High-efficiency single cell encapsulation and size selective capture of cells in picoliter droplets based on hydrodynamic micro-vortices

Deterministic Single-Cell Encapsulation in PEG Norbornene Microgels for Promoting Anti-Inflammatory Response and Therapeutic Delivery of Mesenchymal Stromal Cells

Tissue engineering at single-cell resolution has enhanced therapeutic efficacy. Droplet microfluidics offers a powerful platform that allows deterministic single-cell encapsulation into aqueous droplets, yet the direct encapsulation of cells into microgels remains challenging. Here, the design of a microfluidic device that is capable of single-cell encapsulation within polyethylene glycol norbornene (PEGNB) hydrogels on-chip is reported. Cells are first ordered in media within a straight microchannel via inertial focusing, followed by the introduction of PEGNB solution from two separate, converging channels. Droplets are thoroughly mixed by passage through a serpentine channel, and microgels are formed by photo-photopolymerization. This platform uniquely enables both single-cell encapsulation and excellent cell viability post-photo-polymerization. More than 90% of singly encapsulated mesenchymal stromal cells (MSCs) remain alive for 7 days. Notably, singly encapsulated MSCs have elevated expression levels in genes that code anti-inflammatory cytokines, for example, IL-10 and TGF-β, thus enhancing the secretion of proteins of interest. Following injection into a mouse model with induced inflammation, singly encapsulated MSCs show a strong retention rate in vivo, reduce overall inflammation, and mitigate liver damage. These translational results indicate that deterministic single-cell encapsulation could find use in a broad spectrum of tissue engineering applications.

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.

Incorporation of a Morphologically Controlled Ice Grain Boundary into a Microfluidic Device for Size-Selective Separation of Micro/Nanospheres

A frozen aqueous solution was integrated into a microfluidic device as a size-tunable separation field for the size-selective separation of micro/nanospheres. The width of the ice grain boundaries formed in frozen aqueous solutions could be altered by controlling the operating temperature. A freezing chamber was placed adjacent to the microfluidic channel. A sample-dispersing aqueous sucrose solution was injected into the chamber and frozen, allowing the freeze-concentrated solution (FCS) to run vertically to the microfluidic channel, where the eluting solution flows. The operating temperature can be used to control the physical interaction between the ice wall and micro/nanospheres, enabling size-selective migration. The eluted micro/nanospheres in the microchannel were passed through the eluting solution collected from the outlet. We achieved size-selective separation and collection of microspheres and nanospheres. We separated the exosomes and yeast cells to demonstrate their applicability in bioseparation. The present method is suitable not only for size-selective separation but also for evaluating the biological expression of extracellular vesicles under cryogenic conditions.

Recent advances in microfluidics for single-cell functional proteomics

Single-cell proteomics (SCP) reveals phenotypic heterogeneity by profiling individual cells, their biological states and functional outcomes upon signaling activation that can hardly be probed via other omics characterizations. This has become appealing to researchers as it enables an overall more holistic view of biological details underlying cellular processes, disease onset and progression, as well as facilitates unique biomarker identification from individual cells. Microfluidic-based strategies have become methods of choice for single-cell analysis because they allow facile assay integrations, such as cell sorting, manipulation, and content analysis. Notably, they have been serving as an enabling technology to improve the sensitivity, robustness, and reproducibility of recently developed SCP methods. Critical roles of microfluidics technologies are expected to further expand rapidly in advancing the next phase of SCP analysis to reveal more biological and clinical insights. In this review, we will capture the excitement of the recent achievements of microfluidics methods for both targeted and global SCP, including efforts to enhance the proteomic coverage, minimize sample loss, and increase multiplexity and throughput. Furthermore, we will discuss the advantages, challenges, applications, and future prospects of SCP.

