Recent Advances in the Analysis of Single Cells

Selective Retrieval of Individual Cells from Microfluidic Arrays Combining Dielectrophoretic Force and Directed Hydrodynamic Flow

Hydrodynamic-based microfluidic platforms enable single-cell arraying and analysis over time. Despite the advantages of established microfluidic systems, long-term analysis and proliferation of cells selected in such devices require off-chip recovery of cells as well as an investigation of on-chip analysis on cell phenotype, requirements still largely unmet. Here, we introduce a device for single-cell isolation, selective retrieval and off-chip recovery. To this end, singularly addressable three-dimensional electrodes are embedded within a microfluidic channel, allowing the selective release of single cells from their trapping site through application of a negative dielectrophoretic (DEP) force. Selective capture and release are carried out in standard culture medium and cells can be subsequently mitigated towards a recovery well using micro-engineered hybrid SU-8/PDMS pneumatic valves. Importantly, transcriptional analysis of recovered cells revealed only marginal alteration of their molecular profile upon DEP application, underscored by minor transcriptional changes induced upon injection into the microfluidic device. Therefore, the established microfluidic system combining targeted DEP manipulation with downstream hydrodynamic coordination of single cells provides a powerful means to handle and manipulate individual cells within one device.

Sensitive and specific detection of tumour cells based on a multivalent DNA nanocreeper and a multiplexed fluorescence supersandwich

A self-assembled DNA nanostructure based on a DNA nanocreeper and multiplexed fluorescence supersandwich was designed for the sensitive and specific detection of tumour cells. This nanostructure could improve the binding affinity of current aptamers and trigger signal amplification, which provide potential for the discrimination of low abundant target cells in liquid biopsy.

Probing the Membrane Vibration of Single Living Cells by Using Nanopipettes

The vibration of a cell membrane plays a key role in the regulation of cell shape and the behavior of cells. However, most existing approaches for the measurement of cell vibration require either exogenous modification or sophisticated techniques, and the main challenge lies in developing methods that can monitor membrane vibration of living cells directly. Herein, a noninvasive strategy based on ultrasmall quartz nanopipettes is introduced. With a tip size of less than 100 nm, nanopipettes can be spatially controlled for precision targeting of a specific location on the membrane of single living cells. Surprisingly, by employing a constant voltage, stable cyclic oscillations are observed from the continuous current versus time traces. The time-domain current can be decomposed into two basic waves: the high-frequency one indicates the local membrane vibration driven by the electro-osmotic flow from the nanopipette, whereas the low-frequency one indicates the natural frequency of the whole cell. This provides a simple but reliable method to test local and global membrane vibration of single living cells simultaneously with little damage, which provides a tool for the quantification of drugs, disease, or mutations of the cell structure.

Picoliter enzyme reactor on a nanofluidic device exceeding the bulk reaction rate

A picoliter enzyme reactor using a trypsin immobilized nanochannel realized 25 times faster reaction than the bulk reaction.

A Potential Application of Triangular Microwells to Entrap Single Cancer Cells: A Canine Cutaneous Mast Cell Tumor Model

Cellular heterogeneity is a major hindrance, leading to the misunderstanding of dynamic cell biology. However, single cell analysis (SCA) has been used as a practical means to overcome this drawback. Many contemporary methodologies are available for single cell analysis; among these, microfluidics is the most attractive and effective technology, due to its advantages of low-volume specimen consumption, label-free evaluation, and real-time monitoring, among others. In this paper, a conceptual application for microfluidic single cell analysis for veterinary research is presented. A microfluidic device is fabricated with an elastomer substrate, polydimethylsiloxane (PDMS), under standard soft lithography. The performance of the microdevice is high-throughput, sensitive, and user-friendly. A total of 53.1% of the triangular microwells were able to trap single canine cutaneous mast cell tumor (MCT) cells. Of these, 38.82% were single cell entrapments, while 14.34% were multiple cell entrapments. The ratio of single-to-multiple cell trapping was high, at 2.7:1. In addition, 80.5% of the trapped cells were viable, indicating that the system was non-lethal. OCT4A-immunofluorescence combined with the proposed system can assess OCT4A expression in trapped single cells more precisely than OCT4A-immunohistochemistry. Therefore, the results suggest that microfluidic single cell analysis could potentially reduce the impact of cellular heterogeneity.

