Large-scale arrays of picolitre chambers for single-cell analysis of large cell populations

Recent Advances in Microscale Electroporation

Electroporation (EP) is a commonly used strategy to increase cell permeability for intracellular cargo delivery or irreversible cell membrane disruption using electric fields. In recent years, EP performance has been improved by shrinking electrodes and device structures to the microscale. Integration with microfluidics has led to the design of devices performing static EP, where cells are fixed in a defined region, or continuous EP, where cells constantly pass through the device. Each device type performs superior to conventional, macroscale EP devices while providing additional advantages in precision manipulation (static EP) and increased throughput (continuous EP). Microscale EP is gentle on cells and has enabled more sensitive assaying of cells with novel applications. In this Review, we present the physical principles of microscale EP devices and examine design trends in recent years. In addition, we discuss the use of reversible and irreversible EP in the development of therapeutics and analysis of intracellular contents, among other noteworthy applications. This Review aims to inform and encourage scientists and engineers to expand the use of efficient and versatile microscale EP technologies.

Large-scale patterning of single cells and cell clusters in hydrogels

Biophysical properties of the extracellular matrix (ECM) are known to play a significant role in cell behavior. To gain a better understanding of the effects of the biophysical microenvironment on cell behavior, the practical challenge is longitudinally monitoring behavioral variations within a population to make statistically powerful assessments. Population-level measurements mask heterogeneity in cell responses, and large-scale individual cell measurements are often performed in a one-time, snapshot manner after removing cells from their matrix. Here we present an easy and low-cost method for large-scale, longitudinal studies of heterogeneous cell behavior in 3D hydrogel matrices. Using a platform we term "the drop-patterning chip", thousands of cells were simultaneously transferred from microwell arrays and fully embedded, only using the force of gravity, in precise patterns in 3D collagen I or Matrigel. This method allows for throughputs approaching 2D patterning methods that lack phenotypic information on cell-matrix interactions, and does not rely on special equipment and cell treatments that may result in a proximal stiff surface. With a large and yet well-organized group of cells captured in 3D matrices, we demonstrated the capability of locating selected individual cells and monitoring cell division, migration, and proliferation for multiple days.

3D-Printed seed planter and well array for high-throughput seed germination screening

A 3D-printed miniaturized well array and seed planter have been developed for in-field studies of seed quality and screening of conditions for seedlings.

Laser-fabricated cell patterning stencil for single cell analysis

Precise spatial positioning and isolation of mammalian cells is a critical component of many single cell experimental methods and biological engineering applications. Although a variety of cell patterning methods have been demonstrated, many of these methods subject cells to high stress environments, discriminate against certain phenotypes, or are a challenge to implement. Here, we demonstrate a rapid, simple, indiscriminate, and minimally perturbing cell patterning method using a laser fabricated polymer stencil. The stencil fabrication process requires no stencil-substrate alignment, and is readily adaptable to various substrate geometries and experiments.

Single cell patterning for high throughput sub-cellular toxicity assay

Cell population based toxicity assays cannot distinguish responses of single cells and sub-cellular organelles; while single cell assays are limited by low statistical power due to small number of cells examined. This article reports a new single cell array based toxicity assay, in which cell responses at population level, single cell level and sub-cellular level can be obtained simultaneously at high throughput. The single cell array was produced by microcontact printing and selected area cell attachment, and exposed to damaging X-ray radiation, which was followed by fluorescence imaging after staining. Two image processing softwares written in Python and MATLAB were used to determine the expressions of proteins associated with cell migration and invasion, and production of reactive oxygen species (ROS), respectively. The results showed significant differences in responses at single cell level and distinctive molecular heterogeneity at sub-cellular level in a large population of cells upon exposure to radiation.

Massive Parallel Analysis of Single Cells in an Integrated Microfluidic Platform

New tools that facilitate the study of cell-to-cell variability could help uncover novel cellular regulation mechanisms. We present an integrated microfluidic platform to analyze a large number of single cells in parallel. To isolate and analyze thousands of individual cells in multiplexed conditions, our platform incorporates arrays of microwells (7 pL each) in a multilayered microfluidic device. The device allows the simultaneous loading of cells into 16 separate chambers, each containing 4640 microwells, for a total of 74 240 wells per device. We characterized different parameters important for the operation of the microfluidic device including flow rate, solution exchange rate in a microchamber, shear stress, and time to fill up a single microwell with molecules of different molecular weight. In general, after ∼7.5 min of cell loading our device has an 80% microwell occupancy with 1-4 cells, of which 36% of wells contained a single cell. To test the functionality of our device, we carried out a cell viability assay with adherent and nonadherent cells. We also studied the production of neutrophil extracellular traps (NETs) from single neutrophils isolated from peripheral blood, observing the existence of temporal heterogeneity in NETs production, perhaps having implications in the type of the neutrophil response to an infection or inflammation. We foresee our platform will have a variety of applications in drug discovery and cellular biology by facilitating the characterization of phenotypic differences in a monoclonal cell population.

