antibody-DNA Conjugates Research Articles

Simultaneous detection of membrane protein and mRNA at single extracellular vesicle level by droplet microfluidics for cancer diagnosis

IntroductionSimultaneous detection of proteins and mRNA within a single extracellular vesicle (EV) enables comprehensive analysis of specific EVs subpopulations, significantly advancing cancer diagnostics. However, developing a sensitive and user-friendly approach for simultaneously detecting multidimensional biomarkers in single EV is still challenging. ObjectivesTo facilitate the analysis of multidimensional biomarkers in EVs and boost its clinical application, we present a versatile droplet digital system facilitating the concurrent detection of membrane proteins and mRNA at the single EV level with high sensitivity and specificity. MethodsThe antibody-DNA conjugates were firstly prepared for EVs protein biomarkers recognition and signal transformation. Coupling with the assembled triplex droplet digital PCR system, a versatile droplet digital analysis assay for simultaneous detection of membrane protein and mRNA at a single EV level was developed. ResultsOur new droplet digital system displayed high sensitivity and specificity. Additionally, its clinical application was validated in a breast cancer cohort. As expected, this assay has demonstrated superior performance in distinguishing breast cancer from healthy individuals and benign controls through combined detection of EVs protein and mRNA markers compared to any single kind marker detections, especially for patients with breast cancer at early stage (AUC=0.9229). ConclusionConsequently, this study proposes a promising strategy for accurately identifying and analyzing specific EV subgroups through the co-detection of proteins and mRNA at the single EV level, holding significant potential for future clinical applications.

Multiplexed in situ protein imaging using DNA-barcoded antibodies with extended hybridization chain reactions.

Antibodies have long served as vital tools in biological and clinical laboratories for the specific detection of proteins. Conventional methods employ fluorophore or horseradish peroxidase-conjugated antibodies to detect signals. More recently, DNA-conjugated antibodies have emerged as a promising technology, capitalizing on the programmability and amplification capabilities of DNA to enable highly multiplexed and ultrasensitive protein detection. However, the nonspecific binding of DNA-conjugated antibodies has impeded the widespread adoption of this approach. Here, we present a novel DNA-conjugated antibody staining protocol that addresses these challenges and demonstrates superior performance in suppressing nonspecific signals compared to previously published protocols. We further extend the utility of DNA-conjugated antibodies for signal-amplified in situ protein imaging through the hybridization chain reaction (HCR) and design a novel HCR DNA pair to expand the HCR hairpin pool from the previously published 5 pairs to 13, allowing for flexible hairpin selection and higher multiplexing. Finally, we demonstrate highly multiplexed in situ protein imaging using these techniques in both cultured cells and tissue sections.

Sensitive detection of multiple blood biomarkers via immunomagnetic exosomal PCR for the diagnosis of Alzheimer's disease.

Blood exosomes are emerging as potential biomarkers for diagnosing brain diseases such as Alzheimer's disease (AD). There is currently a lack of an ultrasensitive technology for identifying core AD biomarkers in blood exosomes to optimize the utility of biomarkers in clinical practice. Here, an immunomagnetic exosomal polymerase chain reaction (iMEP) platform was developed using DNA-conjugated antibodies for the rapid detection of amyloid-β (Aβ1-40 and Aβ1-42) and phosphorylated tau (p-tau396,404 and p-tau181) in clinical blood exosomes. The toehold shift-mediated DNA affinity pulldown eliminates the high detection background, which allows the detection of biomarkers at concentrations down to 10 femtograms per milliliter. With the iMEP assay, exosomal Aβ1-42 was more accurate in differentiating patients with AD from healthy individuals compared with exosomal p-tau181 and p-tau396,404, with a sensitivity of 95.0% and a specificity of 95.0%. The iMEP technique is also adept at quantifying the levels of different exosomal biomarkers associated with disease pathogenesis.