Single-cell identification by microfluidic-based in situ extracting and online mass spectrometric analysis of phospholipids expression

This work describes a microfluidic system for in situ extraction of a single-cell and its phosphatidylcholine analysis through mass spectrometry. This approach uncovered cellular heterogeneity among seemingly identical cells and provided a new platform for identification and classification of cells.

Toward Personalized Cancer Treatment: From Diagnostics to Therapy Monitoring in Miniaturized Electrohydrodynamic Systems

Historically, cancer was seen and treated as a single disease. Over the years, this image has shifted, and it is now generally accepted that cancer is a complex and dynamic disease that engages multiple progression pathways in each patient. The shift from treating cancer as single disease to tailoring the therapy based on the individual's characteristic cancer profile promises to improve the clinical outcome and has also given rise to the field of personalized cancer treatment. To advise a suitable therapy plan and adjust personalized treatment, a reliable and fast diagnostic strategy is required. The advances in nanotechnology, microfluidics, and biomarker research have spurred the development of powerful miniaturized diagnostic systems that show high potential for use in personalized cancer treatment. These devices require only minute sample volumes and have the capability to create instant cancer snapshots that could be used as tool for cancer risk indication, early detection, tumor classification, and recurrence. Miniaturized systems can combine a whole sample-to-answer workflow including sample handling, preparation, analysis, and detection. As such, this concept is also often referred to as "lab-on-a-chip". An inherit challenge of monitoring personalized cancer treatment using miniaturized systems is that cancer biomarkers are often only detectable at trace concentrations present in a complex biological sample rich in interfering molecules, necessitating highly specific and sensitive biosensing strategies. To address the need for trace level detection, highly sensitive fluorescence, absorbance, surface-enhanced Raman spectroscopy (SERS), electrochemical, mass spectrometric, and chemiluminescence approaches were developed. To reduce sample matrix interferences, ingenious device modifications including coatings and nanoscopic fluid flow manipulation have been developed. Of the latter, our group has exploited the use of alternating current electrohydrodynamic (ac-EHD) fluid flows as an efficient strategy to reduce nonspecific nontarget biosensor binding and speed-up assay times. ac-EHD provides fluid motion induced by an electric field with the ability to generate surface shear forces in nanometer distance to the biosensing surface (known as nanoshearing phenomenon). This is ideally suited to increase the collision frequency of cancer biomarkers with the biosensing surface and shear off nontarget molecules thereby minimizing nonspecific binding. In this Account, we review recent advancements in miniaturized diagnostic system development with potential use in personalized cancer treatment and monitoring. We focus on integrated microfluidic structures for controlled sample flow manipulation followed by on-device biomarker interrogation. We further highlight the progress in our group, emphasis fundamentals and applications of ac-EHD-enhanced miniaturized systems, and outline promising detection concepts for comprehensive cancer biomarker profiling. The advances are discussed based on the type of cancer biomarkers and cover circulating tumor cells, proteins, extracellular vesicles, and nucleic acids. The potential of miniaturized diagnostic systems for personalized cancer treatment and monitoring is underlined with representative examples including device illustrations. In the final section, we critically discuss the future of personalized diagnostics and what challenges should be addressed to make these devices clinically translatable.

Ultrasonically-guided flow focusing generates precise emulsion droplets for high-throughput single cell analyses

Emulsion-based techniques have dramatically advanced our understanding of single-cell biology and complex single-cell features over the past two decades. Most approaches for precise single cell isolation rely on microfluidics, which has proven highly effective but requires substantial investment in equipment and expertise that can be difficult to access for researchers that specialize in other areas of bioengineering and molecular biotechnology. Inspired by the robust droplet generation technologies in modern flow cytometry instrumentation, here we established a new platform for high-throughput isolation of single cells within droplets of tunable sizes by combining flow focusing with ultrasonic vibration for rapid and effective droplet formation. Application of ultrasonic pressure waves to the flowing jet provided enhanced control of emulsion droplet size, permitting capture of 25,000 to 50,000 single cells per minute. As an example application, we applied this new droplet generation platform to sequence the antibody variable region heavy and light chain pairings (VH:VL) from large repertoires of single B cells. We demonstrated the recovery of > 40,000 paired CDRH3:CDRL3 antibody clusters from a single individual, validating that these droplet systems can enable the genetic analysis of very large single-cell populations. These accessible new technologies will allow rapid, large-scale, and precise single-cell analyses for a broad range of bioengineering and molecular biotechnology applications.

