Mapping receptor density on live cells by using fluorescence correlation spectroscopy

Single-molecule analysis reveals the phosphorylation of FLS2 governs its spatiotemporal dynamics and immunity

The Arabidopsis thaliana FLAGELLIN-SENSITIVE2 (FLS2), a typical receptor kinase, recognizes the conserved 22 amino acid sequence in the N-terminal region of flagellin (flg22) to initiate plant defense pathways, which was intensively studied in the past decades. However, the dynamic regulation of FLS2 phosphorylation at the plasma membrane after flg22 recognition needs further elucidation. Through single-particle tracking, we demonstrated that upon flg22 treatment the phosphorylation of Ser-938 in FLS2 impacts its spatiotemporal dynamics and lifetime. Following Förster resonance energy transfer-fluorescence lifetime imaging microscopy and protein proximity indexes assays revealed that flg22 treatment increased the co-localization of GFP-tagged FLS2/FLS2S938D but not FLS2S938A with AtRem1.3-mCherry, a sterol-rich lipid marker, indicating that the phosphorylation of FLS2S938 affects FLS2 sorting efficiency to AtRem1.3-associated nanodomains. Importantly, we found that the phosphorylation of Ser-938 enhanced flg22-induced FLS2 internalization and immune responses, demonstrating that the phosphorylation may activate flg22-triggered immunity through partitioning FLS2 into functional AtRem1.3-associated nanodomains, which fills the gap between the FLS2S938 phosphorylation and FLS2-mediated immunity.

Recent progress in quantitative technologies for the analysis of cancer-related exosome proteins

Exosomes are a kind of extracellular vesicles, which play a significant role in intercellular communication and molecular exchange. Cancer-derived exosomes are potential and ideal biomarkers for the early diagnosis and treatment monitoring of cancers because of their abundant biological information and contribution to the interaction between cancer cells and the tumor microenvironment. However, there are a number of drawbacks, such as low sensitivity and tedious steps, in conventional detection techniques. Furthermore, exosome quantification is not enough to accurately distinguish cancer patients from healthy individuals. Therefore, developing efficient, accurate, and inexpensive exosome surface protein analysis techniques is necessary and critical. In recent years, a considerable number of researchers have presented novel detection strategies in this field. This review summarizes the recent progress in quantitative technologies for the analysis of cancer-related exosome proteins, mainly including the detection methods based on aptamers, nanomaterials, and antibodies, discusses a roadmap for future developments, and aims to offer an innovative perspective of exosome research.

Reconstitution of morphogen shuttling circuits

Developing tissues form spatial patterns by establishing concentration gradients of diffusible signaling proteins called morphogens. The bone morphogenetic protein (BMP) morphogen pathway uses a family of extracellular modulators to reshape signaling gradients by actively "shuttling" ligands to different locations. It has remained unclear what circuits are sufficient to enable shuttling, what other patterns they can generate, and whether shuttling is evolutionarily conserved. Here, using a synthetic, bottom-up approach, we compared the spatiotemporal dynamics of different extracellular circuits. Three proteins-Chordin, Twsg, and the BMP-1 protease-successfully displaced gradients by shuttling ligands away from the site of production. A mathematical model explained the different spatial dynamics of this and other circuits. Last, combining mammalian and Drosophila components in the same system suggests that shuttling is a conserved capability. Together, these results reveal principles through which extracellular circuits control the spatiotemporal dynamics of morphogen signaling.

Quantitative Evaluation of a Multimodal Aptamer-Targeted Long-Circulating Polymer for Tumor Targeting

Aptamers are promising targeting agents for imaging and therapy of numerous diseases, including cancer. However, a significant shortcoming of aptamers is their poor stability and fast excretion, limiting their application in vivo. Common strategies to overcome these challenges is to chemically modify aptamers in order to increase their stability and/or to apply formulation technologies such as conjugating them to polymers or nanocarriers in order to increase their circulation half-life. This is expected to result in improved cellular uptake or retention to passively targeted nanomedicines. Herein, we report a modular conjugation strategy based on click chemistry between functionalized tetrazines and trans-cyclooctene (TCO), for the modification of high molecular weight hyperbranched polyglycerol (HPG) with sgc8 aptamer, fluorescent dyes, and ¹¹¹In. Our data indicate strong affinity of sgc8 against a range of solid tumor-derived cell lines that have previously not been tested with this aptamer. Nevertheless, nonspecific uptake of scrambled ssDNA-functionalized HPG in cells highlights inherent challenges of aptamer-targeted probes that remain to be solved for clinical translation. We validate HPG-sgc8 as a nontoxic nanoprobe with high affinity against MDA-MB-468 breast and A431 lung cancer cells and show significantly increased plasma stability compared to free sgc8. In vivo quantitative SPECT/CT imaging indicates EPR-mediated tumor uptake of HPG-sgc8 and nontargeted or scrambled ssDNA-conjugated HPG but no statistically significant difference between these formulations in terms of total tumor uptake or retention. Our study emphasizes the need for stringent controls and quantification in the evaluation of aptamer-targeted probes. For this purpose, our versatile synthesis strategy provides a simple approach for the design and evaluation of long-circulating aptamer-conjugated nanoformulations.

Ligand Dilution Analysis Facilitates Aptamer Binding Characterization at the Single-Molecule Level

Cell-specific aptamers offer a powerful tool to study membrane receptors at the single-molecule level. Most target receptors of aptamers are highly expressed on the cell surface, but difficult to analyze in situ because of dense distribution and fast velocity. Therefore, we herein propose a random sampling-based analysis strategy termed ligand dilution analysis (LDA) for easily implemented aptamer-based receptor study. Receptor density on the cell surface can be calculated based on a regression model. By using a synergistic ligand dilution design, colocalization and differentiation of aptamer and monoclonal antibody (mAb) binding on a single receptor can be realized. Once this is accomplished, precise binding site and detailed aptamer-receptor binding mode can be further determined using molecular docking and molecular dynamics simulation. The ligand dilution strategy also sets the stage for an aptamer-based dynamics analysis of two- and three-dimensional motion and fluctuation of highly expressed receptors on the live cell membrane.