Micro/extended-nano sampling interface from a living single cell

Single-cell analysis is of increasing importance in many fields, but is challenging due to the ultra-small volumes (picoliters) of single cells. Indeed, analysis of a specific analyte might require the analysis of a single molecule or several molecules. Analytical processes usually include sampling, chemical processing, and detection. Although several papers have reported chemical processing and detection methods for single cells, a sampling method compatible with maintaining the viability of a single cell during sampling has yet to be developed. Here, we propose a femtoliter sampling method from a living single cell using micro/nanofluidic device technology. The sampling of 39 fL of cytoplasm from a single human aortic endothelial cell was demonstrated and its viability after sampling was confirmed.

Microfluidic Platform for Parallel Single Cell Analysis for Diagnostic Applications

Cell populations are heterogeneous: they can comprise different cell types or even cells at different stages of the cell cycle and/or of biological processes. Furthermore, molecular processes taking place in cells are stochastic in nature. Therefore, cellular analysis must be brought down to the single cell level to get useful insight into biological processes, and to access essential molecular information that would be lost when using a cell population analysis approach. Furthermore, to fully characterize a cell population, ideally, information both at the single cell level and on the whole cell population is required, which calls for analyzing each individual cell in a population in a parallel manner. This single cell level analysis approach is particularly important for diagnostic applications to unravel molecular perturbations at the onset of a disease, to identify biomarkers, and for personalized medicine, not only because of the heterogeneity of the cell sample, but also due to the availability of a reduced amount of cells, or even unique cells. This chapter presents a versatile platform meant for the parallel analysis of individual cells, with a particular focus on diagnostic applications and the analysis of cancer cells. We first describe one essential step of this parallel single cell analysis protocol, which is the trapping of individual cells in dedicated structures. Following this, we report different steps of a whole analytical process, including on-chip cell staining and imaging, cell membrane permeabilization and/or lysis using either chemical or physical means, and retrieval of the cell molecular content in dedicated channels for further analysis. This series of experiments illustrates the versatility of the herein-presented platform and its suitability for various analysis schemes and different analytical purposes.

Fast and Inexpensive Detection of Bacterial Viability and Drug Effectiveness through Metabolic Monitoring

Conventional methods for the detection of bacterial infection such as DNA or immunoassays are expensive, time consuming, or not definitive and thus may not provide all the information sought by medical professionals. In particular, it is difficult to obtain information about viability or drug effectiveness, which is crucial to formulate a treatment. Bacterial culture tests are the “gold standard” because they are inexpensive and do not require extensive sample preparation, and most importantly, provide all the necessary information sought by healthcare professionals, such as bacterial presence, viability and drug effectiveness. These conventional culture methods, however, have a long turnaround time, anywhere between 1 day and 4 weeks. Here, we solve this problem by monitoring the growth of bacteria in thousands of nanowells simultaneously to more quickly identify their presence in the sample and their viability. The segmentation of a sample with low bacterial concentration into thousands of nanoliter wells digitizes the samples and increases the effective concentration in those wells that contain bacteria. We monitor the metabolism of aerobic bacteria by using an oxygen-sensitive fluorophore, ruthenium tris (2,2’-diprydl) dichloride hexahydrate (RTDP), which allows us to monitor the dissolved oxygen concentration in the nanowells. Using E. coli K12 as a model pathogen, we demonstrate that the detection time of E. coli can be as fast as 35–60 min with sample concentrations varying from 10⁴ (62 min for detection), 10⁶ (42 min) and 10⁸ cells/mL (38 min). More importantly, we also demonstrate that reducing the well size can reduce the detection time. Finally we show that drug effectiveness information can be obtained in this format by loading the wells with the drug and monitoring the metabolism of the bacteria. The method that we have developed is low cost, simple, requires minimal sample preparation and can potentially be used with a wide variety of samples in a resource-poor setting to detect bacterial infections such as tuberculosis.