Recent advances in microfluidic platforms for single-cell analysis in cancer biology, diagnosis and therapy

Understanding molecular, cellular, genetic and functional heterogeneity of tumors at the single-cell level has become a major challenge for cancer research. The microfluidic technique has emerged as an important tool that offers advantages in analyzing single-cells with the capability to integrate time-consuming and labour-intensive experimental procedures such as single-cell capture into a single microdevice at ease and in a high-throughput fashion. Single-cell manipulation and analysis can be implemented within a multi-functional microfluidic device for various applications in cancer research. Here, we present recent advances of microfluidic devices for single-cell analysis pertaining to cancer biology, diagnostics, and therapeutics. We first concisely introduce various microfluidic platforms used for single-cell analysis, followed with different microfluidic techniques for single-cell manipulation. Then, we highlight their various applications in cancer research, with an emphasis on cancer biology, diagnosis, and therapy. Current limitations and prospective trends of microfluidic single-cell analysis are discussed at the end.

Optical Imaging Approaches to Monitor Static and Dynamic Cell-on-Chip Platforms: A Tutorial Review

Miniaturized laboratories on chip platforms play an important role in handling life sciences studies. The platforms may contain static or dynamic biological cells. Examples are a fixed medium of an organ-on-a-chip and individual cells moving in a microfluidic channel, respectively. Due to feasibility of control or investigation and ethical implications of live targets, both static and dynamic cell-on-chip platforms promise various applications in biology. To extract necessary information from the experiments, the demand for direct monitoring is rapidly increasing. Among different microscopy methods, optical imaging is a straightforward choice. Considering light interaction with biological agents, imaging signals may be generated as a result of scattering or emission effects from a sample. Thus, optical imaging techniques could be categorized into scattering-based and emission-based techniques. In this review, various optical imaging approaches used in monitoring static and dynamic platforms are introduced along with their optical systems, advantages, challenges, and applications. This review may help biologists to find a suitable imaging technique for different cell-on-chip studies and might also be useful for the people who are going to develop optical imaging systems in life sciences studies.

Recent advances in single cell manipulation and biochemical analysis on microfluidics

Single cell analysis has become of great interest with unprecedented capabilities for the systematic investigation of cell-to-cell variation in large populations. Rapid and multi-parametric analysis of intercellular biomolecules at the single-cell level is imperative for the improvement of early disease diagnosis and personalized medicine. However, the small size of cells and the low concentration levels of target biomolecules are critical challenges for single cell analysis. In recent years, microfluidic platforms capable of handling small-volume fluid have been demonstrated to be powerful tools for single cell analysis. In addition, microfluidic techniques allow for precise control of the localized microenvironment, which yield more accurate outcomes. Many different microfluidic techniques have been greatly improved for highly efficient single-cell manipulation and highly sensitive detection over the past few decades. To date, microfluidics-based single cell analysis has become the hot research topic in this field. In this review, we particularly highlight the advances in this field during the past three years in the following three aspects: (1) microfluidic single cell manipulation based on microwells, micropatterns, droplets, traps and flow cytometric methods; (2) detection methods based on fluorescence, mass spectrometry, electrochemical, and polymerase chain reaction-based analysis; (3) applications in the fields of small molecule detection, protein analysis, multidrug resistance analysis, and single cell sequencing with droplet microfluidics. We also discuss future research opportunities by focusing on key performances of throughput, multiparametric target detection and data processing.

Semi-automated on-demand control of individual droplets with a sample application to a drug screening assay

Automated control of individual droplets in microfluidic channels offers tremendous potential for applications requiring high accuracy and minimal user involvement. The feasibility of active droplet control has been previously demonstrated with pressure-driven flow control and visual feedback, but the manual operation required to perform droplet manipulations limited the accuracy, repeatability, and throughput. The present study improves upon the aforementioned challenges with a higher-level algorithm capturing the dynamics of droplet motion for a semi-automated control system. With a simple T junction geometry, droplets can now be automatically and precisely controlled on-demand. Specifically, there is ±10% accuracy for droplet generation, ±1.3% monodispersity for 500 μm long droplets and ±4% accuracy for splitting ratios. On-demand merging, mixing, and sorting are also demonstrated as well as the application of a drug screening assay related to neurodegenerative disorders. Overall, this system serves as a foundation for a fully automated system that does not require valves, embedded electrodes, or complex multi-layer fabrication.