Virus Mimetic Framework DNA as a Non-LNP Gene Carrier for Modulated Cell Endocytosis and Apoptosis

Mimicking the size and shape of spherical viruses, we constructed a soccer-ball shaped virus-inspired DNA origami (ViDO) framework as a programmable non-LNP (lipid nanoparticle) gene carrier. The DNA framework was decorated with precisely controlled recognition molecules outside and loaded with adequate genetic molecules inside. Five variants were constructed to systematically investigate their cell uptake and modulated gene silencing efficiency. Cellular uptake was enhanced with an increasing number of aptamers, while with a median number of aptamer supply, dispersed distribution performed better than the clustered pattern. Intriguingly, the transfection efficiency was maximized using the ViDO with clustered five aptamers, which exhibited a competitive RNA silencing effect induced by Lipo2000 with low cytotoxicity. Our results revealed the effects of aptamer distribution patterns on endocytosis and transfection, thus providing a programmable platform for meticulous optimization of the gene delivery system.

Receptor-ligand non-equilibrium kinetics (RLNEK) 1.0: An integrated Trackmate laminar flow chamber analysis

Although parallel plate flow chamber assays are widely performed, extraction of kinetic parameters is limited to specialized labs with mathematical expertise and customized video-microscopy tracking tools. The recent development of Trackmate has increased researcher accessibility to tracking particles in video-microscopy experiments; however, there is a lack of tools that analyze this tracking information. We report a software tool, compatible with Trackmate, that extracts Receptor Ligand Non-Equilibrium Kinetic (RLNEK) parameters from video-microscopy data. This software should be of particular interest to the community of researchers and scientists interrogating the target-specific binding and release of immune cells.

Dynamic in Situ Confinement Triggers Ligand-Free Neuropeptide Receptor Signaling

Membrane receptor clustering is fundamental to cell-cell communication; however, the physiological function of receptor clustering in cell signaling remains enigmatic. Here, we developed a dynamic platform to induce cluster formation of neuropeptide Y₂ hormone receptors (Y₂R) in situ by a chelator nanotool. The multivalent interaction enabled a dynamic exchange of histidine-tagged Y₂R within the clusters. Fast Y₂R enrichment in clustered areas triggered ligand-independent signaling as determined by an increase in cytosolic calcium and cell migration. Notably, the calcium and motility response to ligand-induced activation was amplified in preclustered cells, suggesting a key role of receptor clustering in sensitizing the dose response to lower ligand concentrations. Ligand-independent versus ligand-induced signaling differed in the binding of arrestin-3 as a downstream effector, which was recruited to the clusters only in the presence of the ligand. This approach allows in situ receptor clustering, raising the possibility to explore different receptor activation modalities.

Cell imaging with multi-color DNA framework probes

Utilizing the programmability of the fractal DNA frameworks, multi-color probes were constructed by arranging fluorescent molecules and nucleic acid aptamers on the structure. Multiplexed cell imaging and classification was realized through pattern recognition.

Study Progress of Important Agricultural Heritage Systems (IAHS): A Literature Analysis

Important Agricultural Heritage Systems (IAHS), as a new type of heritage, has received extensive attention from the international scientific communities. With the increase of IAHS research, reviews on it have been conducted by many scholars. However, visualized research to show future research trends of IAHS are lacking. Therefore, using metrology analysis methods, this study aims at presenting the progress of research and the general development trends of Globally Important Agricultural Heritage Systems (GIAHS) in the world from 2006 to 2020 to provide ideas for the development of countries or regions in the future. This study mapped 292 literatures from Web of Science core collections from 2006 to 2020 by CiteSpace software. The results show that research on IAHS from 2006 to 2020 experienced two stages: the fluctuating increase stage, and the steady growth stage. Author groups from China, Italy, the USA, Japan, etc., contributed many papers on IAHS. Institutions including the Chinese Academy of Sciences, the University of Florence and the University of Padua in Italy, etc., have a relatively high influence on international IAHS research. Agriculture Ecosystems & Environment is the most cited journal. Agricultural Heritage Systems, regeneration, agriculture, agroforestry, dry-stone wall, social capital, instability, and agricultural biodiversity have been hotspots in the past 15 years. The research themes mainly focus on GIAHS, tourism, livelihood assets, and direct georeferencing. Authors in different regions concern different research themes. In the future, the fields of applications and microscopic views, social sciences, applications of standardized quantitative research methods, and broadened international cooperation should be paid more attention.

Metabolic limits on classical information processing by biological cells

Biological information processing is generally assumed to be classical. Measured cellular energy budgets of both prokaryotes and eukaryotes, however, fall orders of magnitude short of the power required to maintain classical states of protein conformation and localization at the Å, fs scales predicted by single-molecule decoherence calculations and assumed by classical molecular dynamics models. We suggest that decoherence is limited to the immediate surroundings of the cell membrane and of intercompartmental boundaries within the cell, and that bulk cellular biochemistry implements quantum information processing. Detection of Bell-inequality violations in responses to perturbation of recently-separated sister cells would provide a sensitive test of this prediction. If it is correct, modeling both intra- and intercellular communication requires quantum theory.

Experimental and theoretical explorations of nanocarriers' multistep delivery performance for rational design and anticancer prediction

The poor understanding of the complex multistep process taken by nanocarriers during the delivery process limits the delivery efficiencies and further hinders the translation of these systems into medicine. Here, we describe a series of six self-assembled nanocarrier types with systematically altered physical properties including size, shape, and rigidity, as well as both in vitro and in vivo analyses of their performance in blood circulation, tumor penetration, cancer cell uptake, and anticancer efficacy. We also developed both data and simulation-based models for understanding the influence of physical properties, both individually and considered together, on each delivery step and overall delivery process. Thus, beyond finding that nanocarriers that are simultaneously endowed with tubular shape, short length, and low rigidity outperformed the other types, we now have a suit of theoretical models that can predict how nanocarrier properties will individually and collectively perform in the multistep delivery of anticancer therapies.

