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

Highly efficient combination of multiple single cells using a deterministic single-cell combinatorial reactor

Compartmentalization of multiple single cells and/or single microbeads holds significant potential for advanced biological research including single-cell transcriptome analysis or cell-cell interactions. To ensure reliable analysis and prevent misinterpretation, it is essential to achieve highly efficient pairing or combining of single objects. In this paper, we introduce a novel microfluidic device coupled with a multilayer interconnect Si/SiO2 control circuit, named the deterministic single-cell combinatorial reactor (DSCR) device, for the highly efficient combination of multiple single cells. The deterministic combination of multiple single cells is realized by sequentially introducing and trapping each cell population into designated trap-wells within each DSCR. These cell-sized trap-wells, created by etching the SiO2 passivation layer, generate a highly localized electric field that facilitates deterministic single-cell trapping. The device's multilayer interconnection of electrodes enables the sequential operation of each trap-well, allowing precise trapping of each cell population into designated trap-wells within an array of combinatorial reactors. We demonstrated the feasibility of the DSCR by sequentially trapping three distinct groups of PC3 cells, each stained with a different fluorescent dye (blue, green, or red). This method achieved a 93 ± 2% pairing efficiency for two cell populations and an 82 ± 7% combination efficiency for three cell populations. Our innovative system offers promising applications for analyzing multiple cell-cell communications and combinatorial indexing of single cells.

On-chip dielectrophoretic single-cell manipulation

Bioanalysis at a single-cell level has yielded unparalleled insight into the heterogeneity of complex biological samples. Combined with Lab-on-a-Chip concepts, various simultaneous and high-frequency techniques and microfluidic platforms have led to the development of high-throughput platforms for single-cell analysis. Dielectrophoresis (DEP), an electrical approach based on the dielectric property of target cells, makes it possible to efficiently manipulate individual cells without labeling. This review focusses on the engineering designs of recent advanced microfluidic designs that utilize DEP techniques for multiple single-cell analyses. On-chip DEP is primarily effectuated by the induced dipole of dielectric particles, (i.e., cells) in a non-uniform electric field. In addition to simply capturing and releasing particles, DEP can also aid in more complex manipulations, such as rotation and moving along arbitrary predefined routes for numerous applications. Correspondingly, DEP electrodes can be designed with different patterns to achieve different geometric boundaries of the electric fields. Since many single-cell analyses require isolation and compartmentalization of individual cells, specific microstructures can also be incorporated into DEP devices. This article discusses common electrical and physical designs of single-cell DEP microfluidic devices as well as different categories of electrodes and microstructures. In addition, an up-to-date summary of achievements and challenges in current designs, together with prospects for future design direction, is provided.

Automating CAR-T Transfection with Micro and Nano-Technologies

Cancer poses a significant health challenge, with traditional treatments like surgery, radiotherapy, and chemotherapy often lacking in cell specificity and long-term curative potential. Chimeric antigen receptor T cell (CAR-T) therapy,utilizing genetically engineered T cells to target cancer cells, is a promising alternative. However, its high cost limits widespread application. CAR-T manufacturing process encompasses three stages: cell isolation and activation, transfection, and expansion.While the first and last stages have straightforward, commercially available automation technologies, the transfection stage lags behind. Current automated transfection relies on viral vectors or bulk electroporation, which have drawbacks such as limited cargo capacity and significant cell disturbance. Conversely, micro and nano-tool methods offer higher throughput and cargo flexibility, yet their automation remains underexplored.In this perspective, the progress in micro and nano-engineering tools for CAR-T transfection followed by a discussion to automate them is described. It is anticipated that this work can inspire the community working on micro and nano transfection techniques to examine how their protocols can be automated to align with the growing interest in automating CAR-T manufacturing.

Optoelectronic Tweezers Micro-Well System for Highly Efficient Single-Cell Trapping, Dynamic Sorting, and Retrieval

Single-cell arrays have emerged as a versatile method for executing single-cell manipulations across an array of biological applications. In this paper, an innovative microfluidic platform is unveiled that utilizes optoelectronic tweezers (OETs) to array and sort individual cells at a flow rate of 20 µL min-1. This platform is also adept at executing dielectrophoresis (DEP)-based, light-guided single-cell retrievals from designated micro-wells. This presents a compelling non-contact method for the rapid and straightforward sorting of cells that are hard to distinguish. Within this system, cells are individually confined to micro-wells, achieving an impressive high single-cell capture rate exceeding 91.9%. The roles of illuminating patterns, flow velocities, and applied electrical voltages are delved into in enhancing the single-cell capture rate. By integrating the OET system with the micro-well arrays, the device showcases adaptability and a plethora of functions. It can concurrently trap and segregate specific cells, guided by their dielectric signatures. Experimental results, derived from a mixed sample of HepG2 and L-O2 cells, reveal a sorting accuracy for L-O2 cells surpassing 91%. Fluorescence markers allow for the identification of sequestered, fluorescence-tagged HepG2 cells, which can subsequently be selectively released within the chip. This platform's rapidity in capturing and releasing individual cells augments its potential for future biological research and applications.