Genetically Encoded Fluorescent Proteins Enable High-Throughput Assignment of Cell Cohorts Directly from MALDI-MS Images

Matrix-assisted laser desorption/ionization (MALDI) mass spectrometry imaging (MSI) provides a unique in situ chemical profile that can include drugs, nucleic acids, metabolites, lipids, and proteins. MSI of individual cells (of a known cell type) affords a unique insight into normal and disease-related processes and is a prerequisite for combining the results of MSI and other single-cell modalities (e.g. mass cytometry and next-generation sequencing). Technological barriers have prevented the high-throughput assignment of MSI spectra from solid tissue preparations to their cell type. These barriers include obtaining a suitable cell-identifying image (e.g. immunohistochemistry) and obtaining sufficiently accurate registration of the cell-identifying and MALDI-MS images. This study introduces a technique that overcame these barriers by assigning cell type directly from mass spectra. We hypothesized that, in MSI from mice with a defined fluorescent protein expression pattern, the fluorescent protein's molecular ion could be used to identify cell cohorts. A method was developed for the purification of enhanced yellow fluorescent protein (EYFP) from mice. To determine EYFP's molecular mass for MSI studies, we performed intact mass analysis and characterized the protein's primary structure and post-translational modifications through various techniques. MALDI-MSI methods were developed to enhance the detection of EYFP in situ, and by extraction of EYFP's molecular ion from MALDI-MS images, automated, whole-image assignment of cell cohorts was achieved. This method was validated using a well-characterized mouse line that expresses EYFP in motor and sensory neurons and should be applicable to hundreds of commercially available mice (and other animal) strains comprising a multitude of cell-specific fluorescent labels.

Live sperm trap microarray for high throughput imaging and analysis

There is a growing appreciation and understanding of cell-to-cell variability in biological samples. However, research and clinical practice in male fertility has relied on population, or sample-based characteristics. Single-cell resolution is particularly important given the winner-takes-all nature of both natural and in vitro fertilization: it is the properties of a single cell, not the population, that are passed to the next generation. While there are a range of methods for single cell analysis, arraying a larger number of live sperm has not been possible due to the strong locomotion of the cells. Here we present a 103-trap microarray that traps, aligns and arrays individual live sperm. The method enables high-resolution imaging of the aligned cell head, the application of dye-based DNA and mitochondrial analyses, and the quantification of motility characteristics, such as tail beat. In testing, a 2400-post array trapped ∼400 sperm for individual analyses of tail beating frequency and amplitude, DNA integrity via acridine orange staining, and mitochondrial activity via staining. While literature results are mixed regarding a possible correlation between motility and DNA integrity of sperm at sample-level, results here find no statistical correlation between tail beat characteristics and DNA integrity at the cell-level. The trap array uniquely enables the high-throughput study of individual live sperm in semen samples - assessing the inherently single-cell selection process of fertilization, with single-cell resolution.

Nano-Sampling and Reporter Tools to Study Metabolic Regulation in Zebrafish

In the past years, evidence has emerged that hallmarks of human metabolic disorders can be recapitulated in zebrafish using genetic, pharmacological or dietary interventions. An advantage of modeling metabolic diseases in zebrafish compared to other "lower organisms" is the presence of a vertebrate body plan providing the possibility to study the tissue-intrinsic processes preceding the loss of metabolic homeostasis. While the small size of zebrafish is advantageous in many aspects, it also has shortcomings such as the difficulty to obtain sufficient amounts for biochemical analyses in response to metabolic challenges. A workshop at the European Zebrafish Principal Investigator meeting in Trento, Italy, was dedicated to discuss the advantages and disadvantages of zebrafish to study metabolic disorders. This perspective article by the participants highlights strategies to achieve improved tissue-resolution for read-outs using "nano-sampling" approaches for metabolomics as well as live imaging of zebrafish expressing fluorescent reporter tools that inform on cellular or subcellular metabolic processes. We provide several examples, including the use of reporter tools to study the heterogeneity of pancreatic beta-cells within their tissue environment. While limitations exist, we believe that with the advent of new technologies and more labs developing methods that can be applied to minimal amounts of tissue or single cells, zebrafish will further increase their utility to study energy metabolism.

