The aptamers generated from HepG2 cells

Cell-SELEX and application research of a DNA aptamer against esophageal squamous cell carcinoma (ESCC) cell line TE-1

Esophageal cancer is a common cancer with high morbidity and mortality that severely threatens the safety and quality of human life. The strong metastatic nature of esophageal cancer enables it to metastasize more quickly and covertly, making it difficult for current diagnostic and treatment methods to achieve efficient early screening, as well as timely and effective treatment. As a promising solution, nucleic acid aptamers, a kind of special single-stranded DNA or RNA oligonucleotide selected by the Systematic Evolution of Ligands by Exponential Enrichment (SELEX) technology, can specifically bind with different molecular targets. In this paper, random DNA single-stranded oligonucleotides were used as the initial library. Using TE-1 cells and HEEC cells as targets, specific binding sequences were selected by 15 rounds of the cell-SELEX method, and the aptamer sequence that binds to TE-1 cells with the most specificity was obtained and named Te4. The Te4 aptamer was further validated for binding specificity, binding affinity, type of target, in vitro cytotoxicity when conjugated with DOX(Te4-DOX), and in vivo distribution. Results of in vitro validation showed that Te4 has outstanding binding specificity with a Kd value of 51.16 ± 5.52 nM, and the target type of Te4 was preliminarily identified as a membrane protein. Furthermore, the cytotoxicity experiment showed that Te4-DOX has specific cytotoxicity towards cultured TE-1 cells. Finally, the results of the in vivo distribution experiment showed that the Te4 aptamer is able to specifically target tumor regions in nude mice, showing great potential to be applied in future diagnosis and targeted therapy of esophageal cancer.

Aptamers in cancer therapy: problems and new breakthroughs

Aptamers, a class of oligonucleotides that can bind with molecular targets with high affinity and specificity, have been widely applied in research fields including biosensing, imaging, diagnosing, and therapy of diseases. However, compared with the rapid development in the research fields, the clinical application of aptamers is progressing at a much slower speed, especially in the therapy of cancer. Obstructions including nuclease degradation, renal clearance, a complex selection process, and potential side effects have inhibited the clinical transformation of aptamer-conjugated drugs. To overcome these problems, taking certain measures to improve the biocompatibility and stability of aptamer-conjugated drugs in vivo is necessary. In this review, the obstructions mentioned above are thoroughly discussed and the methods to overcome these problems are introduced in detail. Furthermore, landmark research works and the most recent studies on aptamer-conjugated drugs for cancer therapy are also listed as examples, and the future directions of research for aptamer clinical transformation are discussed.

Identification of PHB2 as a Potential Biomarker of Luminal A Breast Cancer Cells Using a Cell-Specific Aptamer

Precise diagnosis of breast cancer molecular subtypes remains a great challenge in clinics. The present molecular biomarkers are not specific enough to classify breast cancer subtypes precisely, which requests for more accurate and specific molecular biomarkers to be discovered. Aptamers evolved by the cell-systematic evolution of ligands by exponential enrichment (SELEX) method show great potential in the discovery and identification of cell membrane targets via aptamer-based cell membrane protein pull-down, which has been regarded as a novel and powerful weapon for the discovery and identification of new molecular biomarkers. Herein, a cell membrane protein PHB2 was identified as a potential molecular biomarker specifically expressed in the cell membranes of MCF-7 breast cancer cells using a DNA aptamer MF3Ec. Further experiments demonstrated that the PHB2 protein is differentially expressed in the cell membranes of MCF-7, SK-BR-3, and MDA-MB-231 breast cancer cells and MCF-10A cells, and the binding molecular domains of aptamer MF3Ec and anti-PHB2 antibodies to the PHB2 protein are different due to there being no obvious competitions between aptamer MF3Ec and anti-PHB2 antibodies in the binding to the cell membranes of target MCF-7 cells. Due to those four cells belonging to luminal A, HER2-positive, and triple-negative breast cancer cell subtypes and human normal mammary epithelial cells, respectively, the PHB2 protein in the cell membrane may be a potential biomarker for precise diagnosis of the luminal A breast cancer cell subtype, which is endowed with the ability to differentiate the luminal A breast cancer cell subtype from HER2-positive and triple-negative breast cancer cell subtypes and human normal mammary epithelial cells, providing a new molecular biomarker and therapeutic target for the accurate and precise classification and diagnostics and personalized therapy of breast cancer.

