DNA-encoded antibody libraries: a unified platform for multiplexed cell sorting and detection of genes and proteins

Whether for pathological examination or for fundamental biology studies, different classes of biomaterials and biomolecules are each measured from a different region of a typically heterogeneous tissue sample, thus introducing unavoidable sources of noise that are hard to quantitate. We describe the method of DNA-encoded antibody libraries (DEAL) for spatially multiplexed detection of ssDNAs and proteins as well as for cell sorting, all on the same diagnostic platform. DEAL is based upon the coupling of ssDNA oligomers onto antibodies which are then combined with the biological sample of interest. Spotted DNA arrays, which are found to inhibit biofouling, are utilized to spatially stratify the biomolecules or cells of interest. We demonstrate the DEAL technique for (1) the rapid detection of multiple proteins within a single microfluidic channel, and, with the additional step of electroless amplification of gold-nanoparticle labeled secondary antibodies, we establish a detection limit of 10 fM for the protein IL-2, 150 times more sensitive than the analogue ELISA; (2) the multiplexed, on-chip sorting of both immortalized cell lines and primary immune cells with an efficiency that exceeds surface-confined panning approaches; and (3) the co-detection of ssDNAs, proteins, and cell populations on the same platform.     

Cell surface glycoprotein profiling of cancer cells based on bioorthogonal chemistry

Bioorthogonal chemistry refers to chemical reactions that can occur within a living system without altering native biochemical processes. Applications of this concept extend to studies on a group of biomolecules that includes glycans, proteins, and lipids. In this study, a strategy for isolating cell surface glycoproteins and based on bioorthogonal chemistry was employed to identify new cancer-related glycoproteins. A novel alkyne reagent containing one disulfide bond was synthesized for the enrichment of glycoproteins metabolized with peracetylated N-azidoacetylmannosamine, which was applied on three different cancer cell lines, and all isolated proteins were analyzed by high-performance liquid chromatography-tandem mass spectrometry. The strategy of purifying cell surface glycoproteins introduced in this article was shown to be reliable, and a total of 56 cell surface glycoproteins were identified. Neuronal cell adhesion molecule was found uniquely expressed in A549 lung adenocarcinoma, and its expression in non-small-cell lung carcinomas was detected by immunohistochemistry. Furthermore, a significant increase of neuronal cell adhesion molecule expression was identified in non-small-cell lung adenocarcinoma compared with adjacent noncancerous tissues, and could be a novel potential target and marker in cancer treatment and detection.     

Cell receptor and surface ligand density effects on dynamic states of adhering circulating tumor cells

Dynamic states of cancer cells moving under shear flow in an antibody-functionalized microchannel are investigated experimentally and theoretically. The cell motion is analyzed with the aid of a simplified physical model featuring a receptor-coated rigid sphere moving above a solid surface with immobilized ligands. The motion of the sphere is described by the Langevin equation accounting for the hydrodynamic loadings, gravitational force, receptor-ligand bindings, and thermal fluctuations; the receptor-ligand bonds are modeled as linear springs. Depending on the applied shear flow rate, three dynamic states of cell motion have been identified: (i) free motion, (ii) rolling adhesion, and (iii) firm adhesion. Of particular interest is the fraction of captured circulating tumor cells, defined as the capture ratio, via specific receptor-ligand bonds. The cell capture ratio decreases with increasing shear flow rate with a characteristic rate. Based on both experimental and theoretical results, the characteristic flow rate increases monotonically with increasing either cell-receptor or surface-ligand density within certain ranges. Utilizing it as a scaling parameter, flow-rate dependent capture ratios for various cell-surface combinations collapse onto a single curve described by an exponential formula.     