Random and aligned electrospun PLGA nanofibers embedded in microfluidic chips for cancer cell isolation and integration with air foam technology for cell release

BACKGROUND

Circulating tumor cells (CTCs) comprise the high metastatic potential population of cancer cells in the blood circulation of humans; they have become the established biomarkers for cancer diagnosis, individualized cancer therapy, and cancer development. Technologies for the isolation and recovery of CTCs can be powerful cancer diagnostic tools for liquid biopsies, allowing the identification of malignancies and guiding cancer treatments for precision medicine.

METHODS

We have used an electrospinning process to prepare poly(lactic-co-glycolic acid) (PLGA) nanofibrous arrays in random or aligned orientations on glass slips. We then fabricated poly(methyl methacrylate) (PMMA)-based microfluidic chips embedding the PLGA nanofiber arrays and modified their surfaces through sequential coating with using biotin-(PEG)7-amine through EDC/NHS activation, streptavidin (SA), and biotinylated epithelial-cell adhesion-molecule antibody (biotin-anti-EpCAM) to achieve highly efficient CTC capture. When combined with an air foam technology that induced a high shear stress and, thereby, nondestructive release of the captured cells from the PLGA surfaces, the proposed device system operated with a high cell recovery rate.

RESULTS

The morphologies and average diameters of the electrospun PLGA nanofibers were characterized using scanning electron microscopy (SEM) and confocal Raman imaging. The surface chemistry of the PLGA nanofibers conjugated with the biotin-(PEG)7-amine was confirmed through time-of-flight secondary ion mass spectrometry (ToF-SIMS) imaging. The chip system was studied for the effects of the surface modification density of biotin-(PEG)7-amine, the flow rates, and the diameters of the PLGA nanofibers on the capture efficiency of EpCAM-positive HCT116 cells from the spiked liquid samples. To assess their CTC capture efficiencies in whole blood samples, the aligned and random PLGA nanofiber arrays were tested for their abilities to capture HCT116 cells, providing cancer cell capture efficiencies of 66 and 80%, respectively. With the continuous injection of air foam into the microfluidic devices, the cell release efficiency on the aligned PLGA fibers was 74% (recovery rate: 49%), while it was 90% (recovery rate: 73%) on the random PLGA fibers, from tests of 200 spiked cells in 2 mL of whole blood from healthy individuals. Our study suggests that integrated PMMA microfluidic chips embedding random PLGA nanofiber arrays may be suitable devices for the efficient capture and recovery of CTCs from whole blood samples.

Microfluidic Platform for Multimodal Analysis of Enzyme Secretion in Nanoliter Droplet Arrays

High-throughput screening of cell-secreted proteins is essential for various biotechnological applications. In this article, we show a microfluidic approach to perform the analysis of cell-secreted proteins in nanoliter droplet arrays by two complementary methods, fluorescence microscopy and mass spectrometry. We analyzed the secretion of the enzyme phytase, a phosphatase used as an animal feed additive, from a low number of yeast cells. Yeast cells were encapsulated in nanoliter volumes by droplet microfluidics and deposited on spatially defined spots on the surface of a glass slide mounted on the motorized stage of an inverted fluorescence microscope. During the following incubation for several hours to produce phytase, the droplets can be monitored by optical microscopy. After addition of a fluorogenic substrate at a defined time, the relative concentration of phytase was determined in every droplet. Moreover, we demonstrate the use of matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) to monitor the multistep conversion of the native substrate phytic acid by phytase secreted in 7 nL droplets containing 50-100 cells. Our method can be adapted to various other protocols. As the droplets are easily accessible, compounds such as assay reagents or matrix molecules can be added to all or to selected droplets only, or part of the droplet volume could be removed. Hence, this platform is a versatile tool for questions related to cell secretome analysis.