Abstract 6169: High throughput in-situ spatial sequencing of proteins and RNA in FFPE tissue

Abstract We have developed an high throughput high resolution in situ multi-omic platform to enable studies in the rapidly evolving landscape of oncology and immunology research. Despite the potential of existing tools, the speed and throughput of current methodologies pose significant limitations. Here, we introduce a novel spatial sequencing platform employing a rapid 4-color SBS chemistry with sub-micron resolution imaging and an ultra-high throughput capacity. The platform simultaneously profiles RNA transcripts and proteins within formalin-fixed paraffin-embedded (FFPE) tissues. With up to 40 cm^2 of tissue area imaging within a 24-hour timeframe, the platform can power extensive, multi-omic studies in cancer research. To evaluate the performance of the platform, we prepared 5 um serial sections from healthy and tumor kidney FFPE block and used a novel tool to precisely position multiple tissue sections on a slide. Following probe binding and amplification, we used SBS readout to profile 105 transcripts and 6 proteins (via DNA-conjugated antibodies). Images were analyzed using a custom pipeline for feature detection and decoding, and cell segmentation using Cellpose. Results showed strong correlation to single-cell transcription profiles and cell type signatures defined by scRNA-Seq. Additionally, we see good agreement between single cell transcript and protein profiles. Existing spatial biology platforms are known to struggle with degraded and challenging clinical sample types (e.g. decalcified bone marrow), due to RNA fragmentation. We successfully profiled immune cells in FFPE-embedded bone marrow biopsies, measuring 143 transcript targets and 8 proteins. We believe this represents a significant step forward for in-situ analysis of bone marrow samples, and could be valuable for studying the pathology and response to treatment in blood cancers such as AML and CML. In-situ sequencing of antibody genes and T-cell receptors provides a deeper view of cellular immune response. As a step towards this goal, we demonstrated in-situ sequencing of antibody heavy and light chains within a B cell line, resulting in accurate readout of 28 bases within the CDR3 regions. In conclusion, we present an SBS-based approach for in-situ detection of targeted gene transcripts and proteins at an unprecedented throughput, and its application to the analysis of human kidney and bone marrow FFPE tissue samples. The capability to deeply profile tissues at high throughput could enable larger translational studies, and assembly of 3D maps of gene and protein expression at sub-cellular resolution. Citation Format: Michael Lawson, Yuji Ishitsuka, Andrew Pawlowski, Zhenmin Hong, Jake Koh, Kenneth Gouin, Nathan Ing, Richard Que, Yeoan Youn, Sara Ding, Tony Facchini, Ryan Costello, Katelyn Nelson, Jamie Stover, Howon Lee, Sarthak Duggal, Taylor Plaziak, Kaitlin Cameron, Mimi Abdu, Daan Witters, Martin Fabani, Eli Glezer. High throughput in-situ spatial sequencing of proteins and RNA in FFPE tissue [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 6169.

Proximity Sequencing Enables Measurement of Protein Complexes in Single Cells.