"Willow Branch" DNA Self-Assembly for Cancer Dual-Target and Proliferation Inhibition

DNA nanotechnology is beginning to yield unique advantages in the area of drug delivery. For the dual-targeting and proliferation suppression of cancer cells, a "willow branch" DNA assembly based on rolling circle amplification (RCA) was built. Three single-stranded DNAs, including antibody modified cDNAs, aptamer cDNAs, and simple cDNAs, were employed in the DNA self-assembly, along with the RCA scaffolds (every 63 bases is a repeat unit). "Willow branch" DNA (WB DNA) assembly successfully linked multiple antibodies and aptamers together to achieve dual targeting of cancer cells. Binding of CD44 antibodies and S2.2 aptamers to receptors on the cell membrane inhibits both pathways, β-catenin signaling and nuclear factor-kappa B-specific transcription activity, through feedback regulation. Results demonstrated that WB DNA assembly could effectively exert multivalency clustering cell-surface receptors, modulating signal pathways and inhibiting proliferation. This study proposes a new approach for cancer dual-target and proliferation inhibition by clustering multivalent receptors.

A comprehensive review on electrochemical and optical aptasensors for organophosphorus pesticides

There has been a rise in pesticide use as a result of the growing industrialization of agriculture. Organophosphorus pesticides have been widely applied as agricultural and domestic pest control agents for nearly five decades, and they remain as health and environmental hazards in water supplies, vegetables, fruits, and processed foods causing serious foodborne illness. Thus, the rapid and reliable detection of these harmful organophosphorus toxins with excellent sensitivity and selectivity is of utmost importance. Aptasensors are biosensors based on aptamers, which exhibit exceptional recognition capability for a variety of targets. Aptasensors offer numerous advantages over conventional approaches, including increased sensitivity, selectivity, design flexibility, and cost-effectiveness. As a result, interest in developing aptasensors continues to expand. This paper discusses the historical and modern advancements of aptasensors through the use of nanotechnology to enhance the signal, resulting in high sensitivity and detection accuracy. More importantly, this review summarizes the principles and strategies underlying different organophosphorus aptasensors, including electrochemical, electrochemiluminescent, fluorescent, and colorimetric ones.

Applications of Aptamer-Bound Nanomaterials in Cancer Therapy

Cancer is still a major disease that threatens human life. Although traditional cancer treatment methods are widely used, they still have many disadvantages. Aptamers, owing to their small size, low toxicity, good specificity, and excellent biocompatibility, have been widely applied in biomedical areas. Therefore, the combination of nanomaterials with aptamers offers a new method for cancer treatment. First, we briefly introduce the situation of cancer treatment and aptamers. Then, we discuss the application of aptamers in breast cancer treatment, lung cancer treatment, and other cancer treatment methods. Finally, perspectives on challenges and future applications of aptamers in cancer therapy are discussed.

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.

A review on methods for diagnosis of breast cancer cells and tissues

Breast cancer has seriously been threatening physical and mental health of women in the world, and its morbidity and mortality also show clearly upward trend in China over time. Through inquiry, we find that survival rate of patients with early‐stage breast cancer is significantly higher than those with middle‐ and late‐stage breast cancer, hence, it is essential to conduct research to quickly diagnose breast cancer. Until now, many methods for diagnosing breast cancer have been developed, mainly based on imaging and molecular biotechnology examination. These methods have great contributions in screening and confirmation of breast cancer. In this review article, we introduce and elaborate the advances of these methods, and then conclude some gold standard diagnostic methods for certain breast cancer patients. We lastly discuss how to choose the most suitable diagnostic methods for breast cancer patients. In general, this article not only summarizes application and development of these diagnostic methods, but also provides the guidance for researchers who work on diagnosis of breast cancer.

Cell-SELEX, an Effective Way to the Discovery of Biomarkers and Unexpected Molecular Events

Cell-SELEX can not only generate aptamers for specific cell isolation/detection, diagnosis, and therapy, but also lead to the discovery of biomarkers and unexpected molecular events. However, most cell-SELEX research is concentrated on aptamer generation and applications. In this progress report, recent research progress with cell-SELEX in terms of the discovery of biomarkers and unexpected molecular events is highlighted. In particular, the key technical challenges for cell-SELEX-based biomarker discovery, namely, the methods for identification and validation of target proteins of aptamers, are discussed in detail. Finally, the prospects of the applications of cell-SELEX in this field now and in the near future are described. It is expected that this report will attract attention to the benefit of cell-SELEX and provide a practical reference for biomedical researchers.