Extracting lipid vesicles from plasma membranes via self-assembly of clathrin-inspired scaffolding nanoparticles

Single-cell analysis is a new and rapidly expanding field, the goal of which is obtaining fresh information from individual cells to understand the regulatory mechanisms of cell development and diseases. Conventional approaches generally rely on the cell lysis which, however, is destructive to cells and against multiple sampling from the living cell. Here, we propose and design a scaffolding nanoparticle (NP) system that enables us to sample cytoplasmic contents without rupturing the cellular membrane, by mimicking the unusual features of clathrin. Our simulation results reveal the design principles, following which scaffolding NPs can extract lipid vesicles from plasma membranes, with both the pathway and the mechanism resembling the clathrin-mediated endocytosis, i.e. multiple NPs deposit at the membrane, assembling into cage-like structures to deform the membrane into a vesicle shape. As important design parameters, the interaction between different NPs should be properly stronger than that between each NP and the membrane to ensure the cage formation, and optimal NP concentration and the membrane surface tension are also requisite for extracting lipid vesicles. Our results provide useful guidelines for design of bio-inspired scaffolding NPs as an intelligent machine for practical use in but not limited to the single-cell analysis.

Single-cell assay on microfluidic devices

Advances in microfluidic techniques have prompted researchers to study the inherent heterogeneity of single cells in cell populations.

Single-cell protein profiling in microchambers with barcoded beads

Single-cell profiling provides insights into cellular behaviour that macroscale cell cultures and bulk measurements cannot reveal. In the context of personalized cancer treatment, the profiling of individual tumour cells may lead to higher success rates for therapies by rapidly selecting the most efficacious drugs. Currently, genomic analysis at the single-cell level is available through highly sensitive sequencing approaches. However, the identification and quantification of intracellular or secreted proteins or metabolites remains challenging. Here, we introduce a microfluidic method that facilitates capture, automated data acquisition and the multiplexed quantification of proteins from individual cells. The microfluidic platform comprises 1026 chambers with a volume of 152 pL each, in which single cells and barcoded beads are co-immobilized. We demonstrated multiplexed single-cell protein quantification with three different mammalian cell lines, including two model breast cancer cell lines. We established on-chip immunoassays for glyceraldehyde-3-phosphate dehydrogenase (GAPDH), galectin-3 (Gal-3) and galectin-3 binding protein (Gal-3bp) with detection limits as low as 7.0 × 10⁴, 2.3 × 10⁵ and 1.8 × 10³ molecules per cell, respectively. The three investigated cell types had high cytosolic levels of GAPDH and could be clearly differentiated by their expression levels of Gal-3 and Gal-3bp, which are important factors that contribute to cancer metastasis. Because it employed commercially available barcoded beads for this study, our platform could be easily used for the single-cell protein profiling of several hundred different targets. Moreover, this versatile method is applicable to the analysis of bacteria, yeast and mammalian cells and nanometre-sized lipid vesicles.

Advances in mass spectrometry based single-cell metabolomics

Single cell metabolomics using mass spectrometry can contribute to understanding biological activities in health and disease.

Codetermination of Sphingomyelin and Cholesterol in Cellular Plasma Membrane in Sphingomyelin-Depletion-Induced Cholesterol Efflux

Quantification of multiple lipids with different contents in plasma membrane in single cells is significant, but challenging, for investigating lipid interactions and the role of dominant protein transporters. In this paper, comonitoring the alteration of low-content sphingomyelin (SM) and high-content cholesterol in plasma membrane of one living cell is realized by use of luminol electrochemiluminescence (ECL) for the first time. Concentrations of SM as low as 0.5 μM are detected, which permits the measurement of low-content membrane SM in single cells. More membrane cholesterol is observed in individual cells after depletion of membrane SM, providing direct evidence about SM-depletion-induced cholesterol efflux. The upregulation of ATP-binding cassette transporters A1 (ABCA1) and G1 (ABCG1) in SM-depleted cells induces a further increase in membrane cholesterol. These results imply that higher expression of ABCA1/G1 promotes cholesterol trafficking, which offers additional information to solve the debate about ABC transporters in cholesterol efflux. Moreover, the established approach offers a special strategy to investigate the correlation of membrane lipids and the role of transporters in cholesterol trafficking.

Electrochemical Biosensing System for Single Cells, Cellular Aggregates and Microenvironments

Applications of electrochemical biosensing for surveying intact cells and tissues have been focus of attention. Two experimental approaches have been used when performing amperometric measurements on biological cells, the stylus-type microelectrode probes and the electrode-integrated microdevices based on lithographic technologies. For the probe scanning approach, various types of microsensors were developed to monitor localized physical or chemical natures at a variety of surfaces in situ under wet conditions. Scanning electrochemical microscopy (SECM) has been applied for monitoring local oxygen, enzyme activity, and collection of transcripts. For the non-scanning type of approach, electrode array devices allow very rapid response, parallel monitoring, and multi-analyte assay. Sveral topics of on-chip-culture system were introduced especially concerning on gene expression monitoring by reporter system and reconstruction of in vivo-like nature by controlling microenvironments. Electrochemical reporter assay has been demonstrated to monitor the gene expression process of the gene-modified cultured cells. Long-term monitoring of cellular function of spheroids and three dimensionally-cultured cells were carried out by controlling microenvironments on the cellular chip.