Advances in single-cell sequencing technology have transformed our understanding of cellular heterogeneity and identity, providing insight on topics ranging from the diversity of microbial ecosystems to tumor biological behaviors. However, accurate measurement of protein complexes in single cells remains challenging as relatively few proteins can form large numbers of complexes that must be distinguished accurately. The inability to accurately differentiate protein complexes hinders in-depth study of critical biological functions such as immune signaling and cellular differentiation. In a recent article in Nature Methods, Vistain et al. (1) present a solution to this problem by combining proximity ligation assay (PLA) with single-cell RNA sequencing (scRNA-seq). This method, which they call proximity sequencing (Prox-seq), can measure hundreds of protein complexes and mRNAs in single cells simultaneously. Prox-seq introduces pairs of DNA-conjugated antibodies to single-cell sequencing methods. When proteins enter a complex, the DNA oligomers on the antibodies come into proximity and are ligated. These ligated DNA oligomers (PLA products) are then sequenced to retrieve protein complex information. Prox-seq also generates transcriptome data through mRNA sequencing, allowing multimodal analyses of single cells. To validate this assay, the authors first demonstrated Prox-seq’s ability to differentiate T and B cells in a mixed population using probes designed for 11 cell-specific protein targets. Prox-seq measurements showed that T and B cells could be accurately differentiated using mRNAs, proteins, or total PLA products. An orthogonal method of flow cytometry was used to confirm that the enriched PLA products in each cell type were cell-specific proteins. This confirmed that PLA products can be measured using scRNA-seq, and PLA data displays cell type-specific differences in protein expression. Quantification of protein expression analysis in the same cell types with a different panel of 13 Prox-seq probes showed high correlation with flow cytometry which confirmed accurate protein characterization and quantification by Prox-seq in single cells. The authors also tested Prox-seq’s ability to measure large numbers of protein complexes in 8700 human peripheral blood mononuclear cells with a panel of probe pairs targeting 38 immune cell markers, and up to 741 unique protein complexes. The data showed 37 protein complexes and measurements identifying the expected cell types. In addition, they identified a novel CD8 and CD9 interaction in naïve CD8 T cells. Lastly, authors demonstrated that the assay can identify variability of receptor components in individual human macrophages after activation of an innate immunity signaling pathway by measuring PLA products detected within a panel designed for 15 pathway-specific protein targets.

An Electrochemical Proximity Assay (ECPA) Based Sensor for Antibody Detection

Biomarker detection is vitally important for disease diagnosis. Critical biomarkers which are present in ultra-low concentrations in body fluids have been detected with immunoassays such as ELISA and improved versions such as Alpha-LISA and digital ELISA. Although these techniques have fM-pM range detection limits, the requirement of special instruments, reagents, and labor-intensive workflows have directed researchers to develop simpler assay techniques. The ideal alternative assay will be cost effective, with simple mix-and-read workflows, yet will not compromise its specificity and sensitivity. Analyte-driven hybridization of short complementary DNA strands have gained substantial attention for these reasons. Molecular pincer assays and proximity ligation assays (PLA) have successfully demonstrated sensitivities comparable to ELISA, using antibody-DNA conjugates. These techniques rely on fluorescence detection, which is sensitive and specific, but is challenging in terms of miniaturization and point-of-care (POC) use. Electrochemical (EC) detection, on the contrary, can be easily miniaturized and employs simple instrumentation with high sensitivity. We have previously introduced the electrochemical proximity assay (ECPA), where insulin and thrombin have been detected at fM or pM concentrations, respectively. ECPA leverages target driven hybridization of a methylene blue (redox reporter) tagged DNA to a thiolated DNA attached to a gold surface. In this work, we have developed a novel assay for antibody detection, leveraging the ECPA concept. Here, simultaneous binding of recognition elements to paratopes of the antibody results in hybridization of methylene blue (MB) tagged DNA to thiolated-DNA (see schematic), and generated current is proportional to the antibody concentration. Using free-solution, thermoflourimetric analysis (TFA) of similar strands, we showed that probe flexibility is very important for sensor response, where ssDNA with polyethylene glycol (PEG) linkers improved sensitivities significantly. Using information from TFA, we used the same modification and demonstrated that analyte-dependent EC current was increased after ssDNA attachments to the electrode were substituted with more flexible PEG linkers (see data). This modification was introduced to both the MB-DNA and thiolated-DNA, allowing direct antibody sensing of 45 nM. With optimization in the near future, this new ECPA-based antibody sensor should be useful for clinical monitoring of the immune response. Figure 1

A method for Boolean analysis of protein interactions at a molecular level

Determining the levels of protein–protein interactions is essential for the analysis of signaling within the cell, characterization of mutation effects, protein function and activation in health and disease, among others. Herein, we describe MolBoolean – a method to detect interactions between endogenous proteins in various subcellular compartments, utilizing antibody-DNA conjugates for identification and signal amplification. In contrast to proximity ligation assays, MolBoolean simultaneously indicates the relative abundances of protein A and B not interacting with each other, as well as the pool of A and B proteins that are proximal enough to be considered an AB complex. MolBoolean is applicable both in fixed cells and tissue sections. The specific and quantifiable data that the method generates provide opportunities for both diagnostic use and medical research.