Detection of membrane receptors on per tumor cell by nonimmobilized cell capillary electrophoresis and a mathematic model

Folate receptors (FRs) are a class of valuable therapeutic target which is highly expressed on a variety of cancers. The accurate detection of the expression of FRs in different cells is conducive to improve the accuracy of FR targeted tumor therapy. Herein, a method based on nonimmobilized cell capillary electrophoresis (NICCE) combined with a mathematic model to quantify FRs on each single tumor cell was developed. At first, we studied the interactions between FA and A549, HT-29, HepG2, and U87MG cells by NICCE respectively, and calculated the kinetic parameters (Ka, k', ka, and kd). Next, we established a mathematic model to accurately determine the number of moles of FRs on per A549, HT-29, HepG2, and U87MG cell for the first time, that were (10.44 ± 0.53) × 10-19 mol, (34.32 ± 1.33) × 10-19 mol, (337.14 ± 10.11) × 10-19 mol, and (37.31 ± 2.13) × 10-19 mol. Then, these re-sults were proved to be consistent with the results of enzyme-linked immunosorbent assay (ELISA). Therefore, this method is simple, rapid, sensitive, and without protein separation or purification, which is expected to achieve clinical detection of cell membrane receptor expression level of cell membrane receptors on a single cell, which may be greatly beneficial to further clinical diagnosis and therapy.

Endophilin recruitment drives membrane curvature generation through coincidence detection of GPCR loop interactions and negative lipid charge

Endophilin plays key roles during endocytosis of cellular receptors, including generating membrane curvature to drive internalization. Electrostatic interactions between endophilin's BIN/Amphiphysin/Rvs domain and anionic membrane lipids have been considered the major driving force in curvature generation. However, the SH3 domain of endophilin also interacts with the proline-rich third intracellular loop (TIL) of various G-protein-coupled receptors (GPCRs), and it is unclear whether this interaction has a direct role in generating membrane curvature during endocytosis. To examine this, we designed model membranes with a membrane density of 1400 receptors per μm2 represented by a covalently conjugated TIL region from the β1-adrenergic receptor. We observed that TIL recruits endophilin to membranes composed of 95 mol% of zwitterionic lipids via the SH3 domain. More importantly, endophilin recruited via TIL tubulates vesicles and gets sorted onto highly curved membrane tubules. These observations indicate that the cellular membrane bending and curvature sensing activities of endophilin can be facilitated through detection of the TIL of activated GPCRs in addition to binding to anionic lipids. Furthermore, we show that TIL electrostatically interacts with membranes composed of anionic lipids. Therefore, anionic lipids can modulate TIL/SH3 domain binding. Overall, our findings imply that an interplay between TIL, charged membrane lipids, BAR domain, and SH3 domain could exist in the biological system and that these components may act in coordination to regulate the internalization of cellular receptors.

Towards understanding the messengers of extracellular space: Computational models of outside-in integrin reaction networks

The interactions between cells and their extracellular matrix (ECM) are critically important for homeostatic control of cell growth, proliferation, differentiation and apoptosis. Transmembrane integrin molecules facilitate the communication between ECM and the cell. Since the characterization of integrins in the late 1980s, there has been great advancement in understanding the function of integrins at different subcellular levels. However, the versatility in molecular pathways integrins are involved in, the high diversity in their interaction partners both outside and inside the cell as well as on the cell membrane and the short lifetime of events happening at the cell-ECM interface make it difficult to elucidate all the details regarding integrin function experimentally. To overcome the experimental challenges and advance the understanding of integrin biology, computational modeling tools have been used extensively. In this review, we summarize the computational models of integrin signaling while we explain the function of integrins at three main subcellular levels (outside the cell, cell membrane, cytosol). We also discuss how these computational modeling efforts can be helpful in other disciplines such as biomaterial design. As such, this review is a didactic modeling summary for biomaterial researchers interested in complementing their experimental work with computational tools or for seasoned computational scientists that would like to advance current in silico integrin models.

Quantifying the adhesive strength between the SARS-CoV-2 S-proteins and human receptor and its effect in therapeutics

The binding affinity and adhesive strength between the spike (S) glycoproteins of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), and the human angiotensin-converting enzyme 2 (ACE2) receptor is computed using molecular dynamics (MD) simulations. The calculations indicate that the binding affinity is [Formula: see text] [Formula: see text] with a maximum adhesive force of [Formula: see text] pN. Our analysis suggests that only 27 (13 in S-protein, 14 in ACE2) residues are active during the initial fusion process between the S-protein and ACE2 receptor. With these insights, we investigated the effect of possible therapeutics in the size and wrapping time of virus particles by reducing the binding energy. Our analysis indicates that this energy has to be reduced significantly, around 50% or more, to block SARS-CoV-2 particles with radius in the order of [Formula: see text] nm. Our study provides concise target residues and target binding energy reduction between S-proteins and receptors for the development of new therapeutics treatments for COVID-19 guided by computational design.

Artificial Aquaporin That Restores Wound Healing of Impaired Cells

Artificial aquaporins are synthetic molecules that mimic the structure and function of natural aquaporins (AQPs) in cell membranes. The development of artificial aquaporins would provide an alternative strategy for treatment of AQP-related diseases. In this report, an artificial aquaporin has been constructed from an amino-terminated tubular molecule, which operates in a unimolecular mechanism. The artificial channel can work in cell membranes with high water permeability and selectivity rivaling those of AQPs. Importantly, the channel can restore wound healing of the cells that contain function-lost AQPs.

Development of a DNA aptamer to detect Brucella abortus and Brucella melitensis through cell SELEX

BACKGROUND

Brucellosis is a zoonosis, caused by Brucella spp. which are small aerobic intracellular coccobacilli, localized in the reproductive organs of host animals, causing abortion and sterility. The diagnosis of this zoonosis is based on microbiological, serological or real time-polymerase chain reaction (RT-PCR) laboratory tests. Although the common microbiological and serological based assays have advantages, they are not able to solve the diagnosis problems.

AIMS

To overcome some of the limitations of present techniques, in this study, we developed an aptamer through whole-cell systematic evolution of Ligands by EXponential enrichment (SELEX) procedures to detect Brucella.

METHODS

We used mixture of Brucella melitensis and Brucella abortus as the target. In order to prepare the single-stranded DNA (ssDNA) aptamer, the DNA library was amplified with 5´-phosphorylated reverse primer and treated with lambda exonuclease. The SELEX procedure was performed by incubating the ssDNA pool with a bacterial suspension in a binding buffer. The selected procedures were monitored by flow cytometry using FITC-labelled forward primer. Aptamers with the highest binding affinity towards the target and the lowest to other strains were selected.