Efficient analysis of a small number of cancer cells at the single-cell level using an electroactive double-well array

Analysis of the intracellular materials of a small number of cancer cells at the single-cell level is important to improve our understanding of cellular heterogeneity in rare cells. To analyze an extremely small number of cancer cells (less than hundreds of cells), an efficient system is required in order to analyze target cells with minimal sample loss. Here, we present a novel approach utilizing an advanced electroactive double-well array (EdWA) for on-chip analysis of a small number of cancer cells at the single-cell level with minimal loss of target cells. The EdWA consisted of cell-sized trap-wells for deterministic single-cell trapping using dielectrophoresis and high aspect ratio reaction-wells for confining the cell lysates extracted by lysing trapped single cells via electroporation. We demonstrated a highly efficient single-cell arraying (a cell capture efficiency of 96 ± 3%) by trapping diluted human prostate cancer cells (PC3 cells). On-chip single-cell analysis was performed by measuring the intracellular β-galactosidase (β-gal) activity after lysing the trapped single cells inside a tightly enclosed EdWA in the presence of a fluorogenic enzyme substrate. The PC3 cells showed large cell-to-cell variations in β-gal activity although they were cultured under the same conditions in a culture dish. This simple and effective system has great potential for high throughput single-cell analysis of rare cells.

Single cells in confined volumes: microchambers and microdroplets

Microfluidic devices capable of manipulating and guiding small fluid volumes open new methodical approaches in the fields of biology, pharmacy, and medicine. They have already proven their extraordinary value for cell analysis. The emergence of microfluidic platforms has paved the way to novel analytical strategies for the positioning, treatment and observation of living cells, for the creation of chemically defined liquid environments, and for tailoring biomechanical or physical conditions in small volumes. In this article, we particularly focus on two complementary approaches: (i) the isolation of cells in small chambers defined by microchannels and integrated valves and (ii) the encapsulation of cells in microdroplets. We review the advantages and limitations of both approaches and discuss their potential for single-cell analysis and related fields. Our intention is also to give a recommendation on which platform is most appropriate for a new question, i.e., a guideline to choose the most suitable platform.

Sub-population analysis of deformability distribution in heterogeneous red blood cell population

We present a method for sub-population analysis of deformability distribution using single-cell microchamber array (SiCMA) technology. It is a unique method allowing the correlation of overall cellular characteristics with surface and cytosolic characteristics to define the distribution of individual cellular characteristics in heterogeneous cell populations. As a proof of principle, reticulocytes, the immature sub-population of red blood cells (RBC), were recognized from RBC population by a surface marker and different characteristics on deformability between these populations were characterized. The proposed technology can be used in a variety of applications that would benefit from the ability to measure the distribution of cellular characteristics in complex populations, especially important to define hematologic disorders.

Biomechanical properties of red blood cells in health and disease towards microfluidics

Red blood cells (RBCs) possess a unique capacity for undergoing cellular deformation to navigate across various human microcirculation vessels, enabling them to pass through capillaries that are smaller than their diameter and to carry out their role as gas carriers between blood and tissues. Since there is growing evidence that red blood cell deformability is impaired in some pathological conditions, measurement of RBC deformability has been the focus of numerous studies over the past decades. Nevertheless, reports on healthy and pathological RBCs are currently limited and, in many cases, are not expressed in terms of well-defined cell membrane parameters such as elasticity and viscosity. Hence, it is often difficult to integrate these results into the basic understanding of RBC behaviour, as well as into clinical applications. The aim of this review is to summarize currently available reports on RBC deformability and to highlight its association with various human diseases such as hereditary disorders (e.g., spherocytosis, elliptocytosis, ovalocytosis, and stomatocytosis), metabolic disorders (e.g., diabetes, hypercholesterolemia, obesity), adenosine triphosphate-induced membrane changes, oxidative stress, and paroxysmal nocturnal hemoglobinuria. Microfluidic techniques have been identified as the key to develop state-of-the-art dynamic experimental models for elucidating the significance of RBC membrane alterations in pathological conditions and the role that such alterations play in the microvasculature flow dynamics.

Quantifying genetically inserted fluorescent protein in single iPS cells to monitor Nanog expression using electroactive microchamber arrays

Interest in the gene expression levels of pluripotent stem cells has increased in order to precisely understand cellular differentiation. Here, we propose a method utilizing a large number of arrayed microchambers to quantitatively measure an intracellular fluorescence protein that is genetically inserted to monitor a pluripotency marker protein, Nanog, in pluripotent stem cells. Individual cells are isolated and lysed by inducing an electric potential on the cell membrane within the tightly enclosed microchambers. The microchambers have a size that is comparable to the target cells, making it possible to trap single cells and restrict the dilution of the cell lysate. The amount of intracellular fluorescence proteins in a single cell is precisely quantified inside the well-defined volume of each microchamber. Our method will be a useful tool for high-throughput and parallelized read-outs of gene expression levels in individual cells in a large population of cells.