Aptamer-based fluorescence polarization assay for separation-free exosome quantification

Tumor-derived exosomes have emerged as promising cancer biomarkers and attracted increasing interest in non-invasive cancer diagnosis and treatment monitoring. However, the identification and quantification of exosomes in clinical samples such as blood remains challenging due to the difficulty in trade-off between recognition specificity and isolation efficiency. Here we have developed an aptamer-based fluorescence polarization assay for exosome quantification, which is a separation-free, amplification-free and sensitive approach enabling direct quantification of exosomes in human plasma. While the key specificity of this assay is based on the aptamer's inherent affinity to membrane proteins on exosomes, exosomes' inherent huge mass/volume acts as mass-based fluorescence polarization amplifier. Our assay allows quantitative analysis of exosomes in the range of 5 × 10² to 5 × 10⁵ particles per μL with a detect limitation of 500 particles per μL for the cell line deprived exosomes. The total assay time is about 30 min with just one mix-and-read step to achieve high sensitivity. We have also demonstrated quantification of exosomes from lung cancer patients and healthy donors in clinical samples. This work describes a new and simple liquid biopsy assay to directly detect exosomes in the biological matrix, which facilitates cancer diagnosis and therapy monitoring.

Differentiating breast cancer molecular subtypes using a DNA aptamer selected against MCF-7 cells

Aptamers are single-stranded DNA or RNA oligonucleotides selected by systematic evolution of ligands by exponential enrichment (SELEX), which show great potential in the diagnosis and personalized therapy of cancers, due to their specific advantages over antibodies. In the past years, though great progress has been made in molecular subtyping of breast cancer, it remains a challenge in clinical medicine, which plays a crucial role in the treatment. In this study, a ssDNA aptamer MF3 against MCF-7 breast cancer cells was developed by Cell-SELEX for differentiating breast cancer molecular subtypes, which showed favorable specificity and binding affinity towards MCF-7 cells with a Kd value of 82.25 ± 25.14 nM. The aptamer could not only successfully distinguish MCF-7 breast cancer cells from MDA-MB-231 and SK-BR-3 breast cancer cells and MCF-10A human normal mammary epithelial cells, but also could differentiate MCF-7 cells from other cancer cells or normal cells. Moreover, both in vivo and in vitro fluorescence imaging studies demonstrated that aptamer MF3 was able to distinguish tumor-bearing mice and xenograft tissue sections of MCF-7 breast cancer cells from that of MDA-MB-231 and SK-BR-3 breast cancer cells. All these results suggested that aptamer MF3 is a potential tool for differentiating molecular subtypes and diagnosis of breast cancer.

Aptasensors for pesticide detection

Pesticide contamination has become one of the most serious problems of public health in the world, due to their wide application in agriculture industry to guarantee the crop yield and quality. The detection of pesticide residues plays an important role in food safety management and environment protection. However, the conventional detection methodologies cannot realize highly sensitive, selective and on-site detection, which limits their applications. Aptamers are short single-stranded oligonucleotides (RNA or DNA) selected by SELEX method, which can selectively bind to their targets with high affinity. Compared with the commonly used antibodies or enzymes in designing biosensors, aptamers exhibit better stability, low molecular weight, easy modification and low cost, and were regarded as excellent candidates for developing aptasensors for pesticide detection. In this review, application of aptamers for pesticide detection was reviewed. Firstly, aptamers specifically bind to various pesticides were first summarized. Secondly, the progresses and highlights of developing aptasensors for highly-sensitive and selective detection of pesticide residues were systematically provided. Finally, the present challenges and future perspectives for developing novel highly-effective aptasensor for the detection of pesticide residues were discussed.

Prediction of the binding affinity of aptamers against the influenza virus

Thousands of investigations on quantitative structure-activity/property relationships (QSARs/QSPRs) have been reported. However, few publications can be found that deal with QSARs for aptamers, because calculating two-dimensional and three-dimensional descriptors directly from aptamers (typically with 15-45 nucleotides) is difficult. This paper describes calculating molecular descriptors from amino acid sequences that are translated from DNA aptamer sequences with DNAMAN software, and developing QSAR models for the aptamers' binding affinity to the influenza virus. General regression neural network (GRNN) based on Parzen windows estimation was used to build the QSAR model by applying six molecular descriptors. The optimal spreading factor σ of Gaussian function of 0.3 was obtained with the circulation method. The correlation coefficients r from the GRNN model were 0.889 for the training set and 0.892 for the test set. Compared with the existing model for aptamers' binding affinity to the influenza virus, our model is accurate and competes favourably. The feasibility of calculating molecular descriptors from an amino acid sequence translated from DNA aptamer sequences to develop a QSAR model for the anti-influenza aptamers was demonstrated.