RESULTS

Two aptamers namely B20 and B21 showed significant binding affinity toward B. melitensis and B. abortus. The dissociation constant (K_d) for aptamers B20 and B21 was 40.179 ± 3.06 pM and 184.396 ± 465 pM, respectively.

CONCLUSION

The isolated aptamers were able to identify B. melitensis and B. abortus with a remarkable binding efficiency and appropriated K_d in a picoMolar range and therefore can be good candidates in the development of any rapid assay test implanted on routine brucellosis diagnoses.

Highly Effective Drug Delivery and Cell Imaging Using Fluorescent Double-Imprinted Nanoparticles by Targeting Recognition of the Epitope of Membrane Protein

Nanocarriers with both targeting ability and stable loading of drugs can more effectively deliver drugs to precise tumor sites for therapeutic effects. Accordingly, we have rationally designed fluorescent molecularly imprinted polymer nanoparticles (FMIPs), which use N-terminal epitope of P32 membrane protein as the primary template and doxorubicin (DOX) as the secondary template. The DOX imprinted cavity can stably carry the drug and the epitope-imprinted cavity allows FMIPs to actively recognize the P32-positive 4T1 cancer cells. The targeted therapeutic effect of DOX-loaded FMIPs (FMIPs@DOX) is investigated in vitro and in vivo. The FMIPs@DOX only causes apoptosis in 4T1 cancer cells compared to C8161 cells (expressing low level of P32). In addition, highly effective inhibition of 4T1 malignant breast tumors using FMIPs@DOX is achieved in the model of tumor-bearing mice. Importantly, the antitumor effect achieved by intravenous injection of FMIPs@DOX is almost identical to that by intratumoral injection. Furthermore, the FMIPs can serve as a targeted fluorescence imaging agent due to the high specificity of the epitope-imprinted cavity and the stable fluorescence of the embedded silicon nanoparticles. These results demonstrate the effectiveness of the FMIPs for active targeted drug delivery and imaging. Furthermore, the FMIPs provide a direction for drug-loaded nanocarrier.

The Increased PTK7 Expression Is a Malignant Factor in Cervical Cancer

Cervical cancer is one of the most common malignant neoplasms in gynecology. Protein tyrosine kinase 7 (PTK7) with an inactive kinase domain is an important regulator of multiple Wnt pathways under normal and various pathological conditions and overexpressed in various tumors; however, the clinical and biological significance of PTK7 in cervical cancer is still unknown. In the present study, the protein expression level of PTK7 was detected in clinical cervical cancer patient samples, and the relationship between PTK7 expression and clinicopathological features was analyzed. In addition, the Kaplan-Meier method was performed to estimate the overall survival (OS) and progression-free survival (PFS) of patients to investigate the clinicopathological significance of PTK7 expression. Functional assays demonstrated that knocking down PTK7 might inhibit the ability of cancer cells to proliferate and invade or migrate, both in vivo and in vitro. Thus, PTK7 might serve as a potential target for cervical cancer.

An exploration of aptamer internalization mechanisms and their applications in drug delivery

INTRODUCTION

As 'chemical antibodies', aptamers have some advantages, such as lack of immunogenicity, rapid tissue penetration, cell internalization and so on. Consequently, more and more aptamers have been screened out by the systematic evolution of ligands through exponential enrichment for the desired cells or membrane receptors. On the basis of the result, researchers use aptamers to guide drug targeting to the desired cells and internalization in vivo.

AREAS COVERED

In this review, we explore the mechanisms of cargo- or aptamer-mediated internalization, and then briefly summarize five strategies for exploring the mechanism of aptamer internalization. Finally, we focus on four types of applications involving aptamer internalization: aptamers as drugs, aptamers as chemical drug-delivery systems, aptamer-based chimeras and aptamer-conjugated nanoparticles or block copolymer micelles.

EXPERT OPINION

Two aptamer-internalization mechanisms are known, namely receptor-mediated endocytosis and macropinocytosis. The latter mechanism, which is has only been verified in the internalization of nucleolin aptamer shuttles between the nucleus and cytoplasm, may be important for nuclear internalization and cargo molecule escape from the endosomal compartment. Thus, it is feasible to use some strategies to further explore the macropinocytosis internalization mechanism and then to screen for aptamers similar to the nucleolin aptamer for use with the desired cell types as a targeted delivery tool.

Membrane Wrapping Efficiency of Elastic Nanoparticles during Endocytosis: Size and Shape Matter

Using coarse-grained molecular dynamics simulations, we systematically investigate the receptor-mediated endocytosis of elastic nanoparticles (NPs) with different sizes, ranging from 25 to 100 nm, and shapes, including sphere-like, oblate-like, and prolate-like. Simulation results provide clear evidence that the membrane wrapping efficiency of NPs during endocytosis is a result of competition between receptor diffusion kinetics and thermodynamic driving force. The receptor diffusion kinetics refer to the kinetics of receptor recruitment that are affected by the contact edge length between the NP and membrane. The thermodynamic driving force represents the amount of required free energy to drive NPs into a cell. Under the volume constraint of elastic NPs, the soft spherical NPs are found to have similar contact edge lengths to rigid ones and to less efficiently be fully wrapped due to their elastic deformation. Moreover, the difference in wrapping efficiency between soft and rigid spherical NPs increases with their sizes, due to the increment of their elastic energy change. Furthermore, because of its prominent large contact edge length, the oblate ellipsoid is found to be the least sensitive geometry to the variation in NP's elasticity among the spherical, prolate, and oblate shapes during the membrane wrapping. In addition, simulation results indicate that conflicting experimental observations on the efficiency of cellular uptake of elastic NPs could be caused by their different mechanical properties. Our simulations provide a detailed mechanistic understanding about the influence of NPs' size, shape, and elasticity on their membrane wrapping efficiency, which serves as a rational guidance for the design of NP-based drug carriers.

In situ fluorescent profiling of living cell membrane proteins at a single-molecule level

A signal amplification method is developed for visualization analysis of membrane proteins on living cells at a single-molecule level.