一种基于硝酸纤维素膜的新颖便捷的芯片对循环肿瘤细胞的高效捕获

开发了一种新颖便捷的循环肿瘤细胞(CTC)捕获芯片用于癌细胞的分离和检测。CTC芯片以硝酸纤维素膜为基底制备,利用其对蛋白质的超强吸附能力来结合抗体,简便高效,便于将来大规模的推广应用。以非小肺癌细胞NCI-H1650为目标靶细胞,证明了CTC芯片对癌细胞具有很高的捕获效能。向1 mL正常人血液中加入500个癌细胞模拟病人血样的分析中成功检测到了182个癌细胞,预示了CTC芯片将来在临床应用上的巨大潜力。     

Effects of monoclonal antibody anti-EGF receptor on human nasopharyngeal carcinoma cell and other tumor cells

Three anti-EGF receptor MoAbs were used in these studies. Administration of MoAbs 3 and 176 inhibited tumor formation in nude mice by CNE-2, a poorly differentiated nasopharyngeal carcinoma cell line and A431, an epidermoid carcinoma cell line. When the same MoAbs were used in treatment against HeLa, a cervical carcinoma, tumor growth was not affected. The number of EGF receptors and apparent dissociation constants for 125I-EGF on CNE-2 and A431 was 1.3 x 10(5)/cell (Kd 7.7 x 10(-8) mol/L) and 1.4 x 10(6)/cell (Kd 2.4 x 10(-9) mol/L), respectively. Both MoAbs 3 and 176, capable of competing with EGF for receptor binding, showed significant tumor growth inhibition. MoAb 101 was incapable of blocking the binding of EGF to its receptor, and not as effective as MoAbs 3 and 176 in tumor growth inhibition. Our observation is that the MoAb anti-EGF receptor is cytostatic rather than cytocidal, in vitro against CNE-2 and A431.     

Nanoemulsions to support ex vivo cell culture of breast cancer circulating tumor cells

The culture and expansion of circulating tumor cells (CTCs) for ex vivo assays plays an important role in precision medicine. However, it still represents a big challenge in translational research. Generating knowledge about the characteristics of CTCs can help to shed light about the metastasis process. Furthermore, ex vivo culture of CTCs might allow performing functional analyses and testing different drugs, to guide clinical therapies. In this work, we present a new methodology based on the use of nanosystems to support ex vivo culture of CTCs. We have formulated oil-in-water (O/W) nanoemulsions (NEs) composed by lipids and fatty acids, and have demonstrated that they can help increasing cell viability on different breast cancer cell lines. Moreover, we have generated a CTC model from breast cancer mice xenografts, to prove the ability of the NEs to facilitate their culture and expansion. Additionally, we have postulated a mechanism of action based on the cell consumption of the NEs, which are acting as energy suppliers, driving proliferation. This work corroborates the potential of nanotechnology to provide valuable tools for precision oncology, and the ability of our NEs to improve proliferation of breast cancer CTCs for the establishment of CTCs culture protocols.     

Microfluidic applications on circulating tumor cell isolation and biomimicking of cancer metastasis

The prognosis of malignant tumors is challenged by insufficient means to effectively detect tumors at early stage. Liquid biopsy using circulating tumor cells (CTCs) as biomarkers demonstrates a promising solution to tackle the challenge, because CTCs play a critical role in cancer metastatic process via intravasation, circulation, extravasation, and formation of secondary tumor. However, the effectiveness of the solution is compromised by rarity, heterogeneity, and vulnerability associated with CTCs. Among a plethora of novel approaches for CTC isolation and enrichment, microfluidics leads to isolation and detection of CTCs in a cost-effective and operation-friendly way. Development of microfluidics also makes it feasible to model the cancer metastasis in vitro using a microfluidic system to mimick the in vivo microenvironment, thereby enabling analysis and monitor of tumor metastasis. This paper aims to review the latest advances for exploring the dual-roles microfluidics has played in early cancer diagnosis via CTC isolation and investigating the role of CTCs in cancer metastasis; the merits and drawbacks for dominating microfluidics-based CTC isolation methods are discussed; biomimicking cancer metastasis using microfluidics are presented with example applications on modelling of tumor microenvironment, tumor cell dissemination, tumor migration, and tumor angiogenesis. The future perspectives and challenges are discussed.     