Single-cell trapping and retrieval in open microfluidics

Among various single-cell analysis platforms, hydrodynamic cell trapping systems remain relevant because of their versatility. Among those, deterministic hydrodynamic cell-trapping systems have received significant interest; however, their applications are limited because trapped cells are kept within the closed microchannel, thus prohibiting access to external cell-picking devices. In this study, we develop a hydrodynamic cell-trapping system in an open microfluidics architecture to allow external access to trapped cells. A technique to render only the inside of a polydimethylsiloxane (PDMS) microchannel hydrophilic is developed, which allows the precise confinement of spontaneous capillary flow in the open-type microchannel with a width on the order of several tens of micrometers. Efficient trapping of single beads and single cells is achieved, in which trapped cells can be retrieved via automated robotic pipetting. The present system can facilitate the development of new single-cell analytical systems by bridging between microfluidic devices and macro-scale apparatus used in conventional biology.

Massively Parallel High-Throughput Single-Cell Patterning and Large Biomolecular Delivery in Mammalian Cells Using Light Pulses

The recent advancements of single-cell analysis have significantly enhanced the ability to understand cellular physiology when compared to bulk cellular analysis. Here a massively parallel single-cell patterning and very large biomolecular delivery is reported. Micro-pillar polydimethyl siloxane stamp with different diameters (40-100 µm with 1 cm × 1 cm patterning area) is fabricated and then imprint distinct proteins and finally pattern single-cell to small clusters of cells depending on the micro-pillar diameters. The maximum patterning efficiency is achieved 99.7% for SiHa, 96.75% for L929, and 98.6% for MG63 cells, for the 100 µm micro-pillar stamp. For intracellular delivery of biomolecules into the patterned cells, a titanium micro-dish device is aligned on top of the cells and exposed by infrared light pulses. The platform successfully delivers small to very large biomolecules such as PI dyes (668 Da), dextran 3000 Da, siRNA (20-24 bp), and large size enzymes (464 KDa) in SiHa, L929 and MG63 cells. The delivery efficiency for PI dye, Dextran 3000, siRNA, and enzyme for patterned cells are ≈95 ± 3%, 97 ± 1%, 96 ± 1% and 94 ± 3%, with cell viability of 98 ± 1%. Thus, the platform is compact, robust, easy for printing, and potentially applicable for single-cell therapy and diagnostics.

Dielectrophoretic trapping of nanosized biomolecules on plasmonic nanohole arrays for biosensor applications: simple fabrication and visible-region detection

Surface plasmon resonance is an optical phenomenon that can be applied for label-free, real-time sensing to directly measure biomolecular interactions and detect biomarkers in solutions. Previous studies using plasmonic nanohole arrays have monitored and detected various biomolecules owing to the propagating surface plasmon polaritons (SPPs). Extraordinary optical transmission (EOT) that occurs in the near-infrared (NIR) and infrared (IR) regions is usually used for detection. Although these plasmonic nanohole arrays improve the sensitivity and throughput for biomolecular detection, these arrays have the following disadvantages: (1) molecular diffusion in the solution (making the detection of biomolecules difficult), (2) the device fabrication's complexities, and (3) expensive equipments for detection in the NIR or IR regions. Therefore, there is a need to fabricate plasmonic nanohole arrays as biomolecular detection platforms using a simple and highly reproducible procedure based on other SPP modes in the visible region instead of the EOT in the NIR or IR regions while suppressing molecular diffusion in the solution. In this paper, we propose the combination of a polymer-based gold nanohole array (Au NHA) obtained through an easy process as a simple platform and dielectrophoresis (DEP) as a biomolecule manipulation method. This approach was experimentally demonstrated using SPP and LSPR modes (not EOT) in the visible region and simple, label-free, rapid, cost-effective trapping and enrichment of nanoparticles (trapping time: <50 s) and bovine serum albumin (trapping time: <1000 s) was realized. These results prove that the Au NHA-based DEP devices have great potential for real-time digital and Raman bioimaging, in addition to biomarker detection.

Quantification of capture efficiency, purity, and single-cell isolation in the recovery of circulating melanoma cells from peripheral blood by dielectrophoresis

This paper describes a dielectrophoretic method for selection of circulating melanoma cells (CMCs), which lack reliable identifying surface antigens and are extremely rare in blood. This platform captures CMCs individually by dielectrophoresis (DEP) at an array of wireless bipolar electrodes (BPEs) aligned to overlying nanoliter-scale chambers, which isolate each cell for subsequent on-chip single-cell analysis. To determine the best conditions to employ for CMC isolation in this DEP-BPE platform, the static and dynamic dielectrophoretic response of established melanoma cell lines, melanoma cells from patient-derived xenografts (PDX) and peripheral blood mononuclear cells (PBMCs) were evaluated as a function of frequency using two established DEP platforms. Further, PBMCs derived from patients with advanced melanoma were compared with those from healthy controls. The results of this evaluation reveal that each DEP method requires a distinct frequency to achieve capture of melanoma cells and that the distribution of dielectric properties of PBMCs is more broadly varied in and among patients versus healthy controls. Based on this evaluation, we conclude that 50 kHz provides the highest capture efficiency on our DEP-BPE platform while maintaining a low rate of capture of unwanted PBMCs. We further quantified the efficiency of single-cell capture on the DEP-BPE platform and found that the efficiency diminished beyond around 25% chamber occupancy, thereby informing the minimum array size that is required. Importantly, the capture efficiency of the DEP-BPE platform for melanoma cells when using optimized conditions matched the performance predicted by our analysis. Finally, isolation of melanoma cells from contrived (spike-in) and clinical samples on our platform using optimized conditions was demonstrated. The capture and individual isolation of CMCs, confirmed by post-capture labeling, from patient-derived samples suggests the potential of this platform for clinical application.