Direct visualization of single-molecule membrane protein interactions in living cells

Interactions between membrane proteins are poorly understood despite their importance in cell signaling and drug development. Here, we present a co-immunoimmobilization assay (Co-II) enabling the direct observation of membrane protein interactions in single living cells that overcomes the limitations of currently prevalent proximity-based indirect methods. Using Co-II, we investigated the transient homodimerizations of epidermal growth factor receptor (EGFR) and beta-2 adrenergic receptor (β2-AR) in living cells, revealing the differential regulation of these receptors’ dimerizations by molecular conformations and microenvironment in a plasma membrane. Co-II should provide a simple, rapid, and robust platform for visualizing both weak and strong protein interactions in the plasma membrane of living cells.

Protein–protein interactions govern cellular processes. The majority of these physical interactions previously identified are strong/permanent interactions, which typically remain unbroken even after purification. The weak/transient interactions between proteins have been implicated in the control of dynamic cellular process that maintain cellular homeostasis and trigger signaling cascades upon environmental changes. However, these interactions are poorly investigated, mainly due to the methodological limitations. Here, we have developed a co-immunoimmobilization assay called Co-II that enables the direct visualization of protein–protein interactions in the membrane of living cells at the single-molecule level. Co-II is based on the intuitive concept that if the protein of interest is immobilized, the interacting protein must be co-immobilized. The use of intrinsic protein diffusivity fundamentally overcomes the limitations of proximity-based methods. Using Co-II, we study the transient homodimerizations of EGFR and β2-AR in living cells, which have been implicated in several types of cancers and heart diseases. We show that the dimerization of these receptors is differently regulated by molecular conformations and the microenvironment in the plasma membrane.

Comprehensive Regression Model for Dissociation Equilibria of Cell-Specific Aptamers

A comprehensive nonlinear regression model for dissociation equilibria of cell-specific aptamers is proposed by considering the effect of receptor expression level. Benefiting from the global regression of simultaneous equations, the fitted parameters reach a very significant level, indicating the statistical validity of this updated model. According to the fitting results, we found that dissociation constants fitted using the previous model are obviously larger than the updated values, which can be explained by the effect of receptor number on curve fitting. In addition, equivalent receptor density can be estimated using the updated model, which may lead to some new judgments about reported results of cell-SELEX.

DNA nanotriangle-scaffolded activatable aptamer probe with ultralow background and robust stability for cancer theranostics

Activatable aptamers have emerged as promising molecular tools for cancer theranostics, but reported monovalent activatable aptamer probes remain problematic due to their unsatisfactory affinity and poor stability. To address this problem, we designed a novel theranostic strategy of DNA nanotriangle-scaffolded multivalent split activatable aptamer probe (NTri-SAAP), which combines advantages of programmable self-assembly, multivalent effect and target-activatable architecture.

Methods: NTri-SAAP was assembled by conjugating multiple split activatable aptamer probes (SAAPs) on a planar DNA nanotriangle scaffold (NTri). Leukemia CCRF-CEM cell line was used as the model to investigate its detection, imaging and therapeutic effect both in vitro and in vivo. Binding affinity and stability were evaluated using flow cytometry and nuclease resistance assays.

Results: In the free state, NTri-SAAP was stable with quenched signals and loaded doxorubicin, while upon binding to target cells, it underwent a conformation change with fluorescence activation and drug release after internalization. Compared to monovalent SAAP, NTri-SAAP displayed greatly-improved target binding affinity, ultralow nonspecific background and robust stability in harsh conditions, thus affording contrast-enhanced tumor imaging within an extended time window of 8 h. Additionally, NTri-SAAP increased doxorubicin loading capacity by ~5 times, which further realized a high anti-tumor efficacy in vivo with 81.95% inhibition but no obvious body weight loss.

Conclusion: These results strongly suggest that the biocompatible NTri-SAAP strategy would provide a promising platform for precise and high-quality theranostics.

Binding-induced nicking site reconstruction strategy for quantitative detection of membrane protein on living cell

Here, a binding-induced nicking site reconstruction strategy has been fabricated for quantitative detection of membrane protein on living cell. Taking protein tyrosine kinase-7 (PTK7) as model analyst, first, an aptamer probe was designed with an aptamer sequence, a trigger sequence and a nicking site. In the absence of PTK7, the aptamer sequence could partially hybridize with the trigger sequence, forming a stem-loop structure. And the two complementary sequences of the nicking site were separated, which could not be recognized by nicking enzyme. In the presence of PTK7, the aptamer probe and PTK7 binding caused the reconstruction of the probe, leading to the hybridization of the two separated nicking site sequences. Then, the nicking site could be identified and nicked, yielding the release of the trigger sequence. Next, the trigger sequence could initiate the homogeneous cascade amplification, producing multiple G-quadruplex structures. By inserting the N-Methyl Mesoporphyrin IX (NMM), enhanced fluorescence signal could be acquired. Through the binding-induced nicking site reconstruction, the trigger sequence could be released on the surface of living cell and became more accessible. By combining the cascade rolling circle amplification (RCA) and hybridization chain reaction (HCR), high sensitivity was achieved with a detection limit of 0.3 fM. Moreover, Quantitative assay of PTK7 on living cancer cells and normal cells were performed, suggesting that the proposed method was sensitive enough to detect changes in PTK7 expression. Thus, this strategy provided a novel and reliable method for membrane protein expression assay on living cell.

Aptamer/AuNP Biosensor for Colorimetric Profiling of Exosomal Proteins

Exosomes constitute an emerging biomarker for cancer diagnosis because they carry multiple proteins that reflect the origins of parent cells. Assessing exosome surface proteins provides a powerful means of identifying a combination of biomarkers for cancer diagnosis. We report a sensor platform that profiles exosome surface proteins in minutes by the naked eye. The sensor consists of a gold nanoparticle (AuNP) complexed with a panel of aptamers. The complexation of aptamers with AuNPs protects the nanoparticles from aggregating in a high-salt solution. In the presence of exosomes, the non-specific and weaker binding between aptamers and the AuNP is broken, and the specific and stronger binding between exosome surface protein and the aptamer displaces aptamers from the AuNP surface and results in AuNP aggregation. This aggregation results in a color change and generates patterns for the identification of multiple proteins on the exosome surface.