Single-Cell Microgels for Diagnostics and Therapeutics

Cell encapsulation within hydrogel droplets is transforming what is feasible in multiple fields of biomedical science such as tissue engineering and regenerative medicine, in vitro modeling, and cell-based therapies. Recent advances have allowed researchers to miniaturize material encapsulation complexes down to single-cell scales, where each complex, termed a single-cell microgel, contains only one cell surrounded by a hydrogel matrix while remaining <100 μm in size. With this achievement, studies requiring single-cell resolution are now possible, similar to those done using liquid droplet encapsulation. Of particular note, applications involving long-term in vitro cultures, modular bioinks, high-throughput screenings, and formation of 3D cellular microenvironments can be tuned independently to suit the needs of individual cells and experimental goals. In this progress report, an overview of established materials and techniques used to fabricate single-cell microgels, as well as insight into potential alternatives is provided. This focused review is concluded by discussing applications that have already benefited from single-cell microgel technologies, as well as prospective applications on the cusp of achieving important new capabilities.

Precise and convenient size barcode on microfluidic chip for multiplex biomarker detection

The existing multiplex biomarker detection methods are limited by the high demand for coding material and expensive detection equipment. This paper proposes a convenient and precise coding method based on a wedge-shaped microfluidic chip, which can be further applied in multiplex biomarker detection. The proposed microfluidic chip has a microchannel with continuously varying height, which can naturally separate and code microparticles of different sizes. Our data indicate that this method can be applied to code more than 5 or 7 kinds of microparticles, even when their size discrepancies are smaller than 1 μm. Based on these, multiplex biomarker detection can be implemented by using microparticles of different sizes, hence each kind of microparticle that coats one kind of antibody represents the species of targets. This method is simple and easy to operate, with no clogging or sophisticated coding design, showing its significant potential in the area of point-of-care tests (POCT).

Particle encapsulation in aqueous ferrofluid drops and sorting of particle-encapsulating drops from empty drops using a magnetic field

Handling and manipulation of particle-encapsulating droplets (PED) have profound applications in biochemical assays. Herein we report encapsulation of microparticles in aqueous ferrofluid droplets in a primary continuous phase (CP) and sorting of PED from empty droplets (ED) at the interface of the CP in coflow with a second continuous phase using a magnetic field. We find that the encapsulation process results in a size contrast between the PED and ED that depends on the flow regime - squeezing, dripping, or jetting - which in turn is governed by the ratio of the discrete phase to the continuous phase capillary number, Ca_r. The difference between the volume fractions of ferrofluid in the PED and ED, Δα_PED, is utilized for sorting, and is found to depend on the ratio of the capillary numbers, Ca_r. The difference Δα_PED is found to be maximum in the jetting regime, suggesting that the jetting regime is most suitable for encapsulation and sorting. The sorting criterion is represented in terms of a parameter ξ, which is a function of the ratios of the magnetic force to the interfacial force experienced by the PED and ED. Our study revealed that sorting is possible for ξ < 0, which corresponds to Δα_PED > 0.25. The maximum sorting efficiency of our system is found to be ∼95% at a throughput of ∼100 drops per s.

Conformal single cell hydrogel coating with electrically induced tip streaming of an AC cone

Encapsulation of single cells in a thin hydrogel provides a more precise control of stem cell niches and better molecular transport. Despite the recent advances in microfluidic technologies to allow encapsulation of single cells, existing methods rely on special crosslinking agents that are pre-coated on the cell surface and subject to the variation of the cell membrane, which limits their widespread adoption. This work reports a high-throughput single-cell encapsulation method based on the "tip streaming" mode of alternating current (AC) electrospray, with encapsulation efficiencies over 80% after tuned centrifugation. Dripping with multiple cells is curtailed due to gating by the sharp conic meniscus of the tip streaming mode that only allows one cell to be ejected at a time. Moreover, the method can be universally applied to both natural and synthetic hydrogels, as well as various cell types, including human multipotent mesenchymal stromal cells (hMSCs). Encapsulated hMSCs maintain good cell viability over an extended culture period and exhibit robust differentiation potential into osteoblasts and adipocytes. Collectively, electrically induced tip streaming enables high-throughput encapsulation of single cells with high efficiency and universality, which is applicable for various applications in cell therapy, pharmacokinetic studies, and regenerative medicine.