Highly efficient cell-microbead encapsulation using dielectrophoresis-assisted dual-nanowell array

Recent advancements in micro/nanofabrication techniques have led to the development of portable devices for high-throughput single-cell analysis through the isolation of individual target cells, which are then paired with functionalized microbeads. Compared with commercially available benchtop instruments, portable microfluidic devices can be more widely and cost-effectively adopted in single-cell transcriptome and proteome analysis. The sample utilization and cell pairing rate (∼33%) of current stochastic-based cell-bead pairing approaches are fundamentally limited by Poisson statistics. Despite versatile technologies having been proposed to reduce randomness during the cell-bead pairing process in order to statistically beat the Poisson limit, improvement of the overall pairing rate of a single cell to a single bead is typically based on increased operational complexity and extra instability. In this article, we present a dielectrophoresis (DEP)-assisted dual-nanowell array (ddNA) device, which employs an innovative microstructure design and operating process that decouples the bead- and cell-loading processes. Our ddNA design contains thousands of subnanoliter microwell pairs specifically tailored to fit both beads and cells. Interdigitated electrodes (IDEs) are placed below the microwell structure to introduce a DEP force on cells, yielding high single-cell capture and pairing rates. Experimental results with human embryonic kidney cells confirmed the suitability and reproducibility of our design. We achieved a single-bead capture rate of >97% and a cell-bead pairing rate of >75%. We anticipate that our device will enhance the application of single-cell analysis in practical clinical use and academic research.

Dielectrophoresis-Based Selective Droplet Extraction Microfluidic Device for Single-Cell Analysis

We developed a microfluidic device that enables selective droplet extraction from multiple droplet-trapping pockets based on dielectrophoresis. The device consists of a main microchannel, five droplet-trapping pockets with side channels, and drive electrode pairs appropriately located around the trapping pockets. Agarose droplets capable of encapsulating biological samples were successfully trapped in the trapping pockets due to the difference in flow resistance between the main and side channels. Target droplets were selectively extracted from the pockets by the dielectrophoretic force generated between the electrodes under an applied voltage of 500 V. During their extraction from the trapping pockets, the droplets and their contents were exposed to an electric field for 400-800 ms. To evaluate whether the applied voltage could potentially damage the biological samples, the growth rates of Escherichia coli cells in the droplets, with and without a voltage applied, were compared. No significant difference in the growth rate was observed. The developed device enables the screening of encapsulated single cells and the selective extraction of target droplets.

FLUIDOT: A Modular Microfluidic Platform for Single-Cell Study and Retrieval, with Applications in Drug Tolerance Screening and Antibody Mining

Advancements in lab-on-a-chip technologies have revolutionized the single-cell analysis field. However, an accessible platform for in-depth screening and specific retrieval of single cells, which moreover enables studying diverse cell types and performing various downstream analyses, is still lacking. As a solution, FLUIDOT is introduced, a versatile microfluidic platform incorporating customizable microwells, optical tweezers and an interchangeable cell-retrieval system. Thanks to its smart microfluidic design, FLUIDOT is straightforward to fabricate and operate, rendering the technology widely accessible. The performance of FLUIDOT is validated and its versatility is subsequently demonstrated in two applications. First, drug tolerance in yeast cells is studied, resulting in the discovery of two treatment-tolerant populations. Second, B cells from convalescent COVID-19 patients are screened, leading to the discovery of highly affine, in vitro neutralizing monoclonal antibodies against SARS-CoV-2. Owing to its performance, flexibility, and accessibility, it is foreseen that FLUIDOT will enable phenotypic and genotypic analysis of diverse cell samples and thus elucidate unexplored biological questions.

On-Chip Enrichment System for Digital Bioassay Based on Aqueous Two-Phase System

We developed an on-chip enrichment method based on an aqueous two-phase system of dextran/polyethylene glycol mix, DEX/PEG ATPS, for digital bioassay. Accordingly, we prepared an array device of femtoliter reactors that displays millions of uniformly shaped DEX-rich droplets under a PEG-rich medium. The DEX-rich droplets effectively enriched DNA molecules from the PEG-rich medium. To quantify the enrichment power of the system, we performed a digital bioassay of alkaline phosphatase (ALP). Upon genetically tagging ALP molecules with the DEX-binding domain (DBD) derived from dextransucrase, the ALP molecules were enriched 59-fold in the DEX droplets in comparison to that in a conventional digital bioassay. Subsequently, we performed a Cas13-based digital SARS-CoV-2 RNA detection assay to evaluate the performance of this system for a more practical assay. In this assay, the target RNA molecules bound to the DBD-tagged Cas13 molecules were effectively enriched in the DEX droplets. Consequently, an enrichment factor of 31 was achieved. Enrichment experiments for nonlabeled proteins were also performed to test the expandability of this technique. The model protein, nontagged β-galactosidase, was enriched in DEX droplets containing DBD-tagged antibody, with an enrichment factor of over 100. Thus, this system enabled effective on-chip enrichment of target molecules to enhance the detection sensitivity of digital bioassays without using external instruments or an external power source, which would be applicable for on-site bioassays or portable diagnostic tests.