Highly efficient circulating tumor cell isolation from whole blood and label-free enumeration using polymer-based microfluidics with an integrated conductivity sensor

A novel microfluidic device that can selectively and specifically isolate exceedingly small numbers of circulating tumor cells (CTCs) through a monoclonal antibody (mAB) mediated process by sampling large input volumes (>/=1 mL) of whole blood directly in short time periods (<37 min) was demonstrated. The CTCs were concentrated into small volumes (190 nL), and the number of cells captured was read without labeling using an integrated conductivity sensor following release from the capture surface. The microfluidic device contained a series (51) of high-aspect ratio microchannels (35 mum width x 150 mum depth) that were replicated in poly(methyl methacrylate), PMMA, from a metal mold master. The microchannel walls were covalently decorated with mABs directed against breast cancer cells overexpressing the epithelial cell adhesion molecule (EpCAM). This microfluidic device could accept inputs of whole blood, and its CTC capture efficiency was made highly quantitative (>97%) by designing capture channels with the appropriate widths and heights. The isolated CTCs were readily released from the mAB capturing surface using trypsin. The released CTCs were then enumerated on-device using a novel, label-free solution conductivity route capable of detecting single tumor cells traveling through the detection electrodes. The conductivity readout provided near 100% detection efficiency and exquisite specificity for CTCs due to scaling factors and the nonoptimal electrical properties of potential interferences (erythrocytes or leukocytes). The simplicity in manufacturing the device and its ease of operation make it attractive for clinical applications requiring one-time use operation.     

Size-resolved counting of circulating tumor cells on pinched flow-based microfluidic cytometry

Precise cell detecting and counting is meaningful in circulating tumor cells (CTCs) analysis. In this work, a simple cyclic olefin copolymer (COC) microflow cytometer device was developed for size-resolved CTCs counting. The proposed device is constructed by a counting channel and a pinched injection unit having three channels. Through injection flow rate control, microspheres/cells can be focused into the centerline of the counting channel. Polystyrene microspheres of 3, 9, 15, and 20 µm were used for the microspheres focusing characterization. After coupling to laser-induced fluorescence detection technique, the proposed device was used for polystyrene microspheres counting and sizing. A count accuracy up to 97.6% was obtained for microspheres. Moreover, the proposed microflow cytometer was applied to CTCs detecting and counting. To mimic blood sample containing CTCs and CTCs mixture with different subtypes, an MDA-MB-231 (human breast cell line) spiked red blood cells sample and a mixture of MDA-MB-231 and MCF-7 (human breast cell line) sample were prepared, respectively, and then analyzed by the developed pinched flow-based microfluidic cytometry. The simple fabricated and easy operating COC microflow cytometer exhibits the potential in the point-of-care clinical application.     

Surface bio-magnetism on bacterial cells adhesion and surface proteins secretion

Extensive research works have been done on using magnetic fields on biological organism, but the results till date have been controversial [D.O. Carpenter, S. Ayrapetyan (Eds.), Biological Effects of Electric and Magnetic Fields, vol. 1, Academic Press, San Diego, 1994]. In spite of this, the study of surface magnetic effects on bacterial adhesion and cell growth has not been rigorously explored. The effects of surface magnetism, using perpendicularly polarized magnetic media, are evaluated on Bacillus licheniformis, a widely used bacterium in brewery [L. Kandra, a-Amylases of medical and industrial importance. J. Mol. Struct. (Theochem.), in press] and pharmaceutical [H. Ikram-ul et al., Production of alph amylase by Bacillus licheniformis using an economical medium. Bioresour. Technol. 87 (2003) 57-61] industries, by observing its adhesion and growth behavior. At different spin directions, we are able to observe a change on the biofilm formation, protein synthesis, and cell growth rate. Given that surface energy can easily penetrate through cells, this approach is an advantage over existing techniques that require direct physical contact to target cells. It also presents a new technique to cell adhesion and synthesis of surface proteins.     

