A facile single-cell patterning strategy based on harbor-like microwell microfluidics

Single-cell analysis is an effective method for conducting comprehensive heterogeneity studies ranging from cell phenotype to gene expression. The ability to arrange different cells in a predetermined pattern at single-cell resolution has a wide range of applications in cell-based analysis and plays an important role in facilitating interdisciplinary research by researchers in various fields. Most existing microfluidic microwell chips is a simple and straightforward method, which typically use small-sized microwells to accommodate single cells. However, this method imposes certain limitations on cells of various sizes, and the single-cell capture efficiency is relatively low without the assistance of external forces. Moreover, the microwells limit the spatiotemporal resolution of reagent replacement, as well as cell-to-cell communication. In this study, we propose a new strategy to prepare a single-cell array on a planar microchannel based on microfluidic flip microwells chip platform with large apertures (50 μm), shallow channels (50 μm), and deep microwells (50 μm). The combination of three configuration characteristics contributes to multi-cell trapping and a single-cell array within microwells, while the subsequent chip flipping accomplishes the transfer of the single-cell array to the opposite planar microchannel for cells adherence and growth. Further assisted by protein coating of bovine serum albumin and fibronectin on different layers, the single-cell capture efficiency in microwells is achieved at 92.1% ± 1%, while ultimately 85% ± 3.4% on planar microchannel. To verify the microfluidic flip microwells chip platform, the real-time and heterogeneous study of calcium release and apoptosis behaviours of single cells is carried out. To our knowledge, this is the first time that high-efficiency single-cell acquisition has been accomplished using a circular-well chip design that combines shallow channel, large aperture and deep microwell together. The chip is effective in avoiding the shearing force of high flow rates on cells, and the large apertures better allows cells to sedimentation. Therefore, this strategy owns the advantages of easy preparation and user-friendliness, which is especially valuable for researchers from different fields.

Microfluidic platform for omics analysis on single cells with diverse morphology and size: A review

BACKGROUND

Microfluidic techniques have emerged as powerful tools in single-cell research, facilitating the exploration of omics information from individual cells. Cell morphology is crucial for gene expression and physiological processes. However, there is currently a lack of integrated analysis of morphology and single-cell omics information. A critical challenge remains: what platform technologies are the best option to decode omics data of cells that are complex in morphology and size?

RESULTS

This review highlights achievements in microfluidic-based single-cell omics and isolation of cells based on morphology, along with other cell sorting methods based on physical characteristics. Various microfluidic platforms for single-cell isolation are systematically presented, showcasing their diversity and adaptability. The discussion focuses on microfluidic devices tailored to the distinct single-cell isolation requirements in plants and animals, emphasizing the significance of considering cell morphology and cell size in optimizing single-cell omics strategies. Simultaneously, it explores the application of microfluidic single-cell sorting technologies to single-cell sequencing, aiming to effectively integrate information about cell shape and size.

SIGNIFICANCE AND NOVELTY

The novelty lies in presenting a comprehensive overview of recent accomplishments in microfluidic-based single-cell omics, emphasizing the integration of different microfluidic platforms and their implications for cell morphology-based isolation. By underscoring the pivotal role of the specialized morphology of different cells in single-cell research, this review provides robust support for delving deeper into the exploration of single-cell omics data.

Digital PCR for Single-Cell Analysis

Single-cell analysis provides an overwhelming strategy for revealing cellular heterogeneity and new perspectives for understanding the biological function and disease mechanism. Moreover, it promotes the basic and clinical research in many fields at a single-cell resolution. A digital polymerase chain reaction (dPCR) is an absolute quantitative analysis technology with high sensitivity and precision for DNA/RNA or protein. With the development of microfluidic technology, digital PCR has been used to achieve absolute quantification of single-cell gene expression and single-cell proteins. For single-cell specific-gene or -protein detection, digital PCR has shown great advantages. So, this review will introduce the significance and process of single-cell analysis, including single-cell isolation, single-cell lysis, and single-cell detection methods, mainly focusing on the microfluidic single-cell digital PCR technology and its biological application at a single-cell level. The challenges and opportunities for the development of single-cell digital PCR are also discussed.