Advances in precise single-cell capture for analysis and biological applications

Cells are the basic structural and functional units of living organisms. However, conventional cell analysis only averages millions of cell populations, and some important information is lost. It is essential to quantitatively characterize the physiology and pathology of single-cell activities. Precise single-cell capture is an extremely challenging task during cell sample preparation. In this review, we summarize the category of technologies to capture single cells precisely with a focus on the latest development in the last five years. Each technology has its own set of benefits and specific challenges, which provide opportunities for researchers in different fields. Accordingly, we introduce the applications of captured single cells in cancer diagnosis, analysis of metabolism and secretion, and disease treatment. Finally, some perspectives are provided on the current development trends, future research directions, and challenges of single-cell capture.

An electroactive microwell array device to realize simultaneous trapping of single cancer cells and clusters

The importance of circulating tumor cells (CTCs) as biomarkers has been greatly increased for early diagnosis and detection of cancer metastases. Along with a single form of CTCs, CTC clusters have recently attracted much attention due to their characteristics, such as suppression of apoptosis and survival from immune responses with high metastatic potential. Thus, it is highly necessary to investigate not only single cells but clustered cells at the same time to perform precise analysis of the current cancer state and develop suitable treatment. However, no cancer marker-free microfluidic devices have been realized to trap single cells and clusters at the same time in a single device yet. In this paper, we introduced a novel microfluidic device utilizing a microwell-on-electrode (MOE) array to realize simultaneous trapping of a single cell and clustered cells at a single cell/cluster level. Cell-sized microwells fabricated on interdigitated electrodes efficiently arrayed single cells with high trapping efficiency and single-cell occupancy (more than 90%) using dielectrophoresis (DEP). This high single cell trapping performance of MOE allows arraying of single clusters by trapping one of the cells that constitute a cluster. The feasibility of the MOE device for simultaneous arraying of single cancer cells and clusters was demonstrated by trapping a mixture of single cancer cells and clusters and measuring the size distribution of trapped clusters, which was almost identical with that of introduced cell population. Our work demonstrated that the developed MOE device can be one of the promising methods for trapping single cancer cells as well as clusters on a single device for cancer diagnosis and performing further analyses at a single cell/cluster level.

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.

Selective Single-Cell Sorting Using a Multisectorial Electroactive Nanowell Platform

Current approaches in targeted patient treatments often require the rapid isolation of specific rare target cells. Stream-based dielectrophoresis (DEP) based cell sorters have the limitation that the maximum number of sortable cell types is equivalent to the number of output channels, which makes upscaling to a higher number of different cell types technically challenging. Here, we present a microfluidic platform for selective single-cell sorting that bypasses this limitation. The platform consists of 10 000 nanoliter wells which are placed on top of interdigitated electrodes (IDEs) that facilitate dielectrophoresis-driven capture of cells. By use of a multisectorial design formed by 10 individually addressable IDE structures, our platform can capture a large number of different cell types. The sectorial approach allows for fast and straightforward modification to sort complex samples as different cell types are captured in different sectors and therefore removes the need for individual output channels per cell type. Experimental results obtained with a mixed sample of benign (MCF-10A) and malignant (MDA-MB-231) breast cells showed a target to nontarget sorting accuracy of over 95%. We envision that the high accuracy of our platform, in addition to its versatility and simplicity, will aid clinical environments where reliable sorting of varying complex samples is essential.

Highly Efficient Capture and Quantification of the Airborne Fungal Pathogen Sclerotinia sclerotiorum Employing a Nanoelectrode-Activated Microwell Array

In this study, we present a microdevice for the capture and quantification of Sclerotinia sclerotiorum spores, pathogenic agents of one of the most harmful infectious diseases of crops, Sclerotinia stem rot. The early prognosis of an outbreak is critical to avoid severe economic losses and can be achieved by the detection of a small number of airborne spores. However, the current lack of simple and effective methods to quantify fungal airborne pathogens has hindered the development of an accurate early warning system. We developed a device that remedies these limitations based on a microfluidic design that contains a nanothick aluminum electrode structure integrated with a picoliter well array for dielectrophoresis-driven capture of spores and on-chip quantitative detection employing impedimetric sensing. Based on experimental results, we demonstrated a highly efficient spore trapping rate of more than 90% with an effective impedimetric sensing method that allowed the spore quantification of each column in the array and achieved a sensitivity of 2%/spore at 5 kHz and 1.6%/spore at 20 kHz, enabling single spore detection. We envision that our device will contribute to the development of a low-cost microfluidic platform that could be integrated into an infectious plant disease forecasting tool for crop protection.

Miniaturized single-cell technologies for monoclonal antibody discovery

Antibodies (Abs) are among the most important class of biologicals, showcasing a high therapeutic and diagnostic value. In the global therapeutic Ab market, fully-human monoclonal Abs (FH-mAbs) are flourishing thanks to their low immunogenicity and high specificity. The rapidly emerging field of single-cell technologies has paved the way to efficiently discover mAbs by facilitating a fast screening of the antigen (Ag)-specificity and functionality of Abs expressed by B cells. This review summarizes the principles and challenges of the four key concepts to discover mAbs using these technologies, being confinement of single cells using either droplet microfluidics or microstructure arrays, identification of the cells of interest, retrieval of those cells and single-cell sequence determination required for mAb production. This review reveals the enormous potential for mix-and-matching of the above-mentioned strategies, which is illustrated by the plethora of established, highly integrated devices. Lastly, an outlook is given on the many opportunities and challenges that still lie ahead to fully exploit miniaturized single-cell technologies for mAb discovery.