Protein-Templated Reactions Using DNA-Antibody Conjugates.

DNA-templated chemical reactions have found wide applications in drug discovery, programmed multistep synthesis, nucleic acid detection, and targeted drug delivery. The control of these reactions has, however, been limited to nucleic acid hybridization as a means to direct the proximity between reactants. In this work a system capable of translating protein-protein binding events into a DNA-templated reaction which leads to the covalent formation of a product is introduced. Protein-templated reactions by employing two DNA-antibody conjugates that are both able to recognize the same target protein and to colocalize a pair of reactant DNA strands able to undergo a click reaction are achieved. Two individual systems, each responsive to human serum albumin (HSA) and human IgG, are engineered and it is demonstrated that, while no reaction occurs in the absence of proteins, both protein-templated reactions can occur simultaneously in the same solution without any inter-system crosstalk.

A capillary-driven LoC-SERS device integrated with catalytic hairpin assembly amplification technology for NSCLC-related biomarkers detection.

In this study, we apply catalytic hairpin assembly (CHA) as the signal amplification strategy for the quantification of carcinoembryonic antigen (CEA) and cytokeratin fragment antigen 21-1 (CYFRA21-1) with a surface-enhanced Raman scattering (SERS) microfluidic chip (LoC-SERS) as the carrier. Herein, antibody-DNA conjugates are designed to assist the application of CHA amplification in protein detection. In the presence of protein biomarkers, antibody-DNA conjugates can specifically bind to the target proteins, forming the antigen@antibody-DNA conjugates. The terminal free part of the DNA on the conjugates can trigger the CHA events to connect SERS nanotags to capture nanoprobes. Then, micro-magnet can gather the CHA products in a rectangular chamber, resulting in the aggregation of SERS nanotags, which can ultimately generate abundant "hot spots" for SERS signal enhancement. Using this strategy, CEA and CYFRA21-1 can be successfully determined with a limit of detection (LOD) as low as pg mL-1, much lower than recently reported methods. Meanwhile, a non-small cell lung cancer (NSCLC)-xenografted mouse model was established, and SERS was applied to analyze the expression level of CEA and CYFRA21-1 in tumorigenesis and development. The comparison between SERS results and those of the ELISA method demonstrated a high degree of consistency, suggesting that the proposed CHA-assisted LoC-SERS device has satisfying accuracy. Thus, introducing the CHA strategy via the design of antibody-DNA conjugates opens new gates to ultra-sensitive and specific SERS detection of protein biomarkers.

Highly Sensitive Immuno-CRISPR Assay for CXCL9 Detection.

CRISPR-based detection of target DNA or RNA exploits a dual function, including target sequence-specific recognition followed by trans-cleavage activity of a collateral ssDNA linker between a fluorophore (F) and a quencher (Q), which amplifies a fluorescent signal upon cleavage. In this work, we have extended such dual functionality in a modified immunoassay format to detect a target protein, CXCL9, which is markedly elevated in the urine of kidney transplant recipients undergoing acute rejection episodes. To establish the "immuno-CRISPR" assay, we used anti-CXCL9 antibody-DNA barcode conjugates to target CXCL9 and amplify fluorescent signals via Cas12a-based trans-cleavage activity of FQ reporter substrates, respectively, and in the absence of an isothermal amplification step. To enhance detection sensitivity, the DNA barcode system was engineered by introducing multiple Cas12a recognition sites. Use of biotinylated DNA barcodes enabled self-assembly onto streptavidin (SA) to generate SA-DNA barcode complexes to increase the number and density of Cas12a recognition sites attached to biotinylated anti-CXCL9 antibody. As a result, we improved the rate of CXCL9 detection approximately 8-fold when compared to the use of a monomeric DNA barcode. The limit of detection (LOD) for CXCL9 using the immuno-CRISPR assay was 14 pg/mL, which represented an ∼7-fold improvement when compared to traditional HRP-based ELISA. Selectivity was shown with a lack of crossover reactivity with the related chemokine CXCL1. Finally, we successfully evaluated the presence of CXCL9 in urine samples from 11 kidney transplant recipients using the immuno-CRISPR assay, resulting in 100% accuracy to clinical CXCL9 determination and paving the way for use as a point-of-care noninvasive biomarker for the detection of kidney transplant rejection.