Synthesis of vitamin-selenium complex and its effects on proteins and tumor cells

A selenium-vitamin P complex (SEVP) was synthesized and its structure was determined by IR, LC-MS and (1)H NMR. Its biological effects on bovine serum albumin (BSA) and human colon carcinoma tumor cells were studied by molecular spectra, MTT and flow cytometry. The interaction of SEVP and BSA was discussed by fluorescence quenching method and F?rster non-radiation energy transfer theory. The thermodynamic parameters ΔH(θ), ΔG(θ), ΔS(θ) at different temperatures were calculated and the results indicate the interaction is an exothermic as well as entropy-driven process. Hydrogen bond and electrostatic force played major role in the reaction. The binding geometry and conformation changes of BSA were investigated by fluorescence probe technique and circular dichroism (CD) spectra. The effects of SEVP on human colon carcinoma tumor cells HT29 were tested by MTT method and flow cytometry (FCM). The MTT results show the proliferation of HT29 tumor cells were inhibited by SEVP and the inhibition was associated with dose and time. The FCM analysis disclosed SEVP interrupted the DNA synthesis of tumor cells at S phase.     

微流控芯片分选富集循环肿瘤细胞的研究进展

近年来,循环肿瘤细胞(CTCs)研究得到了越来越多的关注,许多研究报告已经证实其在肿瘤转移的早期诊断、治疗方案选择、个体化治疗及探索肿瘤转移机制等方面具有潜在的价值,然而CTCs在循环系统中的含量极低,这成为限制其临床相关应用的主要难点。微流控芯片技术具有低成本、快速、高通量及操作简单等优势,利用微流控芯片可实现CTCs的高速、高回收率、高纯度的分选富集,近年来得到广泛的关注。本文综述了近年来在微流控芯片内进行CTCs分选富集的研究并探讨了各种方法的优缺点,并在本研究团队的研究基础上进行了展望。     

Highly sensitive electrochemical detection of proteins using aptamer-coated gold nanoparticles and surface enzyme reactions

A novel electrochemical detection methodology is described for the femtomolar detection of proteins which utilizes both DNA aptamer-functionalized nanoparticles and a surface enzymatic reaction. Immunoglobulin E (IgE) was used as a model protein biomarker, which possesses two distinct epitopes for antibody (anti-IgE) and DNA aptamer binding. A surface sandwich assay format was utilized involving the specific adsorption of IgE onto a gold electrode surface that was pre-modified with a monolayer of aptamer-nanoparticle conjugates followed by the specific interaction of alkaline phosphatase (ALP) conjugated anti-IgE. To clearly demonstrate the signal enhancement associated with nanoparticle use, anodic current measurements of the ALP catalyzed oxidation of the enzyme substrate 4-aminophenylphosphate (APP) were also compared with electrode surfaces upon which the aptamer was directly attached. The detection of an unlabelled protein at concentrations as low as 5 fM is a significant improvement compared to conventional electrochemical-based immunoassay approaches and provides a foundation for the practical use and incorporation of nanoparticle-enhanced detection into electrochemical biosensing technologies.     

Highly specific quantification of mRNA mutation in single cells based on RNase H cleavage-assisted reverse transcription(RT)-PCR

Accurate quantitation of site-specific mRNA mutation in single cells or in peripheral blood is of great significance for both biological and biomedical studies.How to eliminate the false-positive interference from the abundant normal mRNA is still a big challenge.Herein,we have proposed an LNA(locked nucleic acid)-assisted high-specificity strategy which can selectively guide the RNase H to cleave only the wildtype mRNA(wtRNA) while the mutant mRNA(mutRNA) will remain intact.The intact mutRNA ca...     

Sensitized photomodification of oligonucleotide-binding proteins displayed on the eucaryotic cell surface

Interactions of double-stranded nucleic acids with cell surface proteins, which are involved in binding and transport of extracellular nucleic acids, were studied by the photoaffinity modification with a binary system of oligonucleotide conjugates. The photoreactive double-stranded complex involved an oligonucleotide template and two complementary to adjacent sequences oligonucleotide conjugates. One conjugate contained a photoreagent, viz., 4-azido-2,3,5,6-tetrafluorobenzaldehyde N-(3-aminopropionyl)hydrazone, at the terminus located in proximity to the terminus of another conjugate containing the sensitizer, viz., 9-aminomethylanthracene. Binding of photoreagent and the sensitizer to a single-stranded template yields the photoreactive center. Upon irradiation with visible light (400—580 nm), this photoreactive double-stranded complex forms covalent cross-linkages with oligonucleotide-binding surface proteins of eucaryotic SPEV cells.     