A novel automatic segmentation and tracking method to measure cellular dielectrophoretic mobility from individual cell trajectories for high throughput assay

BACKGROUND AND OBJECTIVE

The dielectrophoresis (DEP) technique is increasingly being recognised as a potentially valuable tool for non-contact manipulation of numerous cells as well as for biological single cell analysis with non-invasive characterisation of a cell's electrical properties. Several studies have attempted to track multiple cells to characterise their cellular DEP mobility. However, they encountered difficulties in simultaneously tracking the movement of a large number of individual cells in a bright-field image sequence because of interference from the background electrode pattern. Consequently, this present study aims to develop an automatic system for imaging-based characterisation of cellular DEP mobility, which enables the simultaneous tracking of several hundred of cells inside a microfluidic device.

METHODS

The proposed method for segmentation and tracking of cells consists of two main stages: pre-processing and particle centre localisation. In the pre-processing stage, background subtraction and contrast enhancement were performed to distinguish the cell region from the background image. In the particle centre localisation stage, the unmarked cell was automatically detected via graph-cut algorithm-based K-means clustering.

RESULTS

Our algorithm enabled segmentation and tracking of numerous Michigan Cancer Foundation-7 (MCF-7) cell trajectories while the DEP force was oscillated between positive and negative. The cell tracking accuracy and cell count capability was at least 90% of the total number of cells with the newly developed algorithm. In addition, the cross-over frequency was measured by analysing the segmented and tracked trajectory data of the cellular movements caused by the positive and negative DEP force. The measured cross-over frequency was compared with previous results. The multi-cellular movements investigation based on the measured cross-over frequency was repeated until the viability of cells was unchanged in the same environment as in a microfluidic device. The results were statistically consistent, indicating that the developed algorithm was reliable for the investigation of DEP cellular mobility.

CONCLUSION

This study developed a powerful platform to simultaneously measure the DEP-induced trajectories of numerous cells, and to investigate in a robust, efficient, and accurate manner the DEP properties at both the single cell and cell ensemble level.

An Integrated Dielectrophoresis-Trapping and Nanowell Transfer Approach to Enable Double-Sub-Poisson Single-Cell RNA Sequencing

Current technologies for high-throughput single-cell RNA sequencing (scRNA-seq) are based upon stochastic pairing of cells and barcoded beads in nanoliter droplets or wells. They are limited by the mathematical principle of the Poisson statistics such that the utilization of either cells or beads or both is no more than ∼33%. Despite the versatile design of microfluidics or microwells for high-yield loading of beads that beats the Poisson limit, subsequent encapsulation of single cells is still determined by stochastic pairing, representing a fundamental limitation in the field of single-cell sequencing. Here, we present dTNT-seq, an integrated dielectrophoresis (DEP)-trapping-nanowell-transfer (dTNT) approach to perform cell trapping and bead loading both in a sub-Poisson manner to facilitate scRNA-seq. A larger-sized 50 μm microwell array was prealigned precisely on top of the 20 μm DEP nanowell array such that single cells trapped by DEP can be readily transferred into the underneath larger wells by flipping the device, followed by subsequent hydrodynamic bead loading and coisolation with transferred single cells. Using a dTNT device composed of 3600 electroactive DEP-nanowell units, we demonstrated a single-cell trapping rate of 91.84%, a transfer efficiency of 82%, and a routine bead loading rate of >99%, which breaks the Poisson limit for the capture of both cells and beads, thus called double-sub-Poisson distribution, prior to encapsulating them in nanoliter wells for cellular mRNA barcoding. This approach was applied to human (HEK) and mouse (3T3) cells. Comparison with a non-DEP-based method through gene expression clustering and regulatory pathway analysis demonstrates consistent patterns and negligible alternation of cellular transcriptional states by DEP. We envision the dTNT-seq device can be modified for studying cell-cell interactions and enable other applications requiring active manipulation of single cells prior to transcriptome sequencing.

Microfluidic Single-Cell Omics Analysis

The commonly existing cellular heterogeneity plays a critical role in biological processes such as embryonic development, cell differentiation, and disease progress. Single-cell omics-based heterogeneous studies have great significance for identifying different cell populations, discovering new cell types, revealing informative cell features, and uncovering significant interrelationships between cells. Recently, microfluidics has evolved to be a powerful technology for single-cell omics analysis due to its merits of throughput, sensitivity, and accuracy. Herein, the recent advances of microfluidic single-cell omics analysis, including different microfluidic platform designs, lysis strategies, and omics analysis techniques, are reviewed. Representative applications of microfluidic single-cell omics analysis in complex biological studies are then summarized. Finally, a few perspectives on the future challenges and development trends of microfluidic-assisted single-cell omics analysis are discussed.

Microfluidic single-cell analysis-Toward integration and total on-chip analysis

Various types of single-cell analyses are now extensively used to answer many biological questions, and with this growth in popularity, potential drawbacks to these methods are also becoming apparent. Depending on the specific application, workflows can be laborious, low throughput, and run the risk of contamination. Microfluidic designs, with their advantages of being high throughput, low in reaction volume, and compatible with bio-inert materials, have been widely used to improve single-cell workflows in all major stages of single-cell applications, from cell sorting to lysis, to sample processing and readout. Yet, designing an integrated microfluidic chip that encompasses the entire single-cell workflow from start to finish remains challenging. In this article, we review the current microfluidic approaches that cover different stages of processing in single-cell analysis and discuss the prospects and challenges of achieving a full integrated workflow to achieve total single-cell analysis in one device.

