type gene to identify any mutations. We have tested cervical and ovarian cancer cells for mutations in the TP53 gene using this technology. This approach offers a way to monitor multiple genetic mutations in the same small population of cells, which is beneficial given the wide diversity in cancer cells, and therefore it requires very few cells to be extracted from a patient sample.

Aptamer-Based Methods for Detection of Circulating Tumor Cells and Their Potential for Personalized Diagnostics

Cancer diagnostics and treatment monitoring rely on sensing and counting of rare cells such as cancer circulating tumor cells (CTCs) in blood. Many analytical techniques have been developed to reliably detect and quantify CTCs using unique physical shape and size of tumor cells and/or distinctive patterns of cell surface biomarkers. Main problems of CTC bioanalysis are in the small number of cells that are present in the circulation and heterogeneity of CTCs. In this chapter, we describe recent progress towards the selection and application of synthetic DNA or RNA aptamers to capture and detect CTCs in blood. Antibody-based approaches for cell isolation and purification are limited because of an antibody's negative effect on cell viability and purity. Aptamers transform cell isolation technology, because they bind and release cells on-demand. The unique feature of anti-CTC aptamers is that the aptamers are selected for cell surface biomarkers in their native state, and conformation without previous knowledge of their biomarkers. Once aptamers are produced, they can be used to identify CTC biomarkers using mass spectrometry. The biomarkers and corresponding aptamers can be exploited to improve cancer diagnostics and therapies .

Aptamer affinity ligands in protein chromatography

The present review deals with the place of single chain oligonucleotide ligands (aptamers) in affinity chromatography applied to proteins. Aptamers are not the only affinity ligands available but they represent an emerging and highly promising route that advantageously competes with antibodies in immunopurification processes. A historical background of affinity chromatography from the beginning of the discipline to the most recent outcomes is first presented. Then the focus is centered on aptamers which represent the last step so far to the long quest for affinity ligands associating very high specificity, availability and strong stability against most harsh cleaning agents required in chromatography. Then technologies of ligand selection from large libraries followed by the most appropriate chemical grafting approaches are described and supported by a number of bibliographic references. Experimental results assembled from relevant published paper are reported; they are selected by their practical applicability and potential use at large scale. The review concludes with specific remarks and future developments that are expected in the near future to turn this technology into a large acceptance for preparative applications.

Aptamer-functionalized nano/micro-materials for clinical diagnosis: isolation, release and bioanalysis of circulating tumor cells

Detection of rare circulating tumor cells (CTCs) in peripheral blood is a challenging, but necessary, task in order to diagnose early onset of metastatic cancer and to monitor treatment efficacy. Over the last decade, step-up produced aptamers have attracted great attention in clinical diagnosis. They have offered great promise for a broader range of cell-specific recognition and isolation. In particular, aptamer-functionalized magnetic particles for selective extraction of target CTCs have shown reduced damage to cells and relatively simple operation. Also, efforts to develop aptamer-functionalized microchannel/microstructures able to efficiently isolate target CTCs are continuing, and these efforts have brought more advanced geometrically designed substrates. Various aptamer-mediated cell release techniques are being developed to enable subsequent biological studies. This article reviews some of these advances in aptamer-functionalized nano/micro-materials for CTCs isolation and methods for releasing captured CTCs from aptamer-functionalized surfaces. Biological studies of CTCs after release are also discussed.

Oligonucleotide aptamers: A next-generation technology for the capture and detection of circulating tumor cells

A critical challenge for treating cancer is the early identification of those patients who are at greatest risk of developing metastatic disease. The number of circulating tumor cells (CTCs) in cancer patients has recently been shown to be a valuable (and non-invasively accessible) diagnostic indicator of the state of metastatic disease. CTCs are rare cancer cells found in the blood circulation of cancer patients believed to provide a means of diagnosing the likelihood for metastatic spread and assessing response to therapy in advanced, as well as early stage disease settings. Numerous technical efforts have been made to reliably detect and quantify CTCs, but the development of a universal assay has proven quite difficult. Notable challenges for developing a broadly useful CTC-based diagnostic assay are the development of easy-to-operate methods that (1) are sufficiently sensitive to reliably detect the small number of CTCs that are present in the circulation and (2) can capture the molecular heterogeneity of tumor cells. In this review, we describe recent progress towards the application of synthetic oligonucleotide aptamers as promising, novel, robust tools for the isolation and detection of CTCs. Advantages and challenges of the aptamer approach are also discussed.

Aptamers: a promising tool for cancer imaging, diagnosis, and therapy

Aptamers are a group of molecules, which can specifically bind, track, and inhibit target molecules, comprising DNA aptamers, RNA aptamers, and peptide aptamers. So far, there are much progress about developing novel aptamers and their expansile applications. This prospect systematically introduces the composition and technological evolution of aptamers, and then focuses on the application of aptamers in cancer diagnosis, imaging, and therapy. Following this, we discuss the potential to harness aptamers in discovering the biomarker of stem cells, which is favorable for us to study the normal developmental or abnormal pathological process of tissue and to deliver drugs into target cells or tissues in the future.

Programmable hydrogels for controlled cell catch and release using hybridized aptamers and complementary sequences

The ability to regulate cell-material interactions is important in various applications such as regenerative medicine and cell separation. This study successfully demonstrates that the binding states of cells on a hydrogel surface can be programmed by using hybridized aptamers and triggering complementary sequences (CSs). In the absence of the triggering CSs, the aptamers exhibit a stable, hybridized state in the hydrogel for cell-type-specific catch. In the presence of the triggering CSs, the aptamers are transformed into a new hybridized state that leads to the rapid dissociation of the aptamers from the hydrogel. As a result, the cells are released from the hydrogel. The entire procedure of cell catch and release during the transformation of the aptamers is biocompatible and does not involve any factor destructive to either the cells or the hydrogel. Thus, the programmable hydrogel is regenerable and can be applied to a new round of cell catch and release when needed.