Tumor cell capture patterns around aptamer-immobilized microposts in microfluidic devices

Circulating tumor cells (CTCs) have shown potential for cancer diagnosis and prognosis. Affinity-based CTC isolation methods have been proved to be efficient for CTC detection in clinical blood samples. One of the popular choices for affinity-based CTC isolation is to immobilize capture agents onto an array of microposts in microchannels, providing high CTC capture efficiency due to enhanced interactions between tumor cells and capture agents on the microposts. However, how the cells interact with microposts under different flow conditions and what kind of capture pattern results from the interactions have not been fully investigated; a full understanding of these interactions will help to design devices and choose experimental conditions for higher CTC capture effeciency. We report our study on their interaction and cell distribution patterns around microposts under different flow conditions. Human acute lymphoblastic leukemia cells (CCRF-CEM) were used as target cancer cells in this study, while the Sgc8 aptamer that has specific binding with CCRF-CEM cells was employed as a capture agent. We investigated the effects of flow rates and micropost shapes on the cell capture efficiency and capture patterns on microposts. While a higher flow rate decreased cell capture efficiency, we found that the capture pattern around microposts also changed, with much more cells captured in the front half of a micropost than at the back half. We also found the ratio of cells captured on microposts to the cells captured by both microposts and channel walls increased as a function of the flow rate. We compared circular microposts with an elliptical shape and found that the geometry affected the capture distribution around microposts. In addition, we have developed a theoretical model to simulate the interactions between tumor cells and micropost surfaces, and the simulation results are in agreement with our experimental observation.

A label-free sensitive method for membrane protein detection based on aptamer and AgNCs transfer

Recently, membrane proteins have been considered as candidate cancer biomarkers and drug targets, due to their important roles in numerous physiological processes. Therefore, a facile, sensitive and quantitative detection of the membrane proteins is crucial for better understanding their roles in cancer cells and further validating their function in clinical research. We report a highly facile and sensitive detection method for membrane proteins on living cells in situ based on membrane protein-triggered release of cytosine (C)-rich single-stranded DNA (ssDNA) sequences, and the subsequent silver nanoclusters (AgNCs) transfer from polymer to C-rich ssDNA. The high-quantum yield and stable DNA-AgNCs allow the accurate detection of membrane proteins with facile operations and a common fluorescence spectrophotometer. The detection of protein tyrosine kinase-7 (PTK7), a membrane protein model, displays a response range from 30pM to 2nM with a detection limit of 12pM. The expression of PTK7 on single Hela cell and CCRF-CEM cell was calculated to be 7.5 × 10^-19mol and 1.8 × 10^-18mol, respectively. Given the simple and facile operation of this method, this detection platform can be applied as a universal strategy for ultrasensitive detection of membrane protein on cell in situ.

Effect of probe diffusion on the SOFI imaging accuracy

Live-cell super-resolution fluorescence imaging is becoming commonplace for exploring biological systems, though sample dynamics can affect the imaging quality. In this work we evaluate the effect of probe diffusion on super-resolution optical fluctuation imaging (SOFI), using a theoretical model and numerical simulations based on the imaging of live cells labelled with photochromic fluorescent proteins. We find that, over a range of physiological conditions, fluorophore diffusion results in a change in the amplitude of the SOFI signal. The magnitude of this change is approximately proportional to the on-time ratio of the fluorophores. However, for photochromic fluorescent proteins this effect is unlikely to present a significant distortion in practical experiments in biological systems. Due to this lack of distortions, probe diffusion strongly enhances the SOFI imaging by avoiding spatial undersampling caused by the limited labeling density.

Sensitive detection of protein biomarkers using silver nanoparticles enhanced immunofluorescence assay

Detection of biomarkers is extremely important for the early diagnosis of diseases. Here, we developed an easy and highly sensitive fluorescence detection system for the determination of biomarkers by combining the rapid separation of magnetic beads and silver nanoparticles labeled antibodies. An ultrasensitive silver ions fluorescence probe 3', 6'-bis (diethylamino)-2-(2-iodoethyl) spiro[isoindoline-1, 9'-xanthen]-3-one (Ag+-FP) was applied to immunoassay. A significant signal amplification was achieved as the AgNPs can be dissolved by H2O2 and generate numerous Ag+, which would turn "on" the fluorescence of Ag+-FP. Using α-fetoprotein (AFP) and C-reactive protein (CRP) as target analytes, good linear responses were obtained from 0.1 to 10 ng mL-1 and the limits of detection (LOD) were as low as 70 pg·mL-1 and 30 pg·mL-1, respectively. In addition, the developed system was further evaluated for the detection of real samples including 30 positive serum specimens obtained from hepatocarcinoma patients and 20 negative serum samples, and performs as well as the commercial electrochemiluminescence immunoassay (ECLI) method with less cost and more convenience. Thus, the designed detection system can be used as a promising platform for the detection of a variety of biomarkers and served as a powerful tool in clinical diagnosis.

Kinetics of receptor-mediated endocytosis of elastic nanoparticles

It is now widely recognized that mechanical properties play critical roles in the cell uptake of nanomaterials. Here we conduct a theoretical study on the kinetics of receptor-mediated endocytosis of elastic nanoparticles that is limited by receptor diffusion, specifically focusing on how the uptake rate depends on the nanoparticle stiffness and size, membrane tension and binding strength between membrane receptors and ligands grafted on the nanoparticle surface. It is shown that, while soft nanoparticles are energetically less prone to full wrapping than stiff ones, the wrapping of the former is kinetically faster than that of the latter. Spherical and cylindrical elastic nanoparticles show dramatic differences in the effect of stiffness on the uptake rate. Additional theoretical analysis is performed to investigate the role of the stochastic receptor-ligand binding in the endocytosis of elastic nanoparticles. The relation between the uptake efficiency and uptake proneness is discussed. This study provides new insight into the elasticity effects on cell uptake and may serve as a design guideline for the controlled endocytosis and diagnostics delivery.