Selective modification of cell surface proteins and thymidine transport in hamster cells exposed to cholera toxin.

The increased adherence and morphological response which occurs in Chinese hamster ovary cells as a result of exposure to cholera toxin is paralleled by modification in the relative exposure of outer proteins. Mild proteolysis treatment of the cells prelabeled with [3H] glucosamine reveals a markedly different kinetics of release of external glycopeptides as a result of exposure to cholera toxin. Selective alterations in external tyrosyl-rich proteins can also be detected by lactoperoxidase-catalyzed radioiodination. The above modifications are accompanied by a decrease in the rate of thymidine uptake by toxin-treated cells.     

Immobilization of antibody fragment for immunosensor application based on surface plasmon resonance

Biosurface fabrication using the Fab′ fragment of immunoglobulin (IgG) was carried out by self-assembly (SA) technique. The pepsin-digested monoclonal antibody (Mab) against bovine insulin containing the F(ab′)₂ fragment and residual proteins was separated using affinity chromatography and dialysis. To prevent the nonspecific binding of F(ab′)₂ onto gold (Au) substrate, the native disulfide bridge was reduced using dithiothreitol (DTT) to convert F(ab′)₂ into Fab′, which made the immobilization to be carried out via the native thiol (–SH) group. The fabricated biosurface using SA technique showed the formation of stable thin film through AFM topography. Through the concentration change of DTT and Fab′, the absorption characteristics against the Au surface were investigated using surface plasmon resonance (SPR) with the flow cell. The amount of immobilized antibody fragment and the antigen binding capacity were regulated with respect to the reduction state and concentration of F(ab′)₂. Based on the biosurface of the fabricated Fab′, the insulin-detection was carried out by the measurement of SPR. The proposed antibody surface could successfully detect the bovine insulin at the concentration from 100 ng/mL to 10 μg/mL.     

Blue fluorescent dye-protein complexes based on fluorogenic cyanine dyes and single chain antibody fragments

Fluoromodules are complexes formed upon the noncovalent binding of a fluorogenic dye to its cognate biomolecular partner, which significantly enhances the fluorescence quantum yield of the dye. Previously, several single-chain, variable fragment (scFv) antibodies were selected from a yeast cell surface-displayed library that activated fluorescence from a family of unsymmetrical cyanine dyes covering much of the visible and near-IR spectrum. The current work expands our repertoire of genetically encodable scFv-dye pairs by selecting and characterizing a group of scFvs that activate fluorogenic violet-absorbing, blue-fluorescing cyanine dyes, based on oxazole and thiazole heterocycles. The dye binds to both yeast cell surface-displayed and soluble scFvs with low nanomolar K(d) values. These dye-protein fluoromodules exhibit high quantum yields, approaching unity for the brightest system. The promiscuity of these scFvs with other fluorogenic cyanine dyes was also examined. Fluorescence microscopy demonstrates that the yeast cell surface-displayed scFvs can be used for multicolor imaging. The prevalence of 405 nm lasers on confocal imaging and flow cytometry systems make these new reagents potentially valuable for cell biological studies.     

Electrical fingerprinting, 3D profiling and detection of tumor cells with solid-state micropores

Solid-state micropores can provide direct information of ex vivo or in vitro cell populations. Micropores are used to detect and discriminate cancer cells based on the translocation behavior through micropores. The approach provides rapid detection of cell types based on their size and mechano-physical properties like elasticity, viscosity and stiffness. Use of a single micropore device enables detection of tumor cells from whole blood efficiently, at 70% CTC detection efficiency. The CTCs show characteristic electrical signals which easily distinguish these from other cell types. The approach provides a gentle and inexpensive instrument that can be used for specific blood analysis in a lab-on-a-chip setting. The device does not require any preprocessing of the blood sample, particles/beads attachment, surface functionalization or fluorescent tags and provides quantitative and objective detection of cancer cells.