Microfluidics Coupled Mass Spectrometry for Single Cell Multi-Omics

Population-level analysis masks significant heterogeneity between individual cells, making it difficult to accurately reflect the true intricacies of life activities. Microfluidics is a technique that can manipulate individual cells effectively and is commonly coupled with a variety of analytical methods for single-cell analysis. Single-cell omics provides abundant molecular information at the single-cell level, fundamentally revealing differences in cell types and biological states among cell individuals, leading to a deeper understanding of cellular phenotypes and life activities. Herein, this work summarizes the microfluidic chips designed for single-cell isolation, manipulation, trapping, screening, and sorting, including droplet microfluidic chips, microwell arrays, hydrodynamic microfluidic chips, and microchips with microvalves. This work further reviews the studies on single-cell proteomics, metabolomics, lipidomics, and multi-omics based on microfluidics and mass spectrometry. Finally, the challenges and future application of single-cell multi-omics are discussed.

Chemical tagging mass spectrometry: an approach for single-cell omics

Single-cell (SC) analysis offers new insights into the study of fundamental biological phenomena and cellular heterogeneity. The superior sensitivity, high throughput, and rich chemical information provided by mass spectrometry (MS) allow MS to emerge as a leading technology for molecular profiling of SC omics, including the SC metabolome, lipidome, and proteome. However, issues such as ionization suppression, low concentration, and huge span of dynamic concentrations of SC components lead to poor MS response for certain types of molecules. It is noted that chemical tagging/derivatization has been adopted in SCMS analysis, and this strategy has been proven an effective solution to circumvent these issues in SCMS analysis. Herein, we review the basic principle and general strategies of chemical tagging/derivatization in SCMS analysis, along with recent applications of chemical derivatization to single-cell metabolomics and multiplexed proteomics, as well as SCMS imaging. Furthermore, the challenges and opportunities for the improvement of chemical derivatization strategies in SCMS analysis are discussed.

Automatic trajectory control of single cells using dielectrophoresis based on visual feedback

This paper deals with the automatic control of the trajectory of T-lymphocytes using dielectrophoretic (DEP) actuation. Dielectrophoresis is a physical phenomenon induced by a non-uniform electric field enabling application of a force on a dielectric object. In most of the cases, it is used in a passive way. The electric field is in a steady state and the force applied on the cells depends on the cell's characteristics and position inside the channel. These systems are limited as cells with similar characteristics will undergo the same forces. To overcome this issue, active devices where the electric field changes over time were developed. However, the voltages that should be applied to generate the desired electric field are mostly computed offline using finite element methods. Thus, there is a low number of devices using automatic approaches with dielectrophoretic actuation where the electric field is computed and updated in real time based on the current position of the cell. We propose here an experimental bench used to study the automatic trajectory control of cells by dielectrophoresis. The computation of the dielectrophoretic force is done online with a model based on the Fourier series depending on the cell's characteristics, position and electric field. This model allows the use of a controller based on visual feedback running at 120 Hz to control the position of cells inside a microfluidic chip. As cells are sensitive to the electric field, the controller limits the norm of the electric field while maximizing the gradient to maximize the DEP force. Experiments have been performed and T-lymphocytes were successfully steered along several types of trajectories at a speed of five times their size per second. The mean error along those trajectories is below 2 μm. The viability of the cells has been checked after the experiments and confirms that this active DEP actuation does not harm the cells.

Single cell quantification of microRNA from small numbers of non-invasively sampled primary human cells

Expression levels of microRNAs (miRNAs) in single cells are low and conventional miRNA detection methods require amplification that can be complex, time-consuming, costly and may bias results. Single cell microfluidic platforms have been developed; however, current approaches are unable to absolutely quantify single miRNA molecules expressed in single cells. Herein, we present an amplification-free sandwich hybridisation assay to detect single miRNA molecules in single cells using a microfluidic platform that optically traps and lyses individual cells. Absolute quantification of miR-21 and miR-34a molecules was achieved at a single cell level in human cell lines and validated using real-time qPCR. The sensitivity of the assay was demonstrated by quantifying single miRNA molecules in nasal epithelial cells and CD3⁺ T-cells, as well as nasal fluid collected non-invasively from healthy individuals. This platform requires ~50 cells or ~30 µL biofluid and can be extended for other miRNA targets therefore it could monitor miRNA levels in disease progression or clinical studies.