Development of a DNA aptamer that binds specifically to group A Streptococcus serotype M3

Group A streptococcus (GAS) is an important Gram-positive pathogen that causes various human diseases ranging from peripheral lesions to invasive infections. The M protein is one of the main virulence factors present on the cell surface and is associated with invasive GAS infections. Compared with other M types, serotype M3 has a predominant role in lethal infections and demonstrates epidemic behaviors, including streptococcal toxic shock syndrome, bacteremia, and necrotizing fasciitis. Traditional methods for M typing are time-consuming, tedious, contradictory, and generally restricted to reference laboratories. Therefore, development of a new M-typing technique is needed. Aptamers with the ability to detect their target with a high degree of accuracy and specificity can be ideal candidates for specific M-typing of Streptococcus pyogenes. In this study DNA aptamers with a high binding affinity towards S. pyogenes serotype M3 were selected through 12 iterative rounds of the Systematic Evolution of Ligands by EXponential (SELEX) enrichment procedure using live cells as a target. We monitored the progress of the SELEX procedure by flow cytometry analysis. Of several aptamer sequences analyzed, 12L18A showed the highest binding efficiency towards S. pyogenes type M3, with an apparent dissociation constant (K_d) of 7.47 ± 1.72 pmol/L being the lowest. Therefore the isolated aptamer can be used in any tool, such as a biosensor, for the detection of S. pyogenes and can be used in the development of a novel M-typing system.

Luminescence switch-on assay of interferon-gamma using a G-quadruplex-selective iridium(III) complex

In this study, we synthesized a series of 9 luminescent iridium(III) complexes and studied their ability to function as luminescent probes for G-quadruplex DNA. The iridium(III) complex 8 [Ir(pbtz)2(dtbpy)]PF6 (where pbtz = 2-phenylbenzo[d]thiazole; dtbpy = 4,4'-di-tert-butyl-2,2'-bipyridine) showed high selectivity for G-quadruplex DNA over single-stranded and double-stranded DNA, and was subsequently utilized for the development of a label-free oligonucleotide-based assay for interferon-gamma (IFN-γ), an important biomarker for a range of immune and infectious diseases, in aqueous solution. We further demonstrated that this assay could monitor IFN-γ levels even in the presence of cellular debris. This assay represents the first G-quadruplex-based assay for IFN-γ detection described in the literature.

Live cell imaging shows hepatocyte growth factor-induced Met dimerization

The canonical model of receptor tyrosine kinase (RTK) activation assumes that ligand-induced dimerization of inactive receptor monomers is a prerequisite for autophosphorylation. For several RTK families, recent results of fluorescence microscopy provided evidence for preformed receptor dimers that may or may not require ligand binding for kinase activity. Here we report, for the first time, the application of advanced quantitative fluorescence microscopy techniques to study changes in the oligomerization state of the RTK Met in response to stimulation by its endogenous ligand hepatocyte growth factor (HGF). We used inducible C-terminal fusions between Met and enhanced green fluorescent protein (EGFP) or red fluorescent protein (RFP) in combination with fluorescence resonance energy transfer (FRET)-based fluorescence-lifetime imaging microscopy (FLIM) and fluorescence correlation spectroscopy (FCS). A small fraction of HGF-independent Met dimers appeared to be present in cells even at low receptor density. At high receptor density, both the fraction of Met dimers and the level of Met autophosphorylation increased in the absence of HGF. Stimulation with HGF at low receptor density significantly increased the fraction of Met dimers on live cells. We found no indications of Met oligomers larger than dimers. Our findings thus confirm a model of Met activation through HGF-induced dimerization and at the same time they support previous reports of Met dimers in unstimulated cells. The tools established in this work will be useful to further characterize the mechanism of Met activation and to define the contribution of co-receptors.

Generating Cell Targeting Aptamers for Nanotheranostics Using Cell-SELEX

Detecting and understanding changes in cell conditions on the molecular level is of great importance for the accurate diagnosis and timely therapy of diseases. Cell-based SELEX (Systematic Evolution of Ligands by EXponential enrichment), a foundational technology used to generate highly-specific, cell-targeting aptamers, has been increasingly employed in studies of molecular medicine, including biomarker discovery and early diagnosis/targeting therapy of cancer. In this review, we begin with a mechanical description of the cell-SELEX process, covering aptamer selection, identification and identification, and aptamer characterization; following this introduction is a comprehensive discussion of the potential for aptamers as targeting moieties in the construction of various nanotheranostics. Challenges and prospects for cell-SELEX and aptamer-based nanotheranostic are also discussed.

Simulation and Theory of Antibody Binding to Crowded Antigen-Covered Surfaces

In this paper we introduce a fully flexible coarse-grained model of immunoglobulin G (IgG) antibodies parametrized directly on cryo-EM data and simulate the binding dynamics of many IgGs to antigens adsorbed on a surface at increasing densities. Moreover, we work out a theoretical model that allows to explain all the features observed in the simulations. Our combined computational and theoretical framework is in excellent agreement with surface-plasmon resonance data and allows us to establish a number of important results. (i) Internal flexibility is key to maximize bivalent binding, flexible IgGs being able to explore the surface with their second arm in search for an available hapten. This is made clear by the strongly reduced ability to bind with both arms displayed by artificial IgGs designed to rigidly keep a prescribed shape. (ii) The large size of IgGs is instrumental to keep neighboring molecules at a certain distance (surface repulsion), which essentially makes antigens within reach of the second Fab always unoccupied on average. (iii) One needs to account independently for the thermodynamic and geometric factors that regulate the binding equilibrium. The key geometrical parameters, besides excluded-volume repulsion, describe the screening of free haptens by neighboring bound antibodies. We prove that the thermodynamic parameters govern the low-antigen-concentration regime, while the surface screening and repulsion only affect the binding at high hapten densities. Importantly, we prove that screening effects are concealed in relative measures, such as the fraction of bivalently bound antibodies. Overall, our model provides a valuable, accurate theoretical paradigm beyond existing frameworks to interpret experimental profiles of antibodies binding to multi-valent surfaces of different sorts in many contexts.

Antibodies are the main working horses of the human immune system. Remarkably, no matter the size or the shape of the pathological intruders, these extremely flexible three-lobe molecules are able to form a complex, thus eliciting an immune response. What makes antibodies so effective? To answer this and other questions, we have developed a simplified computational scheme to simulate the dynamics of many antibodies interacting with each other and with antigens. Coarse-grained models are a great opportunity, as they give access to a true multi-scale approach to biologically relevant problems. In this work, our innovative method allowed us to simulate the binding process of many antibodies to surface-adsorbed antigens. This led us to elucidate and quantify many important physical aspects of their biological function in agreement with experiments, such as the role of their flexibility and crowding effects at the hapten-covered surface, which were shown to finely regulate the avidity.