Magnetic Separation-Based Multiple SELEX for Effectively Selecting Aptamers against Saxitoxin, Domoic Acid, and Tetrodotoxin

In this study, a novel magnetic separation-based multiple systematic evolution of ligands by exponential enrichment (SELEX) was applied to select aptamers simultaneously against three kinds of marine biotoxins, including domoic acid (DA), saxitoxin (STX), and tetrodotoxin (TTX). Magnetic reduced graphene oxide (MRGO) was prepared to adsorb unbound ssDNAs and simplify the separation step. In the multiple SELEX, after the initial twelve rounds of selection against mixed targets and the subsequent four respective rounds of selection against each single target, the three resulting ssDNA pools were cloned, sequenced, and analyzed. Several aptamer candidates were selected and subjected to the binding affinity and specificity test. Finally, DA-06 ( K_d = 62.07 ± 19.97 nM), TTX-07 ( K_d = 44.12 ± 15.38 nM), and STX-41 ( K_d = 61.44 ± 23.18 nM) showed high affinity and good specificity for DA, TTX, and STX, respectively. They were also applied to detect and quantify DA, TTX, and STX successfully. The other two multitarget aptamers, DA-01 and TTX-27, were also obtained, which can bind with either DA or TTX. These aptamers provide alternative recognition molecules to antibodies for biosensor applications.

Hydrothermal synthesis of N,S co-doped carbon nanodots for highly selective detection of living cancer cells

This study presents a facile synthesis method for the preparation of positively charged N,S co-doped carbon nanodots with excellent optical properties, and it develops a selective method for fluorescent detection of living cancer cells. The specific recognition is due to the application of an aptamer sequence, which shows high affinity and specificity to target cells. The aptamer is firstly labeled with BHQ and wraps around the carbon nanodots, then it finally quenches the fluorescence emission of the carbon nanodots. For the sensitive and selective analysis of target cells, the cells are simply mixed with the carbon nanodot-aptamer nanoconjugates, which are then centrifuged at a low speed. The recognition reaction between aptamer and target cells releases the quencher from the surface of the carbon nanodots and the centrifugation process enables the recovery of fluorescence intensity of the suspension, which reflects the level of initial cancer cells. The developed method is simple, highly selective and cost-effective, thus, it may be further exploited in clinical applications in the future.

Competitive electrochemical platform for ultrasensitive cytosensing of liver cancer cells by using nanotetrahedra structure with rolling circle amplification

In this work, a competitive and label-free electrochemical platform was performed for the ultrasensitive cytosensing of liver cancer cells based on DNA nanotetrahedron (NTH) structure and rolling circle amplification (RCA) directed DNAzyme strategy. The multifunctional nanoprobes were fabricated through a DNA primer probe, carboxyfluorescein (FAM) functionalized TLS11a aptamer and horseradish peroxidase (HRP) immobilized on the surfaces of the platinum nanoparticles (PtNPs). Then the NTH-based complementary DNA (cDNA) probe, complementary to the TLS11a aptamer, was attached on a disposable screen-printed gold electrode (SPGE) for increasing the reactivity and accessibility with the prepared nanoprobes. Due to the primer probe and the circular probe with G-quadruplex sequences for RCA, it can lead to the formation of numerous G-quadruplex/hemin DNAzyme, thus generating a remarkable electrochemical response. When the target cells were present, the nanoprobes were released from the SPGE due to the specific recognition of TLS11a aptamers for HepG2 cells, resulting in the electrochemical signal changes. The cytosensor was ultrasensitive for HepG2 tumor cell detection with a detection limit of 3 cell per mL. Furthermore, this strategy was also demonstrated to be applicable for cancer cell imaging. In summary, this electrochemical cytosensor holds great potential for circulating tumor cell detection in the early cancer diagnose.