Microwell array chip-based single-cell analysis

Single-cell profiling is key to uncover the cellular heterogeneity and drives deep understanding of cell fate. In recent years, microfluidics has become an ideal tool for single-cell profiling owing to its benefits of high throughput and automation. Among various microfluidic platforms, microwell has the advantages of simple operation and easy integration with in situ analysis ability, making it an ideal technique for single-cell studies. Herein, recent advances of single-cell analysis based on microwell array chips are summarized. We first introduce the design and preparation of different microwell chips. Then microwell-based cell capture and lysis strategies are discussed. We finally focus on advanced microwell-based analysis of single-cell proteins, nucleic acids, and metabolites. The challenges and opportunities for the development of microwell-based single-cell analysis are also presented.

A High-Throughput Single-Cell Assay on a Valve-Based Microfluidic Platform Applied to Protein Quantification, Immune Response Monitoring, and Drug Discovery

The use of microfluidic technology in single-cell assay has shown potential in biomedical applications like protein quantification, immune response monitoring, and drug discovery. Because of the details of information that can be obtained at single-cell resolution, the single-cell assay has been applied to tackle challenging issues such as cancer treatment. Information like the levels of protein expression, cellular heterogeneity, and unique behaviors within subsets are very important in the biomedical field. For a single-cell assay system, a high-throughput platform that can do on-demand media exchange and real-time monitoring is advantageous in single-cell screening and profiling. In this work, a high-throughput valve-based device is presented, its use in single-cell assay, particularly in protein quantification and surface-marker analysis, and its potential application to immune response monitoring and drug discovery are laid down in detail.

Artificial intelligence-assisted automatic and index-based microbial single-cell sorting system for One-Cell-One-Tube

Identification, sorting, and sequencing of individual cells directly from in situ samples have great potential for in-depth analysis of the structure and function of microbiomes. In this work, based on an artificial intelligence (AI)-assisted object detection model for cell phenotype screening and a cross-interface contact method for single-cell exporting, we developed an automatic and index-based system called EasySort AUTO, where individual microbial cells are sorted and then packaged in a microdroplet and automatically exported in a precisely indexed, "One-Cell-One-Tube" manner. The target cell is automatically identified based on an AI-assisted object detection model and then mobilized via an optical tweezer for sorting. Then, a cross-interface contact microfluidic printing method that we developed enables the automated transfer of cells from the chip to the tube, which leads to coupling with subsequent single-cell culture or sequencing. The efficiency of the system for single-cell printing is >93%. The throughput of the system for single-cell printing is ~120 cells/h. Moreover, >80% of single cells of both yeast and Escherichia coli are culturable, suggesting the superior preservation of cell viability during sorting. Finally, AI-assisted object detection supports automated sorting of target cells with high accuracy from mixed yeast samples, which was validated by downstream single-cell proliferation assays. The automation, index maintenance, and vitality preservation of EasySort AUTO suggest its excellent application potential for single-cell sorting.

A Dual-Channel Microfluidic Chip for Single Tobacco Protoplast Isolation and Dynamic Capture

Protoplasts are widely used in gene function verification, subcellular localization, and single-cell sequencing because of their complete physiological activities. The traditional methods based on tissues and organs cannot satisfy the requirement. Therefore, the isolation and capture of a single protoplast are most important to these studies. In this study, a dual-channel microfluidic chip based on PDMS with multi-capture cavities was designed. The design theory of the dual-channel microfluidic chip's geometry was discussed. The capture mechanism of the single cell in a dual-channel microfluidic chip was studied by simulation analysis. Our results showed that a single polystyrene microsphere or tobacco protoplast was successfully isolated and trapped in this chip. The capture efficiency of the chip was 83.33% for the single tobacco protoplast when the inlet flow rate was 0.75 μL/min. In addition, the dynamic capture of the polystyrene microsphere and tobacco protoplasts was also presented. Overall, our study not only provided a new strategy for the subsequent high throughput single protoplast research, but also laid a theoretical foundation for the capture mechanism of the single cell.

Advances in Single-Cell Toxicogenomics in Environmental Toxicology

The toxicity evaluation system of environmental pollutants has undergone numerous changes due to the application of new technologies. Single-cell toxicogenomics is rapidly changing our view on environmental toxicology by increasing the resolution of our analysis to the level of a single cell. Applications of this technology in environmental toxicology have begun to emerge and are rapidly expanding the portfolio of existing technologies and applications. Here, we first summarized different methods involved in single-cell isolation and amplification in single-cell sequencing process, compared the advantages and disadvantages of different methods, and analyzed their development trends. Then, we reviewed the main advances of single-cell toxicogenomics in environmental toxicology, emphatically analyzed the application prospects of this technology in identifying the target cells of pollutants in early embryos, clarifying the heterogeneous response of cell subtypes to pollutants, and finding pathogenic bacteria in unknown microbes, and highlighted the unique characteristics of this approach with high resolution, high throughput, and high specificity by examples. We also offered a prediction of the further application of this technology and the revolution it brings in environmental toxicology. Overall, these advances will provide practical solutions for controlling or mitigating exogenous toxicological effects that threaten human and ecosystem health, contribute to improving our understanding of the physiological processes affected by pollutants, and lead to the emergence of new methods of pollution control.