A polydopamine nanosphere based highly sensitive and selective aptamer cytosensor with enzyme amplification

With CCRF-CEM as the model cell, a highly sensitive and selective cytosensor was developed by taking advantage of polydopamine nanospheres for the first time. The strategies of aptamer/membrane protein recognition and Exonuclease III assisted cycle amplification were used for improving selectivity and sensitivity. The detection of limit reached was as low as 15 cells per mL.

Luminescence switch-on detection of protein tyrosine kinase-7 using a G-quadruplex-selective probe

A series of luminescent iridium(iii) complexes were synthesised and evaluated for their ability to act as luminescent G-quadruplex-selective probes. The iridium(iii) complex 9 [Ir(pbi)2(5,5-dmbpy)]PF6 (where pbi = 2-phenyl-1H-benzo[d]imidazole; 5,5-dmbpy = 5,5'-dimethyl-2,2'-bipyridine) exhibited high luminescence for G-quadruplex DNA compared to dsDNA and ssDNA, and was employed to construct a G-quadruplex-based assay for protein tyrosine kinase-7 (PTK7) in aqueous solution. PTK7 is an important biomarker for a range of leukemias and solid tumors. In the presence of PTK7, the specific binding of the sgc8 aptamer sequence triggers a structural transition and releases the G-quadruplex-forming sequence. The formation of the nascent G-quadruplex structure is then detected by the G-quadruplex-selective iridium(iii) complex with an enhanced luminescent response. Moreover, the application of the assay for detecting PTK7 in cellular debris and membrane protein extract was demonstrated. To our knowledge, this is the first G-quadruplex-based assay for PTK7.

Structure-Switching Aptamer Triggering Hybridization Chain Reaction on the Cell Surface for Activatable Theranostics

The ability to probe low-abundance biomolecules or transport a high-load drug in target cells is essential for biology and theranostics. We develop a novel activatable theranostic approach by using a structure-switching aptamer triggered hybridization chain reaction (HCR) on the cell surface, which for the first time creates an aptamer platform enabling real-time activation and amplification for fluorescence imaging and targeting therapy. The aptamer probe is designed not to initiate HCR in its free state but trigger HCR on binding to the target cell via structure switching. The HCR not only amplifies fluorescence signals from a fluorescence-quenched probe for activatable tumor imaging but also accumulates high-load prodrugs from a drug-labeled probe and induces its uptake and conversion into cisplatin in cells for selective tumor therapy. An in vitro assay shows that this approach affords efficient signal amplification for fluorescence detection of target protein tyrosine kinase-7 (PTK7) with a detection limit of 1 pM. Live cell studies reveal that it provides high-contrast fluorescence imaging and highly sensitive detection of tumor cells, while renders high-efficiency drug delivery into tumor cells via an endocytosis pathway. The results imply the potential of the developed approach as a promising platform for early stage diagnosis and precise therapy of tumors.

Nucleic acid aptamers for living cell analysis

Cells as the building blocks of life determine the basic functions and properties of a living organism. Understanding the structure and components of a cell aids in the elucidation of its biological functions. Moreover, knowledge of the similarities and differences between diseased and healthy cells is essential to understanding pathological mechanisms, identifying diagnostic markers, and designing therapeutic molecules. However, monitoring the structures and activities of a living cell remains a challenging task in bioanalytical and life science research. To meet the requirements of this task, aptamers, as "chemical antibodies," have become increasingly powerful tools for cellular analysis. This article reviews recent advances in the development of nucleic acid aptamers in the areas of cell membrane analysis, cell detection and isolation, real-time monitoring of cell secretion, and intracellular delivery and analysis with living cell models. Limitations of aptamers and possible solutions are also discussed.

Highly sensitive and homogeneous detection of membrane protein on a single living cell by aptamer and nicking enzyme assisted signal amplification based on microfluidic droplets

Membrane proteins play vital roles in numerous physiological functions. Recently, they have been considered as candidate biomarkers for cancer and recognized as major drug targets. So, accurate, sensitive, and high-throughput quantitative detection of the membrane proteins is crucial for better understanding their roles in cancer cells and further validating their function in clinical research. Here, we report a highly sensitive and homogeneous detection of membrane protein on single living cells by aptamer and nicking enzyme assisted fluorescence signal amplification in microfluidic droplets. The homogeneous reaction based on the membrane protein-triggered conformation alteration of hairpin probe can improve the detection accuracy with elimination of several washing and separation steps. The microfluidic system provides a high-throughput platform for the detection of a single cell, and the highly monodisperse droplet can function as an independent microreactor for the aptamer and nicking enzyme assisted fluorescence signal amplification, coordinating with the small volume of the confined space (a droplet), increased reaction rate, and highly sensitive detection of membrane protein on single cell can be reached.

Recent applications of fluorescence correlation spectroscopy in live systems

Fluorescence correlation spectroscopy (FCS) is a widely used technique in biophysics and has helped address many questions in the life sciences. It provides important advantages compared to other fluorescence and biophysical methods. Its single molecule sensitivity allows measuring proteins within biological samples at physiological concentrations without the need of overexpression. It provides quantitative data on concentrations, diffusion coefficients, molecular transport and interactions even in live organisms. And its reliance on simple fluorescence intensity and its fluctuations makes it widely applicable. In this review we focus on applications of FCS in live samples, with an emphasis on work in the last 5 years, in the hope to provide an overview of the present capabilities of FCS to address biologically relevant questions.

Role of nanoparticle geometry in endocytosis: laying down to stand up

Nanoparticles (NPs) hold great promises for targeted disease diagnosis and therapy. Despite considerable progress in biomimetic design of NP-bioconjugates, the roles of NP size and shape in endocytosis are still not fully understood. Using an efficient coarse-grained molecular dynamics (CGMD) model, we simulate receptor-mediated endocytosis of NPs of various sizes and shapes. Our simulations demonstrate that both NP size and shape modulate the kinetics of endocytosis. For spherical NPs, there exists an optimal size at which endocytosis takes the shortest time. For a spherocylindrical NP with the initial upright docking position on the membrane plane, endocytosis proceeds through a laying-down-then-standing-up sequence. A free energy analysis reveals that NP size primarily determines whether endocytosis can complete, while NP shape breaks the symmetry of curvature energy landscape and hence dictates the endocytic pathway and the angle of entry. The findings shed light on the rational design of NP-based diagnostic and therapeutic agents with improved cellular targeting.