Sequential Cell-Processing System by Integrating Hydrodynamic Purification and Dielectrophoretic Trapping for Analyses of Suspended Cancer Cells

Microfluidic devices employing dielectrophoresis (DEP) have been widely studied and applied in the manipulation and analysis of single cells. However, several pre-processing steps, such as the preparation of purified target samples and buffer exchanges, are necessary to utilize DEP forces for suspended cell samples. In this paper, a sequential cell-processing device, which is composed of pre-processing modules that employ deterministic lateral displacement (DLD) and a single-cell trapping device employing an electroactive microwell array (EMA), is proposed to perform the medium exchange followed by arraying single cells sequentially using DEP. Two original microfluidic devices were efficiently integrated by using the interconnecting substrate containing rubber gaskets that tightly connect the inlet and outlet of each device. Prostate cancer cells (PC3) suspended in phosphate-buffered saline buffer mixed with microbeads were separated and then resuspended into the DEP buffer in the integrated system. Thereafter, purified PC3 cells were trapped in a microwell array by using the positive DEP force. The achieved separation and trapping efficiencies exceeded 94% and 93%, respectively, when using the integrated processing system. This study demonstrates an integrated microfluidic device by processing suspended cell samples, without the requirement of complex preparation steps.

On-chip immunofluorescence analysis of single cervical cells using an electroactive microwell array with barrier for cervical screening

Several specific tests for cervical screening have been developed recently, including p16/Ki67 dual immunostaining for diagnosing high-risk human papillomavirus positive squamous intraepithelial lesion in the cervix. However, manual screening of cells in an entire glass slide is currently a standard clinical procedure for quantification and interpretation of immunocytochemical features of the cells. Here, we developed a microfluidic device containing an electroactive microwell array with barriers (EMAB) for highly efficient single-cell trapping followed by on-chip immunofluorescence analysis with minimum loss of the sample. EMAB utilizes patterned electrodes at the bottom of cell-sized microwells to trap single cells using dielectrophoresis (DEP) and cell-holding structures behind the microwells to stabilize the position of trapped cells even without DEP. Using the device, we evaluated the performance of p16/Ki67 dual immunostaining of HeLa cells on the chip. The device shows 98% cell-trapping efficiency as well as 92% cell-holding efficiency against the fixed HeLa cells, and we successfully demonstrated high-efficiency on-chip immunofluorescence analysis with minimal loss of sample. p16/Ki67 dual immunostaining using EMAB may be useful for complementary tests for cervical screening in confirming the histopathological diagnosis.

Inkjet-Printing Patterned Chip on Sticky Superhydrophobic Surface for High-Efficiency Single-Cell Array Trapping and Real-Time Observation of Cellular Apoptosis

Single-cell assays have broad applications in cellular studies, tissue engineering, fundamental studies of cell-cell interactions, and understanding of cell-to-cell variations. Most existing methods for micron-sized cell patterning are still based on lithography-based microfabrication process. Thus, exploiting new mask-free strategies while maintaining high-precision single-cell patterning is still a great challenge. Here, we presented a facile, low-cost, and mask-free approach for constructing high-resolution patterning on sticky superhydrophobic (SH) substrates based on inkjet printing with ordinary precision. In this work, the SH surface with both high contact angle and relatively high contact angle hysteresis can not only obtain high-resolution spots but also avoid droplets bouncing behavior. We improved the feature size of printed protein spots as small as 4 μm, which is much smaller than protein spots used for single-cell trapping. Moreover, with the assistance of a narrow microchannel, the inkjet-printing patterned chip with fibronectin ink allows for fast and high-efficiency trapping of multiple single-cell arrays. Using this method, single-cell occupancy could reach approximately 81% within 30 min on subcellular-sized patterning chip, and there was no significant effect on cell viability. As a proof of concept, this chip has been applied to study the real-time apoptosis of single cells and demonstrated the potential in cells' heterogeneity analysis.

A Self-Digitization Dielectrophoretic (SD-DEP) Chip for High-Efficiency Single-Cell Capture, On-Demand Compartmentalization, and Downstream Nucleic Acid Analysis

The design and fabrication of a self-digitization dielectrophoretic (SD-DEP) chip with simple components for single-cell manipulation and downstream nucleic acid analysis is presented. The device employed the traditional DEP and insulator DEP to create the local electric field that is tailored to approximately the size of single cells, enabling highly efficient single-cell capture. The multistep procedures of cell manipulation, compartmentalization, lysis, and analysis were performed in the integrated microdevice, consuming minimal reagents, minimizing contamination, decreasing lysate dilution, and increasing assay sensitivity. The platform developed here could be a promising and powerful tool in single-cell research for precise medicine.

Reverse Transcription Polymerase Chain Reaction in Giant Unilamellar Vesicles

We assessed the applicability of giant unilamellar vesicles (GUVs) for RNA detection using in vesicle reverse transcription polymerase chain reaction (RT-PCR). We prepared GUVs that encapsulated one-pot RT-PCR reaction mixture including template RNA, primers, and Taqman probe, using water-in-oil emulsion transfer method. After thermal cycling, we analysed the GUVs that exhibited intense fluorescence signals, which represented the cDNA amplification. The detailed analysis of flow cytometry data demonstrated that rRNA and mRNA in the total RNA can be amplified from 10–100 copies in the GUVs with 5–10 μm diameter, although the fraction of reactable GUV was approximately 60% at most. Moreover, we report that the target RNA, which was directly transferred into the GUV reactors via membrane fusion, can be amplified and detected using in vesicle RT-PCR. These results suggest that the GUVs can be used as biomimetic reactors capable of performing PCR and RT-PCR, which are important in analytical and diagnostic applications with additional functions.