Recent developments in cell-SELEX technology for aptamer selection

BACKGROUND

SELEX technique is employed to select aptamers against wide range of targets. The in vitro method of aptamer selection using live cells as the target is referred as cell-SELEX.

SCOPE OF THE REVIEW

The review provides a comprehensive description on the development of aptamers through various cell-SELEX methods and list of aptamers identified through this method. In addition, it pinpoints the advantages and limitations of the cell-SELEX process and its variants.

MAJOR CONCLUSIONS

The use of aptamers as therapeutic and diagnostic agents is rapidly evolving, selection techniques such as Cell-SELEX could be beneficial in identifying aptamers when the target is in its native conformation and without prior information of the cognate target, thereby bringing the aptamer development one step closer to the clinic.

GENERAL SIGNIFICANCE

The information in this review can serve as a database for the design and development of futuristic oligonucleotide based diagnostics and therapeutics work.

Real-time detection of the interaction between alpha-fetoprotein and its ssDNA aptamer by dual polarization interferometry

A real-time and label-free strategy to understand the interaction between biomarkers and ssDNA aptamers.

Development of Cell-Specific Aptamers: Recent Advances and Insight into the Selection Procedures

Systematic evolution of ligands by exponential enrichment (SELEX) is an established procedure for developing short single-stranded nucleic acid ligands called aptamers against a target of choice. This approach has also been used for developing aptamers specific to whole cells named Cell-SELEX. Aptamers selected by Cell-SELEX have the potential to act as cell specific therapeutics, cell specific markers or cell specific drug delivery and imaging agents. However, aptamer development is a laborious and time-consuming process which is often challenging due to the requirement of frequent optimization of various steps involved in Cell-SELEX procedures. This review provides an insight into various procedures for selection, aptamer enrichment, regeneration and aptamer-binding analysis, in addition to a very recent update on all aptamers selected by Cell-SELEX procedures.

Aptamer selection and applications for breast cancer diagnostics and therapy

Aptamers are short non-coding, single-stranded oligonucleotides (RNA or DNA) developed through Systematic Evolution of Ligands by Exponential enrichment (SELEX) in vitro. Similar to antibodies, aptamers can bind to specific targets with high affinity, and are considered promising therapeutic agents as they have several advantages over antibodies, including high specificity, stability, and non-immunogenicity. Furthermore, aptamers can be produced at a low cost and easily modified, and are, therefore, called "chemical antibodies". In the past years, a variety of aptamers specifically bound to both breast cancer biomarkers and cells had been selected. Besides, taking advantage of nanomaterials, there were a number of aptamer-nanomaterial conjugates been developed and widely investigated for diagnostics and targeted therapy of breast cancer. In this short review, we first present a systematical review of various aptamer selection methods. Then, various aptamer-based diagnostic and therapeutic strategies of breast cancer were provided. Finally, the current problems, challenges, and future perspectives in the field were thoroughly discussed.

Aptamer-Modified Tetrahedral DNA Nanostructure for Tumor-Targeted Drug Delivery

Tetrahedral DNA nanostructures (TDNs) are considered promising drug delivery carriers because they are able to permeate cellular membrane and are biocompatible and biodegradable. Furthermore, they can be modified by functional groups. To improve the drug-delivering ability of TDNs, we chose anticancer aptamer AS1411 to modify TDNs for tumor-targeted drug delivery. AS1411 can specifically bind to nucleolin, which is overexpressed on the cell membrane of tumor cells. Furthermore, AS1411 can inhibit NF-κB signaling and reduce the expression of bcl-2. In this study, we compared the intracellular localization of AS1411-modified TDNs (Apt-TDNs) with that of TDNs in different cells under hypoxic condition. Furthermore, we compared the effects of Apt-TDNs and TDNs on cell growth and cell cycle under hypoxic condition. A substantial amount of Apt-TDNs entered and accumulated in the nucleus of MCF-7 cells; however, the amount of Apt-TDNs that entered L929 cells was comparatively less. TDNs entered in much lower quantity in MCF-7 cells than Apt-TDNs. Moreover, there was little difference in the amount of TDNs that entered L929 cells and MCF-7 cells. Apt-TDNs can inhibit MCF-7 cell growth and promote L929 cell growth, while TDNs can promote both MCF-7 and L929 cell growth. Thus, the results indicate that Apt-TDNs are more effective tumor-targeted drug delivery vehicles than TDNs, with the ability to specifically inhibit tumor cell growth.