Microfluidic single-cell transcriptomics: moving towards multimodal and spatiotemporal omics

Cells are the basic units of life with vast heterogeneity. Single-cell transcriptomics unveils cell-to-cell gene expression variabilities, discovers novel cell types, and uncovers the critical roles of cellular heterogeneity in biological processes. The recent advances in microfluidic technologies have greatly accelerated the development of single-cell transcriptomics with regard to throughput, sensitivity, cost, and automation. In this article, we review state-of-the-art microfluidic single-cell transcriptomics, with a focus on the methodologies. We first summarize six typical microfluidic platforms for isolation and transcriptomic analysis of single cells. Then the on-going trend of microfluidic transcriptomics towards multimodal omics, which integrates transcriptomics with other omics to provide more comprehensive pictures of gene expression networks, is discussed. We also highlight single-cell spatial transcriptomics and single-cell temporal transcriptomics that provide unprecedented spatiotemporal resolution to reveal transcriptomic dynamics in space and time, respectively. The emerging applications of microfluidic single-cell transcriptomics are also discussed. Finally, we discuss the current challenges to be tackled and provide perspectives on the future development of microfluidic single-cell transcriptomics.

Microfluidics applications for high-throughput single cell sequencing

The inherent heterogeneity of individual cells in cell populations plays significant roles in disease development and progression, which is critical for disease diagnosis and treatment. Substantial evidences show that the majority of traditional gene profiling methods mask the difference of individual cells. Single cell sequencing can provide data to characterize the inherent heterogeneity of individual cells, and reveal complex and rare cell populations. Different microfluidic technologies have emerged for single cell researches and become the frontiers and hot topics over the past decade. In this review article, we introduce the processes of single cell sequencing, and review the principles of microfluidics for single cell analysis. Also, we discuss the common high-throughput single cell sequencing technologies along with their advantages and disadvantages. Lastly, microfluidics applications in single cell sequencing technology for the diagnosis of cancers and immune system diseases are briefly illustrated.

Label-free single-cell isolation enabled by microfluidic impact printing and real-time cellular recognition

Analysis of cellular components at the single-cell level is important to reveal cellular heterogeneity. However, current technologies to isolate individual cells are either label-based or have low performance. Here, we present a novel technique by integrating real-time cellular recognition and microfluidic impact printing (MIP) to isolate single cells with high efficiency and high throughput in a label-free manner. Specifically, morphological characteristics of polystyrene beads and cells, computed by an efficient image processing algorithm, are utilized as selection criteria to identify target objects. Subsequently, each detected single-cell object in the suspension is ejected from the microfluidic channel by impact force. It has been demonstrated that the single-cell isolating system has the ability to encapsulate polystyrene beads in droplets with an efficiency of 95%, while for HeLa cells, this has been experimentally measured as 90.3%. Single-cell droplet arrays are generated at a throughput of 2 Hz and 96.6% of the cells remain alive after isolation. This technology has significant potential in various emerging applications, including single-cell omics, tissue engineering, and cell-line development.

Microfluidics-Based Single-Cell Research for Intercellular Interaction

Intercellular interaction between cell-cell and cell-ECM is critical to numerous biology and medical studies, such as stem cell differentiation, immunotherapy and tissue engineering. Traditional methods employed for delving into intercellular interaction are limited by expensive equipment and sophisticated procedures. Microfluidics technique is considered as one of the powerful measures capable of precisely capturing and manipulating cells and achieving low reagent consumption and high throughput with decidedly integrated functional components. Over the past few years, microfluidics-based systems for intercellular interaction study at a single-cell level have become frequently adopted. This review focuses on microfluidic single-cell studies for intercellular interaction in a 2D or 3D environment with a variety of cell manipulating techniques and applications. The challenges to be overcome are highlighted.