Integrated Proteome Analysis Device for Fast Single-Cell Protein Profiling

In our previous work, we have demonstrated an integrated proteome analysis device (iPAD-100) to analyze proteomes from 100 cells. (1) In this work, for the first time, a novel integrated device for single-cell analysis (iPAD-1) was developed to profile proteins in a single cell within 1 h. In the iPAD-1, a selected single cell was directly sucked into a 22 μm i.d. capillary. Then the cell lysis and protein digestion were simultaneously accomplished in the capillary in a 2 nL volume, which could prevent protein loss and excessive dilution. Digestion was accelerated by using elevated temperature with ultrasonication. The whole time of cell treatment was 30 min. After that, single-cell digest peptides were transferred into an LC column directly through a true zero dead volume union, to minimize protein transfer loss. A homemade 22 μm i.d. nano-LC packing column with 3 μm i.d. ESI tip was used in the device to achieve ultrasensitive detection. A 30 min elution program was applied to analysis of the single-cell proteome. Therefore, the total time needed for a single-cell analysis was only 1 h. In an analysis of 10 single HeLa cells, a maximum of 328 proteins were identified in one cell by using an Orbitrap Fusion Tribrid MS instrument, and the detection limit was estimated at around 1.7-170 zmol. Such a sensitivity of the iPAD-1 was ∼120-fold higher than that of our previously developed iPAD-100 system. (1) Prominent cellular heterogeneity in protein expressive profiling was observed. Furthermore, we roughly estimated the phases of the cell cycle of tested HeLa cells by the amount of core histone proteins.

A high precision MUA-spaced single-cell sensor for cellular receptor assay based on bifunctional Au@Cu-PbCQD nanoprobes

A single-cell sensor with a spatial architecture was firstly fabricated for realizing high precision single-cell analysis using an 11-mercaptoundecanoic acid (MUA)-spaced sensing interface to prop up single cells and provide a suitable space for effective nanoprobe labeling. Mercapto acids (MA) with different carbon chain lengths were optimized and MUA was selected to provide optimal interspace on the electrodeposited PANI/AuNP substrates, and its carboxyl could couple with folic acid to capture cancer cells. Bifunctional Au@Cu-PbCQD nanoprobes, in which the AuNP cores were linked with lead-coadsorbed carbon quantum dots (PbCQDs) by a copper(ii) ion bridge, were firstly synthesized and applied as highly sensitive electrochemiluminescence (ECL) probes and electrochemical probes. Hyaluronic acid (HA)-functionalized Au@Cu-PbCQD nanoprobes were labelled on MCF-7 cells via specific recognition to the CD44 receptor, which served as the research model. The ECL response of the sensor was applied to evaluate the validity of nanoprobe labeling. With MUA modified, the sensor was able to enhance the ECL intensity by 37.5 ± 3.9%, indicating the remarkable amelioration of the accuracy of single-cell analysis. To take advantage of the bifunctional nanoprobes, differential pulse voltammetry (DPV) was further applied to confirm the feasibility of the proposed single-cell sensor with a spatial architecture. Therefore, the novel strategy provides a single-cell analysis platform to acquire high-precision analytical results, and more accurately to elucidate cellular heterogeneity and biological function.

Using single cell analysis for translational studies in immune mediated diseases: Opportunities and challenges

The difficulty of studying small tissue samples and rare cell populations have been some of the main limitations in performing efficient translational studies of immune mediated diseases. Many of these conditions are grouped under the name of a single disease whilst there are strong suggestions that disease heterogeneity leads to variable disease progression as well as therapeutic responses. The recent development of single cell techniques, such as single cell RNA sequencing, gene expression profiling, or multiparametric cytometry, is likely to be a turning point. Single cell approaches provide researchers the opportunity to finally dissect disease pathology at a level that will allow mechanistic classifications and precision therapeutic strategies. In this review, we will give an overview of the current and developing repertoire of single cell techniques, the benefits and limitations of each, and provide an example of how single cell techniques can be utilized to understand complex immune mediated diseases and their translation from mouse to human.