Advanced combinational microfluidic multiplexer using multiple levels of control pressures

We propose an advanced combinational microfluidic multiplexing method capable of increasing the number of addressable fluidic channels dramatically. Using only 4 control lines, the proposed advanced combinational multiplexer, utilizing two different levels of control pressure, could address up to 19 fluidic channels, which is at least two times larger than previous multiplexers. The difference between the maximum addressable channels in the present and previous methods increases dramatically when the control lines and control pressure levels increase. The present multiplexer, with its high control efficiency and simple structure for channel addressing, could be used in the application areas of integrated microfluidic systems such as high-throughput analyzers and dynamic pressure generators.

Rapid identification and drug susceptibility screening of ESAT-6 secreting Mycobacteria by a NanoELIwell assay

To meet the global needs of tuberculosis (TB) control, a nanoELIwell device was developed as a multifunctional assay for TB diagnosis and drug susceptibility testing. The device integrates on-chip culturing of mycobacteria, immunoassay, and high-resolution fluorescent imaging. Mycobacterium smegmatis and Mycobacterium kansasii were used as models of Mycobacterium tuberculosis to evaluate device integrity by using antigens, Ag85 and ESAT-6, as biomarkers. As a result, the nanoELIwell device detected antigens released from a single bacterium within 24–48-hour culture. Antimycobacterial drug-treated M. smegmatis showed significant decreased in Ag85 antigen production when treated with ethambutol and no change in antigen production when treated with rifampin, demonstrating drug susceptibility and resistance, respectively. The nanoELIwell assay also distinguished the ESAT-6-secreting M. kansasii from the non-ESAT-6-secreting M. simiae. The combination of microwell technology and ELISA assay holds potential to the development of a rapid, sensitive, and specific diagnostics and susceptibility testing of TB.

Deformation measurement of individual cells in large populations using a single-cell microchamber array chip

We analyze the deformability of individual red blood cells (RBCs) using SiCMA technology. Our approach is adequate to quickly measure large numbers of individual cells in heterogeneous populations. Individual cells are trapped in a large-scale array of micro-wells, and dielectrophoretic (DEP) force is applied to deform the cells. The simple structures of micro-wells and DEP electrodes facilitate the analysis of thousands of RBCs in parallel. This unique method allows the correlation of red cell deformation with cell surface and cytosolic characteristics to define the distribution of individual cellular characteristics in heterogeneous populations.

Trapping cells on a stretchable microwell array for single-cell analysis

There is a need for a technology that can be incorporated into routine laboratory procedures to obtain a continuous, quantitative, fluorescence-based measurement of the dynamic behaviors of numerous individual living cells in parallel, while allowing other manipulations, such as staining, rinsing, and even retrieval of targeted cells. Here, we report a simple, low-cost microarray platform that can trap cells for dynamic single-cell analysis of mammalian cells. The elasticity of polydimethylsiloxane (PDMS) was utilized to trap tens of thousands of cells on an array. The PDMS microwell array was stretched by a tube through which cells were loaded on the array. Cells were trapped on the array by removal of the tube and relaxation of the PDMS. Once that was accomplished, the cells remained trapped on the array without continuous application of an external force and permitted subsequent manipulations, such as staining, rinsing, imaging, and even isolation of targeted cells. We demonstrate the utility of this platform by multicolor analysis of trapped cells and monitoring in individual cells real-time calcium flux after exposure to the calcium ionophore ionomycin. Additionally, a proof of concept for target cell isolation was demonstrated by using a microneedle to locally deform the PDMS membrane in order to retrieve a particular cell from the array.

Analytical technologies for integrated single-cell analysis of human immune responses

The immune system is a network of cells in which the constitutive members interact through dense and sometimes overlapping connections. The extreme complexity of this network poses a significant challenge for monitoring pathological conditions (e.g., food allergies, autoimmunity, and other chronic inflammatory diseases) and for discovering robust signatures of immunological responses that correlate with or predict the efficacy of interventions. The diversity among immune cells found in clinical samples (variations in cellular functions, lineages, and clonotypic breadth) requires approaches for monitoring immune responses with single-cell resolution.In this chapter, we present an engineering approach for integrated single-cell analysis that uses interchangeable modular operations to provide a comprehensive characterization of the phenotypic, functional, and genetic variations for individual cells. We focus on the use of microfabricated devices to isolate and interrogate single cells, and on the analytical components that enable subsequent detection, correlation, and interpretation of multidimensional sets of data. We discuss specific challenges and opportunities in the realization of this concept, and review two examples where it has been implemented. The presented approach should provide a basis for the design and implementation of nonconventional bioanalytical processes for studying specific responses of an immune system.