Dielectrophoresis assisted loading and unloading of microwells for impedance spectroscopy

Dielectric spectroscopy (DS) is a noninvasive, label-free, fast, and promising technique for measuring dielectric properties of biological cells in real time. We demonstrate a microchip that consists of electro-activated microwell arrays for positive dielectrophoresis assisted cell capture, DS measurements, and negative dielectrophoresis driven cell unloading; thus, providing a high-throughput cell analysis platform. To the best of our knowledge, this is the first microfluidic chip that combines electro-activated microwells and DS to analyze biological cells. Device performance is tested using Saccharomyces cerevisiae (yeast) cells. DEP response of yeast cells is determined by measuring their Clausius-Mossotti factor using biophysical models in parallel plate microelectrode geometry. This information is used to determine the excitation frequency to load and unload wells. Effect of yeast cells on the measured impedance spectrum was examined both experimentally and numerically. Good match between the numerical and experimental results establishes the potential use of the microchip device for extracting subcellular properties of biological cells in a rapid and nonexpensive manner.

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.

Label-free single-cell separation and imaging of cancer cells using an integrated microfluidic system

The incidence of cancer is increasing worldwide and metastatic disease, through the spread of circulating tumor cells (CTCs), is responsible for the majority of the cancer deaths. Accurate monitoring of CTC levels in blood provides clinical information supporting therapeutic decision making, and improved methods for CTC enumeration are asked for. Microfluidics has been extensively used for this purpose but most methods require several post-separation processing steps including concentration of the sample before analysis. This induces a high risk of sample loss of the collected rare cells. Here, an integrated system is presented that efficiently eliminates this risk by integrating label-free separation with single cell arraying of the target cell population, enabling direct on-chip tumor cell identification and enumeration. Prostate cancer cells (DU145) spiked into a sample with whole blood concentration of the peripheral blood mononuclear cell (PBMC) fraction were efficiently separated and trapped at a recovery of 76.2 ± 5.9% of the cancer cells and a minute contamination of 0.12 ± 0.04% PBMCs while simultaneously enabling a 20x volumetric concentration. This constitutes a first step towards a fully integrated system for rapid label-free separation and on-chip phenotypic characterization of circulating tumor cells from peripheral venous blood in clinical practice.

One-step micromolding of complex 3D microchambers for single-cell analysis

Herein we examined the extent of replicability of the PDMS microchamber device transferred from the master mold with complex 3D structures fabricated via micro stereolithography. Due to the elastomeric properties of PDMS, the reversely tapered micromold, with the diameter ratio of ∼5 from the largest to the narrowest part, was precisely transferred without breaking. We obtained the mathematical model to estimate the stress exerted on the mold during the demolding process. Finally, we tested the applicability of this unusual microchamber for single-cell trapping and an enzyme assay.

High-Throughput Fabrication and Modular Assembly of 3D Heterogeneous Microscale Tissues

3D hydrogel microstructures that encapsulate cells have been used in broad applications in microscale tissue engineering, personalized drug screening, and regenerative medicine. Recent technological advances in microstructure assembly, such as bioprinting, magnetic assembly, microfluidics, and acoustics, have enabled the construction of designed 3D tissue structures with spatially organized cells in vitro. However, a bottleneck exists that still hampers the application of microtissue structures, due to a lack of techniques that combined high-throughput fabrication and flexible assembly. Here, a versatile method for fabricating customized microstructures and reorganizing building blocks composed of functional components into a combined single geometric shape is demonstrated. The arbitrary microstructures are dynamically synthesized in a microfluidic device and then transferred to an optically induced electrokinetics chip for manipulation and assembly. Moreover, building blocks containing different cells can be arranged into a desired geometry with specific shape and size, which can be used for microscale tissue engineering.

Electroporation for nanomedicine: a review

Here, we present a review of recent advances in electroporation for the delivery of nanomedicine as intracellular carriers by electroporation (NICE) in a drug format with functional nanoparticles.

Microfluidics cell sample preparation for analysis: Advances in efficient cell enrichment and precise single cell capture

Single cell analysis has received increasing attention recently in both academia and clinics, and there is an urgent need for effective upstream cell sample preparation. Two extremely challenging tasks in cell sample preparation-high-efficiency cell enrichment and precise single cell capture-have now entered into an era full of exciting technological advances, which are mostly enabled by microfluidics. In this review, we summarize the category of technologies that provide new solutions and creative insights into the two tasks of cell manipulation, with a focus on the latest development in the recent five years by highlighting the representative works. By doing so, we aim both to outline the framework and to showcase example applications of each task. In most cases for cell enrichment, we take circulating tumor cells (CTCs) as the target cells because of their research and clinical importance in cancer. For single cell capture, we review related technologies for many kinds of target cells because the technologies are supposed to be more universal to all cells rather than CTCs. Most of the mentioned technologies can be used for both cell enrichment and precise single cell capture. Each technology has its own advantages and specific challenges, which provide opportunities for researchers in their own area. Overall, these technologies have shown great promise and now evolve into real clinical applications.