Aptamer-containing surfaces for selective capture of CD4 expressing cells

Aptamers have recently emerged as an excellent alternative to antibodies because of their inherent stability and ease of modification. In this paper, we describe the development of an aptamer-based surface for capture of cells expressing CD4 antigen. The glass or silicon surfaces were modified with amine-terminated silanes and then modified with thiolated RNA aptamer against CD4. Modification of the surface was first characterized by ellipsometry to demonstrate assembly of biointerface components and to show specific capture of recombinant CD4 protein. Subsequently, surfaces were challenged with model lymphocytes (cell lines) that were either positive or negative for CD4 antigen. Our experiments show that aptamer-functionalized surfaces have similar capture efficiency to substrates containing anti-CD4 antibody. To mimick capture of specific T-cells from a complex cell mixture, aptamer-modified surfaces were exposed to binary mixtures containing Molt-3 cells (CD4+) spiked into Daudi B cells (CD4-). 94% purity of CD4 cells was observed on aptamer-containing surfaces from an initial fraction of 15% of CD4. Given the importance of CD4 cell enumeration in HIV/AIDS diagnosis and monitoring, aptamer-based devices may offer an opportunity for novel cell detection strategies and may yield more robust and less expensive blood analysis devices in the future.

Development of an aptamer-based concentration method for the detection of Trypanosoma cruzi in blood

Trypanosoma cruzi, a blood-borne parasite, is the etiological agent of Chagas disease. T. cruzi trypomastigotes, the infectious life cycle stage, can be detected in blood of infected individuals using PCR-based methods. However, soon after a natural infection, or during the chronic phase of Chagas disease, the number of parasites in blood may be very low and thus difficult to detect by PCR. To facilitate PCR-based detection methods, a parasite concentration approach was explored. A whole cell SELEX strategy was utilized to develop serum stable RNA aptamers that bind to live T. cruzi trypomastigotes. These aptamers bound to the parasite with high affinities (8–25 nM range). The highest affinity aptamer, Apt68, also demonstrated high specificity as it did not interact with the insect stage epimastigotes of T. cruzi nor with other related trypanosomatid parasites, L. donovani and T. brucei, suggesting that the target of Apt68 was expressed only on T. cruzi trypomastigotes. Biotinylated Apt68, immobilized on a solid phase, was able to capture live parasites. These captured parasites were visible microscopically, as large motile aggregates, formed when the aptamer coated paramagnetic beads bound to the surface of the trypomastigotes. Additionally, Apt68 was also able to capture and aggregate trypomastigotes from several isolates of the two major genotypes of the parasite. Using a magnet, these parasite-bead aggregates could be purified from parasite-spiked whole blood samples, even at concentrations as low as 5 parasites in 15 ml of whole blood, as detected by a real-time PCR assay. Our results show that aptamers can be used as pathogen specific ligands to capture and facilitate PCR-based detection of T. cruzi in blood.

Label-free detection of prion protein with its DNA aptamer through the formation of T-Hg2+-T configuration

Though rapid tests were developed for mass screening of prion diseases in the last century, bovine spongiform encephalopathy (BSE) was still epidemic in some European countries. The main reason is that the sensitivity of such tests is insufficient for detecting animals that are incubating with prion diseases at the presymptomatic stage. Driven by this, in this contribution, we developed a novel sensitive label-free method taking advantage of DNA aptamer for prion proteins (PrP) detection through the formation of T-Hg(2+)-T configuration. In the presence of Hg(2+) ions, double-strand structures formed due to the strong binding affinity of Hg(2+) ions to the T bases of DNA aptamer, which dramatically enhanced the fluorescence of Syber Green I, a double-strand indicator. With the addition of prion protein, however, the specific interaction between prion protein and its aptamer forced the destruction of the double-strand structures, and thus the fluorescence of Syber Green I decreased. It was found that there is a linear relationship between the decreased fluorescence intensities and prion protein concentration ranging from 13.0 to 156.0 nmol/L. Compared with other methods, the method presented here holds the advantages of being label-free, rapid, highly sensitive, and selective, which shows great promise for clinical application.

Aptamer-enabled efficient isolation of cancer cells from whole blood using a microfluidic device

Circulating tumor cells (CTC) in the peripheral blood could provide important information for diagnosis of cancer metastasis and monitoring treatment progress. However, CTC are extremely rare in the bloodstream, making their detection and characterization technically challenging. We report here the development of an aptamer-mediated, micropillar-based microfluidic device that is able to efficiently isolate tumor cells from unprocessed whole blood. High-affinity aptamers were used as an alternative to antibodies for cancer cell isolation. The microscope-slide-sized device consists of >59,000 micropillars, which enhanced the probability of the interactions between aptamers and target cancer cells. The device geometry and the flow rate were investigated and optimized by studying their effects on the isolation of target leukemia cells from a cell mixture. The device yielded a capture efficiency of ~95% with purity of ~81% at the optimum flow rate of 600 nL/s. Further, we exploited the device for isolating colorectal tumor cells from unprocessed whole blood; as few as 10 tumor cells were captured from 1 mL of whole blood. We also addressed the question of low throughput of a typical microfluidic device by processing 1 mL of blood within 28 min. In addition, we found that ~93% of the captured cells were viable, making them suitable for subsequent molecular and cellular studies.