Expanding the horizons for single-cell applications on lab-on-a-chip devices

Stochastic events in gene expression, protein synthesis, and metabolite synthesis or degradation lead to cellular heterogeneity essential to life. In a tissue as we see in organs, there is strong heterogeneity among the constituting cells critical to its function. Thus, there exists a strong demand to develop new micro/nanosystems that would enable us to conduct single-cell analysis. This field is rapidly growing, as exemplified below with recent emerging technologies that now reveal sensitive single-cell "omics" analysis. We describe in the review some of the most promising technologies that will certainly transform our view of biology in the near future.

Electroactive microwell arrays for highly efficient single-cell trapping and analysis

We present a novel method, implemented in the form of a microfluidic device, for arraying and analyzing large populations of single cells. The device contains a large array of electroactive microwells where manipulation and analysis of large population of cells are carried out. On the device, single cells can be actively trapped in the microwells by dielectrophoresis (DEP) and then lysed by electroporation (EP) for subsequent analysis of the confined cell lysates. The DEP force in the selected dimensions of the microwells could achieve efficient trapping in nearly all the microwells (95%) in less than three minutes. Moreover, the positions of the cells in the microwells are maintained even when unstable flow of liquid is applied. This makes it possible to exchange the DEP buffer to a solution that will be subsequently used for stimulating or analyzing the trapped cells. After closing the microwells, EP is conducted to lyse the trapped cells by applying short electric pulses. Tight enclosure is critical to prevent dilution, diffusion and cross contamination of the cell lysates. We demonstrated the feasibility of our approach with an enzymatic assay measuring the intracellular-galactosidase activity. The use of this method should greatly help analysis of large populations of cells at the single-cell level. Furthermore, the method offers rapidity in the trapping and analysis of multiple cell types in physiological conditions that will be important to ensure the relevance of single cell analyses.

Parallel single-cell analysis microfluidic platform

We report a PDMS microfluidic platform for parallel single-cell analysis (PaSCAl) as a powerful tool to decipher the heterogeneity found in cell populations. Cells are trapped individually in dedicated pockets, and thereafter, a number of invasive or non-invasive analysis schemes are performed. First, we report single-cell trapping in a fast (2-5  min) and reproducible manner with a single-cell capture yield of 85% using two cell lines (P3x63Ag8 and MCF-7), employing a protocol which is scalable and easily amenable to automation. Following this, a mixed population of P3x63Ag8 and MCF-7 cells is stained in situ using the nucleic acid probe (Hoechst) and a phycoerythrin-labeled monoclonal antibody directed at EpCAM present on the surface of the breast cancer cells MCF-7 and absent on the myeloma cells P3x63Ag8 to illustrate the potential of the device to analyze cell population heterogeneity. Next, cells are porated in situ using chemicals in a reversible (digitonin) or irreversible way (lithium dodecyl sulfate). This is visualized by the transportation of fluorescent dyes through the membrane (propidium iodide and calcein). Finally, an electrical protocol is developed for combined cell permeabilization and electroosmotic flow (EOF)-based extraction of the cell content. It is validated here using calcein-loaded cells and visualized through the progressive recovery of calcein in the side channels, indicating successful retrieval of individual cell content.

An electroactive microwell array for trapping and lysing single-bacterial cells

Interest in single-cell analysis has increased because it allows to understand cell metabolism and characterize disease states, cellular adaptation to environmental changes, cell cycles, etc. Here, the authors propose a device to electrically trap and lyse single-bacterial cells in an array format for high-throughput single-cell analysis. The applied electric field is highly deformed and concentrated toward the inside of the microwell structures patterned on the planar electrode. This configuration effectively generates dielectrophoretic force to attract a single cell per well. The microwell has a comparable size to the target bacterial cell making it possible to trap single cells by physically excluding additional cells. Inducing highly concentrated electric potential on the cell membrane can also effectively lyse the trapped single-bacterial cells. The feasibility of the authors' approach was demonstrated by trapping and lysing Escherichia coli cells at the single-cell level. The present microwell array can be used as a basic tool for individual bacterial cell analysis.