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.

A Single-Cell Assay for Time Lapse Studies of Exosome Secretion and Cell Behaviors

To understand the inhomogeneity of cells in biological systems, there is a growing demand on the capability of characterizing the properties of individual single cells. Since single-cell studies require continuous monitoring of the cell behaviors, an effective single-cell assay that can support time lapsed studies in a high throughput manner is desired. Most currently available single-cell technologies cannot provide proper environments to sustain cell growth and, proliferation of single cells and convenient, noninvasive tests of single-cell behaviors from molecular markers. Here, a highly versatile single-cell assay is presented that can accommodate different cellular types, enable easy and efficient single-cell loading and culturing, and be suitable for the study of effects of in vitro environmental factors in combination with drug screening. One salient feature of the assay is the noninvasive collection and surveying of single-cell secretions at different time points, producing unprecedented insight of single-cell behaviors based on the biomarker signals from individual cells under given perturbations. Above all, the acquired information is quantitative, for example, measured by the number of exosomes each single-cell secretes for a given time period. Therefore, our single-cell assay provides a convenient, low-cost, and enabling tool for quantitative, time lapsed studies of single-cell properties.

Micro- and Nanoscale Technologies for Delivery into Adherent Cells

Several recent micro- and nanotechnologies have provided novel methods for biological studies of adherent cells because the small features of these new biotools provide unique capabilities for accessing cells without the need for suspension or lysis. These novel approaches have enabled gentle but effective delivery of molecules into specific adhered target cells, with unprecedented spatial resolution. We review here recent progress in the development of these technologies with an emphasis on in vitro delivery into adherent cells utilizing mechanical penetration or electroporation. We discuss the major advantages and limitations of these approaches and propose possible strategies for improvements. Finally, we discuss the impact of these technologies on biological research concerning cell-specific temporal studies, for example non-destructive sampling and analysis of intracellular molecules.

Innovative Tools and Technology for Analysis of Single Cells and Cell-Cell Interaction

Heterogeneity in single-cell responses and intercellular interactions results from complex regulation of cell-intrinsic and environmental factors. Single-cell analysis allows not only detection of individual cellular characteristics but also correlation of genetic content with phenotypic traits in the same cell. Technological advances in micro- and nanofabrication have benefited single-cell analysis by allowing precise control of the localized microenvironment, cell manipulation, and sensitive detection capabilities. Additionally, microscale techniques permit rapid, high-throughput, multiparametric screening that has become essential for -omics research. This review highlights innovative applications of microscale platforms in genetic, proteomic, and metabolic detection in single cells; cell sorting strategies; and heterotypic cell-cell interaction. We discuss key design aspects of single-cell localization and isolation in microfluidic systems, dynamic and endpoint analyses, and approaches that integrate highly multiplexed detection of various intracellular species.

Trapping and isolation of single prokaryotic cells in a micro-chamber array using dielectrophoresis

The vast majority of prokaryotic species are difficult or impossible to culture in laboratories, which makes it difficult to study these organisms using conventional biochemical techniques.

Dual stimuli-responsive smart beads that allow “on–off” manipulation of cancer cells

Temperature- and electric field-responsive polymer-conjugated polystyrene beads, termed smart beads, are designed to isolate cancer cells.

Highly efficient single cell arraying by integrating acoustophoretic cell pre-concentration and dielectrophoretic cell trapping

To array rare cells at the single-cell level, the volumetric throughput may become a bottleneck in the cell trapping and the subsequent single-cell analysis, since the target cells per definition commonly exist in a large sample volume after purification from the original sample. Here, we present a novel approach for high throughput single cell arraying by integrating two original microfluidic devices: an acoustofluidic chip and an electroactive microwell array. The velocity of the cells is geared down in the acoustofluidic chip while maintaining a high volume flow rate at the inlet of the microsystem, and the cells are subsequently trapped one by one into the microwell array using dielectrophoresis. The integrated system exhibited a 10 times improved sample throughput compared to trapping with the electroactive microwell array chip alone, while maintaining a highly efficient cell recovery above 90%. The results indicate that the serial integration of the acoustophoretic pre-concentration with the dielectrophoretic cell trapping drastically improves the performance of the electroactive microwell array for highly efficient single cell analysis. This simple and effective system for high throughput single cell arraying with further possible integration of additional functions, including cell sorting and downstream analysis after cell trapping, has potential for development to a highly integrated and automated platform for single-cell analysis of rare cells.

Cancer Cell Analyses at the Single Cell-Level Using Electroactive Microwell Array Device

Circulating tumor cells (CTCs), shed from primary tumors and disseminated into peripheral blood, are playing a major role in metastasis. Even after isolation of CTCs from blood, the target cells are mixed with a population of other cell types. Here, we propose a new method for analyses of cell mixture at the single-cell level using a microfluidic device that contains arrayed electroactive microwells. Dielectrophoretic (DEP) force, induced by the electrodes patterned on the bottom surface of the microwells, allows efficient trapping and stable positioning of single cells for high-throughput biochemical analyses. We demonstrated that various on-chip analyses including immunostaining, viability/apoptosis assay and fluorescent in situ hybridization (FISH) at the single-cell level could be conducted just by applying specific reagents for each assay. Our simple method should greatly help discrimination and analysis of rare cancer cells among a population of blood cells.