A Rolling Circle-Amplified G-Quadruplex/Hemin DNAzyme for Chemiluminescence Immunoassay of the SARS-CoV-2 Protein.

Sensitive detection of the SARS-CoV-2 protein remains a great research interest in clinical screening and diagnosis owing to the coronavirus epidemic. Here, an ultrasensitive chemiluminescence (CL) imaging strategy was developed through proximity hybridization to trigger the formation of a rolling circle-amplified G-quadruplex/hemin DNAzyme for the detection of the SARS-CoV-2 protein. The target protein was first recognized by a pair of DNA–antibody conjugates, Ab-1 and Ab-2, to form a proximity-ligated complex, Ab-1/SARS-CoV-2/Ab-2, which contained a DNA sequence complemental to block DNA and thus induced a strand displacement reaction to release the primer from a block/primer complex. The released primer then triggered a rolling circle amplification to form abundant DNAzyme units in the presence of hemin, which produced a strong chemiluminescent signal for the detection of the target protein by catalyzing the oxidation of luminol by hydrogen peroxide. The proposed assay showed a detectable concentration range over 5 orders of magnitude with the detection limit down to 6.46 fg/mL. The excellent selectivity, simple procedure, acceptable accuracy, and intrinsic high throughput of the imaging technique for analysis of serum samples demonstrated the potential applicability of the proposed detection method in clinical screening and diagnosis.

CODEX multiplexed tissue imaging with DNA-conjugated antibodies.

Advances in multiplexed imaging technologies have drastically improved our ability to characterize healthy and diseased tissues at the single-cell level. Co-detection by indexing (CODEX) relies on DNA-conjugated antibodies and the cyclic addition and removal of complementary fluorescently labeled DNA probes and has been used so far to simultaneously visualize up to 60 markers in situ. CODEX enables a deep view into the single-cell spatial relationships in tissues and is intended to spur discovery in developmental biology, disease and therapeutic design. Herein, we provide optimized protocols for conjugating purified antibodies to DNA oligonucleotides, validating the conjugation by CODEX staining and executing the CODEX multicycle imaging procedure for both formalin-fixed, paraffin-embedded (FFPE) and fresh-frozen tissues. In addition, we describe basic image processing and data analysis procedures. We apply this approach to an FFPE human tonsil multicycle experiment. The hands-on experimental time for antibody conjugation is ~4.5 h, validation of DNA-conjugated antibodies with CODEX staining takes ~6.5 h and preparation for a CODEX multicycle experiment takes ~8 h. The multicycle imaging and data analysis time depends on the tissue size, number of markers in the panel and computational complexity.

Antibody Arrays: Barcode Technology.

Antibody microarray is a fundamental, high-content technology for analyzing biomarkers with a multiplexity even at the proteomic level. Recent advancement in this field has driven the antibody array into a new territory related with single-cell analysis. Here we describe a flow pattern-based method for producing a high-density barcode antibody microarray for the detection of proteins in fluidic samples and in single cells. The antibody microarray is fabricated by a perpendicularly oriented flow patterning of single-stranded barcode DNAs, which are then converted into DNA-antibody conjugates. Compared to conventional microarrays, this barcode antibody microarray features a simple and high-throughput assay while achieving both high sensitivity and specificity. This barcode technology provides new clues for developing next-generation antibody microarrays and can be widely used in protein biomarker discovery, cell signaling network analysis, and disease diagnosis and prognosis.

Single Extracellular Vesicle Protein Analysis Using Immuno-Droplet Digital Polymerase Chain Reaction Amplification.