Recent advances in single-cell analysis: Encapsulation materials, analysis methods and integrative platform for microfluidic technology

Traditional cell biology researches on cell populations by their origin, tissue, morphology, and secretions. Because of the heterogeneity of cells, research at the single-cell level can obtain more accurate and comprehensive information that reflects the physiological state and process of the cell, increasing the significance of single-cell analysis. The application of single-cell analysis is faced with the problem of contaminated or damaged cells caused by cell sample transportation. Reversible encapsulation of a single cell can protect cells from the external environment and open the encapsulation shell to release cells, thus preserving cell integrity and improving extraction efficiency of analytes. Meanwhile, microfluidic single cell analysis (MSCA) exhibits integration, miniaturization, and high throughput, which can considerably improve the efficiency of single-cell analysis. The researches on single-cell reversible encapsulation materials, single-cell analysis methods, and the MSCA integration platform are analyzed and summarized in this review. The problems of single-cell viability, network of single-cell signal, and simultaneous detection of multiple biotoxins in food based on single-cell are proposed for future research.

Cell Analysis on Microfluidics Combined with Mass Spectrometry

Cell analysis is of great significance for the exploration of human diseases and health. However, there are not many techniques for high-throughput cell analysis in the simulated cell microenvironment. The high designability of the microfluidic chip enables multiple kinds of cells to be co-cultured on the chip, with other functions such as sample preprocessing and cell manipulation. Mass spectrometry (MS) can detect a large number of biomolecules without labelling. Therefore, the application of the microfluidic chip coupled with MS has represented a major branch of cell analysis over the past decades. Here, we concisely introduce various microfluidic devices coupled with MS used for cell analysis. The main functions of microfluidic devices are described first, followed by introductions of different interfaces with different types of MS. Then, their various applications in cell analysis are highlighted, with an emphasis on cell metabolism, drug screening, and signal transduction. Current limitations and prospective trends of microfluidics coupled with MS are discussed at the end.

Single cell metabolomics using mass spectrometry: Techniques and data analysis

Mass spectrometry (MS) based techniques are gaining popularity for metabolomics research due to their high sensitivity, wide detection range, and capability of molecular identification. Utilizing such powerful technique to explore the cellular metabolism at the single cell level not only appreciates the subtle cell-to-cell difference (i.e., cell heterogeneity), but also gains biological merits corresponding to individual cells or small cell subpopulations. In this review article, we first briefly summarize recent advances in single cell MS experimental techniques, and then emphasize on the single cell metabolomics data analysis approaches. Through implementation of statistical analysis and more advanced data analysis methods, single cell metabolomics is expected to find more potential applications in the translational and clinical fields in the future.

Single-Cell Analysis of Highly Metastatic Circulating Tumor Cells by Combining a Self-Folding Induced Release Reaction with a Cell Capture Microchip

Nondestructive analysis of the single-cell molecular phenotype of circulating tumor cells (CTCs) is of great significance to the precise diagnosis and treatment of cancer but is also a huge challenge. To address this issue, here, we develop a facile analysis system that integrates CTCs' capture and molecular phenotype analysis. An isothermal nucleic acid amplification technique named self-folding induced release reaction (sFiR), which has high-efficiency signal amplification capabilities and can run under physiological conditions, is first developed to meet the high requirements for sensitivity and nondestructivity. By combining the sFiR with immune recognition and a single cell capture microchip, the molecular phenotype analysis of a single CTC is realized. As a model, nondestructive analysis of junction plakoglobin (JUP), an overexpressed membrane protein that is closely related to the metastasis of CTCs, is successfully achieved. Results reveal that this sFiR-based analysis system can clearly distinguish the expression of JUP in different cancer cell lines and can present quantitative information on the expression of JUP. Furthermore, the captured and analyzed CTCs maintain their basic physiological activity and can be used for drug sensitivity testing. Considering the excellent performance and ease of operation of the system, it can provide technical support for CTC-based cancer liquid biopsy and drug development.