Microfluidic and Paper-Based Devices for Disease Detection and Diagnostic Research

Recent developments in microfluidic devices, nanoparticle chemistry, fluorescent microscopy, and biochemical techniques such as genetic identification and antibody capture have provided easier and more sensitive platforms for detecting and diagnosing diseases as well as providing new fundamental insight into disease progression. These advancements have led to the development of new technology and assays capable of easy and early detection of pathogenicity as well as the enhancement of the drug discovery and development pipeline. While some studies have focused on treatment, many of these technologies have found initial success in laboratories as a precursor for clinical applications. This review highlights the current and future progress of microfluidic techniques geared toward the timely and inexpensive diagnosis of disease including technologies aimed at high-throughput single cell analysis for drug development. It also summarizes novel microfluidic approaches to characterize fundamental cellular behavior and heterogeneity.

Single-neuronal cell culture and monitoring platform using a fully transparent microfluidic DEP device

Dielectrophoresis using multi-electrode arrays allows a non-invasive interface with biological cells for long-term monitoring of electrophysiological parameters as well as a label-free and non-destructive technique for neuronal cell manipulation. However, experiments for neuronal cell manipulation utilizing dielectrophoresis have been constrained because dielectrophoresis devices generally function outside of the controlled environment (i.e. incubator) during the cell manipulation process, which is problematic because neurons are highly susceptible to the properties of the physiochemical environment. Furthermore, the conventional multi-electrode arrays designed to generate dielectrophoretic force are often fabricated with non-transparent materials that confound live-cell imaging. Here we present an advanced single-neuronal cell culture and monitoring platform using a fully transparent microfluidic dielectrophoresis device for the unabated monitoring of neuronal cell development and function. The device is mounted inside a sealed incubation chamber to ensure improved homeostatic conditions and reduced contamination risk. Consequently, we successfully trap and culture single neurons on a desired location and monitor their growth process over a week. The proposed single-neuronal cell culture and monitoring platform not only has significant potential to realize an in vitro ordered neuronal network, but also offers a useful tool for a wide range of neurological research and electrophysiological studies of neuronal networks.

Ultrasensitive profiling of multiple biomarkers from single cells by signal amplification mass spectrometry

A signal amplification protocol based on mass spectrometry (MS) was developed to profile simultaneously multiple biomarkers from a single cell using various mass label (ML)-modified Au nanoparticles (AuNPs). The strategy with ultrahigh sensitivity and specificity has potential prospects in the deep exploration of molecular and cellular characterization.

Recent Advances in Scanning Electrochemical Microscopy for Biological Applications

Scanning electrochemical microscopy (SECM) is a chemical microscopy technique with high spatial resolution for imaging sample topography and mapping specific chemical species in liquid environments. With the development of smaller, more sensitive ultramicroelectrodes (UMEs) and more precise computer-controlled measurements, SECM has been widely used to study biological systems over the past three decades. Recent methodological breakthroughs have popularized SECM as a tool for investigating molecular-level chemical reactions. The most common applications include monitoring and analyzing the biological processes associated with enzymatic activity and DNA, and the physiological activity of living cells and other microorganisms. The present article first introduces the basic principles of SECM, followed by an updated review of the applications of SECM in biological studies on enzymes, DNA, proteins, and living cells. Particularly, the potential of SECM for investigating bacterial and biofilm activities is discussed.

Static droplet array for culturing single live adherent cells in an isolated chemical microenvironment

We present here a new method to easily and reliably generate an array of hundreds of dispersed nanoliter-volume semi-droplets for single-cells culture and analysis. The liquid segmentation step occurs directly in indexed traps by a tweezer-like mechanism and is stabilized by spatial confinement. Unlike common droplet-based techniques, the semi-droplet wets its surrounding trap walls thus supporting the culturing of both adherent and non-adherent cells. To eliminate cross-droplet cell migration and chemical cross-talk each semi-droplet is separated from a nearby trap by an ∼80 pL air plug. The overall setup and injection procedure takes less than 10 minutes, is insensitive to fabrication defects and supports cell recovery for downstream analysis. The method offers a new approach to easily capture, image and culture single cells in a chemically isolated microenvironment as a preliminary step towards high-throughput single-cell assays.