There is a need for novel analytical techniques to study the composition of single extracellular vesicles (EV). Such techniques are required to improve the understanding of heterogeneous EV populations, to allow identification of unique subpopulations, and to enable earlier and more sensitive disease detection. Because of the small size of EV and their low protein content, ultrahigh sensitivity technologies are required. Here, an immuno-droplet digital polymerase chain reaction (iddPCR) amplification method is described that allows multiplexed single EV protein profiling. Antibody-DNA conjugates are used to label EV, followed by stochastic microfluidic incorporation of single EV into droplets. In situ PCR with fluorescent reporter probes converts and amplifies the barcode signal for subsequent read-out by droplet imaging. In these proof-of-principle studies, it is shown that multiplex protein analysis is possible in single EV, opening the door for future analyses.

Facile incorporation of DNA-templated quantum dots for sensitive electrochemical detection of the oral cancer biomarker interleukin-8.

Recent studies reveal a great value of interleukin-8 (IL-8), a pro-inflammatory cytokine, as a potent biomarker for early diagnosis of oral cancer. Herein, a new electrochemical method is proposed to detect IL-8 by facilely incorporating DNA-templated quantum dots (QDs). In principle, target IL-8 is first treated with the reducing agent tris(2-carboxyethyl)phosphine (TCEP) to yield active thiols and then captured by antibody-functionalized magnetic beads (MBs). Thereafter, via the Michael addition reaction between the active thiol and maleimide group, a maleimide-modified DNA probe is linked to the surface of MBs, which can initiate a process of rolling circle amplification. In this way, long-range DNA strands are generated on the MB surface, subsequently recruiting DNA-templated CdTe/CdS QDs (DNA-QDs) to act as electrochemical reporters. By tracing the responses of DNA-QDs, the method allows IL-8 detection in a linear range from 5 to 5000fg/mL with a detection limit of 3.36fg/mL. The selectivity, reproducibility, and applicability in complex serum samples are also demonstrated to be favorable, indicating that the method may have a great potential in the future. More importantly, the use of TCEP treatment in the method not only provides a facile way to incorporate DNA-QDs, avoiding the complicated and time-consuming preparation process of antibody-DNA conjugates or functional nanomaterials; but also makes the method capable of being extended to detect other protein biomarkers in view of widespread presence of disulfides, which may hold a broad potential to facilitate efficient biosensing designs.

Development of a Linker-Mediated Immunoassay Using Chemically Transitioned Nanosensors.

Sensitive and specific quantification of protein biomarkers is important in medical diagnostics, academic research, and pharmaceutical development. However, multiple binding steps in conventional sandwich immunoassay protocols result in high assay hands-on-time and delayed results. This is particularly relevant for medical diagnostics, where assay turn-around-time can have an immense impact on patient outcomes. To address this limitation, we report the assembly of nanosensors prepared using DNA-antibody conjugates, which combine capture and detection antibody binding steps by facilitating rapid antigen capture. Following antigen binding, detection antibodies are released using chemically induced complex rearrangement. A panel of 12 chemical additives are characterized to identify melting point depressants capable of rapidly denaturing double stranded DNA (dsDNA) linkers, and 8 compounds are demonstrated to be capable of disrupting dsDNA while maintaining the integrity of protein binding. This technique is then validated for the measurement of the heart attack indicator cardiac troponin I and is shown to successfully combine antigen binding steps while also increasing detection sensitivity 42×. Linker-mediated immunoassays are also demonstrated to provide robust quantification in human serum and are shown to be compatible with each of the most commonly used immunoassay detection modalities.

Fast and Efficient Fc-Specific Photoaffinity Labeling To Produce Antibody-DNA Conjugates.