On-chip protein separation with single-molecule resolution

Accurate identification of both abundant and rare proteins hinges on the development of single-protein sensing methods. Given the immense variation in protein expression levels in a cell, separation of proteins by weight would improve protein classification strategies. Upstream separation facilitates sample binning into smaller groups while also preventing sensor overflow, as may be caused by highly abundant proteins in cell lysates or clinical samples. Here, we scale a bulk analysis method for protein separation, sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE), to the single-molecule level using single-photon sensitive widefield imaging. Single-molecule sensing of the electrokinetically moving proteins is achieved by in situ polymerization of the PAGE in a low-profile fluidic channel having a depth of only ~ 0.6 µm. The polyacrylamide gel restricts the Brownian kinetics of the proteins, while the low-profile channel ensures that they remain in focus during imaging, allowing video-rate monitoring of single-protein migration. Calibration of the device involves separating a set of Atto647N-covalently labeled recombinant proteins in the size range of 14-70 kDa, yielding an exponential dependence of the proteins' molecular weights on the measured mobilities, as expected. Subsequently, we demonstrate the ability of our fluidic device to separate and image thousands of proteins directly extracted from a human cancer cell line. Using single-particle image analysis methods, we created detailed profiles of the separation kinetics of lysine and cysteine -labeled proteins. Downstream coupling of the device to single-protein identification sensors may provide superior protein classification and improve our ability to analyze complex biological and medical protein samples.

How single-cell immunology is benefiting from microfluidic technologies

The immune system is a complex network of specialized cells that work in concert to protect against invading pathogens and tissue damage. Imbalances in this network often result in excessive or absent immune responses leading to allergies, autoimmune diseases, and cancer. Many of the mechanisms and their regulation remain poorly understood. Immune cells are highly diverse, and an immune response is the result of a large number of molecular and cellular interactions both in time and space. Conventional bulk methods are often prone to miss important details by returning population-averaged results. There is a need in immunology to measure single cells and to study the dynamic interplay of immune cells with their environment. Advances in the fields of microsystems and microengineering gave rise to the field of microfluidics and its application to biology. Microfluidic systems enable the precise control of small volumes in the femto- to nanoliter range. By controlling device geometries, surface chemistry, and flow behavior, microfluidics can create a precisely defined microenvironment for single-cell studies with spatio-temporal control. These features are highly desirable for single-cell analysis and have made microfluidic devices useful tools for studying complex immune systems. In addition, microfluidic devices can achieve high-throughput measurements, enabling in-depth studies of complex systems. Microfluidics has been used in a large panel of biological applications, ranging from single-cell genomics, cell signaling and dynamics to cell-cell interaction and cell migration studies. In this review, we give an overview of state-of-the-art microfluidic techniques, their application to single-cell immunology, their advantages and drawbacks, and provide an outlook for the future of single-cell technologies in research and medicine.

Recent Progress of Microfluidic Devices for Hemodialysis

Microfluidic hemodialysis techniques have recently attracted great attention in the treatment of kidney disease due to their advantages of portability and wearability as well as their great potential for replacing clinical hospital-centered blood purification with continuous in-home hemodialysis. This Review summarizes the recent progress in microfluidic devices for hemodialysis. First, the history of kidney-inspired hemodialysis is introduced. Then, recent achievements in the preparation of microfluidic devices and hemodialysis nanoporous membrane materials are presented and categorized. Subsequently, attention is drawn to the recent progress of nanoporous membrane-based microfluidic devices for hemodialysis. Finally, the challenges and opportunities of hemodialysis microfluidic devices in the future are also discussed. This Review is expected to provide a comprehensive guide for the design of hemodialysis microfluidic devices that are closely related to clinical applications.

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.

Methods for Single-Cell Isolation and Preparation

Within the last decade, single-cell analysis has revolutionized our understanding of cellular processes and heterogeneity across all disciplines of life science. As the transcriptome, genome, or epigenome of individual cells can nowadays be analyzed at low cost and in high-throughput within a few days by modern techniques, tremendous improvements in disease diagnosis on the one hand and the investigation of disease-relevant mechanisms on the other were achieved so far. This relies on the parallel development of reliable cell capturing and single-cell sequencing approaches that have paved the way for comprehensive single-cell studies. Apart from single-cell isolation methods in high-throughput, a variety of methods with distinct specializations were developed, allowing for correlation of transcriptomics with cellular parameters like electrophysiology or morphology.For all single-cell-based approaches, accurate and reliable isolation with proper quality controls is prerequisite, whereby different options exist dependent on sample type and tissue properties. Careful consideration of an appropriate method is required to avoid incorrect or biased data that may lead to misinterpretations.In this chapter, we will provide a broad overview of the current state of the art in matters of single-cell isolation methods mostly applied for sequencing-based downstream analysis, and their respective advantages and drawbacks. Distinct technologies will be discussed in detail addressing key parameters like sample compatibility, viability, purity, throughput, and isolation efficiency.