Antibody-DNA conjugates are powerful tools for DNA-assisted protein analysis. Growing usage of these methods demands efficient production of high-quality conjugates. We developed an easy and fast synthesis route yielding covalent antibody-DNA conjugates with a defined conjugation site and low batch-to-batch variability. We utilize the Z domain from protein A, containing the unnatural amino acid 4-benzoylphenylalanine (BPA) for photoaffinity labeling of the antibodies' Fc region. Z(xBPA) domains are C-terminally modified with triple-glycine (G3)-modified DNA-oligonucleotides via enzymatic Sortase A coupling. We show reliable modification of the most commonly used IgG's. To prove our conjugates' functionality, we detected antibody-antigen binding events in an assay called Droplet Barcode Sequencing for Protein analysis (DBS-Pro). It confirms not only retained functionality for both conjugate parts but also the potential of using DBS-Pro for quantifying protein abundances. As intermediates are easily storable and our approach is modular, it offers a convenient strategy for screening various antibody-DNA conjugates using the same starting material.

Profiling surface proteins on individual exosomes using a proximity barcoding assay

Exosomes have been implicated in numerous biological processes, and they may serve as important disease markers. Surface proteins on exosomes carry information about their tissues of origin. Because of the heterogeneity of exosomes it is desirable to investigate them individually, but this has so far remained impractical. Here, we demonstrate a proximity-dependent barcoding assay to profile surface proteins of individual exosomes using antibody-DNA conjugates and next-generation sequencing. We first validate the method using artificial streptavidin-oligonucleotide complexes, followed by analysis of the variable composition of surface proteins on individual exosomes, derived from human body fluids or cell culture media. Exosomes from different sources are characterized by the presence of specific combinations of surface proteins and their abundance, allowing exosomes to be separately quantified in mixed samples to serve as markers for tissue-specific engagement in disease.

Antibody-Functional Microsphere-Integrated Filter Chip with Inertial Microflow for Size-Immune-Capturing and Digital Detection of Circulating Tumor Cells.

Circulating tumor cells (CTCs) in blood is the direct cause of tumor metastasis. The isolation and detection of CTCs in the whole blood is very important and of clinical value in early diagnosis, postoperative review, and personalized treatment. It is difficult to separate all types of CTCs that efficiently rely on a single path due to cancer cell heterogenicity. Here, we designed a new kind of "filter chip" for the retention of CTCs with very high efficiency by integrating the effects of cell size and specific antigens on the surface of tumor cells. The filter chip consists of a semicircle arc and arrays and can separate large-scale CTC microspheres, which combined with CTCs automatically. We synthesized interfacial zinc oxide coating with nanostructure on the surface of the microsphere to increase the specific surface area to enhance the capturing efficiency of CTCs. Microspheres, trapped in the arrays, would entrap CTCs, too. The combination of the three kinds of strategies resulted in more than 90% capture efficiency of different tumor cell lines. Furthermore, it is easy to find and isolate the circulating tumor cells from the chip as tumor cells would be fixed inside the structure of a filter chip. To avoid the high background contamination when a few CTCs are surrounded by millions of nontarget cells, a digital detection method was applied to improve the detection sensitivity. The CTCs in the whole blood were specifically labeled by the antibody-DNA conjugates and detected via the DNA of the conjugates with a signal amplification. The strategy of the antibody-functional microsphere-integrated microchip for cell sorting and detection of CTCs may find broad implications that favor the fundamental cancer biology research, the precise diagnosis, and monitoring of cancer in the clinics.

Aptamer-Directed Conjugation of DNA to Therapeutic Antibodies.

A method for aptamer directed conjugation of DNA to therapeutic antibodies has been developed. In the method, an antibody selective aptamer binds to a specific site in the constant domain of human IgG1 antibodies and is used for both templated and direct conjugation to the antibodies. Through optimization of the design and reaction conditions, the antibody-DNA conjugates could be produced efficiently using equal stoichiometry of protein and DNA. Three different antibodies were evaluated, and the conjugates were characterized by anion exchange chromatography and SDS-PAGE. The conjugation sites for one of the antibodies were determined by MS/MS analysis of the digested conjugate. The antibody-DNA conjugate was also tested for receptor binding on cell surfaces showing retained binding.