Single-molecule measurements in microwells for clinical applications

The ability to detect and analyze proteins, nucleic acids, and other biomolecules is critical for clinical diagnostics and for understanding the underlying mechanisms of disease. Current detection methods in clinical and research laboratories rely upon bulk measurement techniques such as immunoassays, polymerase chain reaction, and mass spectrometry to detect these biomarkers. However, many potentially useful protein or nucleic acid biomarkers in blood, saliva, or other biofluids exist at concentrations well below the detection limits of current methods, necessitating the development of more sensitive technologies. Single-molecule measurements are poised to address this challenge, vastly improving sensitivity for detecting low abundance biomarkers and rare events within a population. Microwell arrays have emerged as a powerful tool for single-molecule measurements, enabling ultrasensitive detection of disease-relevant biomolecules in easily accessible biofluids. This review discusses the development, fundamentals, and clinical applications of microwell-based single-molecule methods, as well as challenges and future directions for translating these methods to the clinic.

Real-Time Imaging of Ammonia Release from Single Live Cells via Liquid Crystal Droplets Immobilized on the Cell Membrane

Tumor cells exhibit prominent metabolic alterations through which they acclimatize to their stressful microenvironment. These cells have a high rate of glutaminolysis and release ammonia (NH3) as a byproduct, which may function as a diffusible signal among cancer cells and can reveal cellular heterogeneity. E7, a nematic liquid crystal (LC), is doped with 4-pentyl-4'-biphenyl carboxylic acid (PBA) and encapsulated in polymeric microcapsules (P-E7PBA), which are then immobilized on cells in a microfluidic channel. Normal human umbilical vein endothelial cells (HUVECs) and myeloma, human primary glioblastoma (U87), human colon carcinoma (Caco-2), and human breast adenocarcinoma (MCF-7) cells are investigated for the release of NH3. The P-E7PBA is able to visualize NH3 release from the cell via a radial-to-bipolar (R-B) orientation change, observed through a polarized optical microscope. The various cell lines significantly differ in their response time required for an R-B change. The mean response times for Caco-2, U87, and MCF-7 cells are 277, 155, and 121 s, respectively. NH3 release from a single cell captured in a microwell flow chip shows a similar R-B change. The P-E7PBA droplets technology could be applied to other multiple targets by functionalizing LCs with different probes.

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.

Single-cell Analysis with Microfluidic Devices

A microfluidic device as a pivotal research tool in chemistry and life science is now widely recognized. Indeed, microfluidic techniques have made significant advancements in fundamental research, such as the inherent heterogeneity of single-cells studies in cell populations, which would be helpful in understanding cellular molecular mechanisms and clinical diagnosis of major diseases. Single-cell analyses on microdevices have shown great potential for precise fluid control, cell manipulation, and signal output with rapid and high throughput. Moreover, miniaturized devices also have open functions such as integrating with traditional detection methods, for example, optical, electrochemical or mass spectrometry for single-cell analysis. In this review, we summarized recent advances of single-cell analysis based on various microfluidic approaches from different dimensions, such as in vitro, ex vivo, and in vivo analysis of single cells.

Mobile Microfluidics

Microfluidics platforms can program small amounts of fluids to execute a bio-protocol, and thus, can automate the work of a technician and also integrate a large part of laboratory equipment. Although most microfluidic systems have considerably reduced the size of a laboratory, they are still benchtop units, of a size comparable to a desktop computer. In this paper, we argue that achieving true mobility in microfluidics would revolutionize the domain by making laboratory services accessible during traveling or even in daily situations, such as sport and outdoor activities. We review the existing efforts to achieve mobility in microfluidics, and we discuss the conditions mobile biochips need to satisfy. In particular, we show how we adapted an existing biochip for mobile use, and we present the results when using it during a train ride. Based on these results and our systematic discussion, we identify the challenges that need to be overcome at technical, usability and social levels. In analogy to the history of computing, we make some predictions on the future of mobile biochips. In our vision, mobile biochips will disrupt how people interact with a wide range of healthcare processes, including medical testing and synthesis of on-demand medicine.

The effect of dielectrophoresis on living cells: crossover frequencies and deregulation in gene expression

This article documents the effect of dielectrophoresis on living cells.

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.