Enhanced single-cell encapsulation in microfluidic devices: From droplet generation to single-cell analysis

Single-cell analysis to investigate cellular heterogeneity and cell-to-cell interactions is a crucial compartment to answer key questions in important biological mechanisms. Droplet-based microfluidics appears to be the ideal platform for such a purpose because the compartmentalization of single cells into microdroplets offers unique advantages of enhancing assay sensitivity, protecting cells against external stresses, allowing versatile and precise manipulations over tested samples, and providing a stable microenvironment for long-term cell proliferation and observation. The present Review aims to give a preliminary guidance for researchers from different backgrounds to explore the field of single-cell encapsulation and analysis. A comprehensive and introductory overview of the droplet formation mechanism, fabrication methods of microchips, and a myriad of passive and active encapsulation techniques to enhance single-cell encapsulation efficiency were presented. Meanwhile, common methods for single-cell analysis, especially for long-term cell proliferation, differentiation, and observation inside microcapsules, are briefly introduced. Finally, the major challenges faced in the field are illustrated, and potential prospects for future work are discussed.

Generation and manipulation of oil-in-water micro-droplets by confined thermocapillary microvortices

Optofluidic manipulation of droplets is critical in droplet-based microfluidic systems for chemistry, biology, and medicine. Here, we reported a thermocapillary microvortices-based manipulation platform for controlling oil-in-water droplets through integrating a photothermal waveguide into a microfluidic chip. The sizes and shapes of the droplets can be controlled by adjusting optical power or positions of the water-oil interface. Here, teardrop-shaped droplets, which can encapsulate and accumulate mesoscopic matters easily, were generated when the water-oil interface and the channel boundaries approached the photothermal waveguide center simultaneously. The results showed that the thermocapillary microvortices have good controllability of droplet positions, droplet volumes, and encapsulated-particle distribution and thus it will be a powerful droplet manipulation strategy for microreactors and microcapsules.

Preserving Single Cells in Space and Time for Analytical Assays

Analytical assays performed within clinical laboratories influence roughly 70% of all medical decisions by facilitating disease detection, diagnosis, and management. Both in clinical and academic research laboratories, single-cell assays permit measurement of cell diversity and identification of rare cells, both of which are important in the understanding of disease pathogenesis. For clinically utility, the single-cell assays must be compatible with the clinical workflow steps of sample collection, sample transportation, pre-analysis processing, and single-cell assay; therefore, it is paramount to preserve cells in a state that resembles that in vivo rather than measuring signaling behaviors initiated in response to stressors such as sample collection and processing. To address these challenges, novel cell fixation (and more broadly, cell preservation) techniques incorporate programmable fixation times, reversible bond formation and cleavage, chemoselective reactions, and improved analyte recovery. These technologies will further the development of individualized, precision therapies for patients to yield improved clinical outcomes.

Asynchronous generation of oil droplets using a microfluidic flow focusing system

Here, we show that long-term exposure of PDMS based microfluidic droplet generation systems to water can reverse their characteristics such that they generate oil-in-water droplets instead of water-in-oil droplets. The competition between two oil columns entering via the two side channels leads to asynchronous generation of oil droplets. We identify various modes of droplet generation, and study the size, gap and generation rate of droplets under different combinations of oil and water pressures. Oil droplets can also be generated using syringe pumps, various oil viscosities, and different combinations of immiscible liquids. We also demonstrate the ability to dynamically change the gap between the oil droplets from a few hundred microns to just a few microns in successive cycles using a latex balloon pressure pump. This method requires no special equipment or chemical treatments, and importantly can be reversed by long-term exposure of the PDMS surfaces to the ambient air.

Microdroplets-on-chip: A review

Single-cell analysis serves as an important approach to study cell functions and interactions. Catering to the demand of Big Data Era, fast reactions for single cells and paralleled high-throughput analysis have become an urgent need. Microdroplet in microfluidics has advantages of modularity and integrity, as well as high throughput and sensitivity, which present great potential in the field of single-cell analysis. This review is carried out on three aspects to introduce microdroplet chips for single-cell analysis: droplet formation, droplet detection and practical functions. Structures of droplet formation are categorized into three types, including T-shaped channel, flow-involved channel and three-dimensional micro-vortice. The detection methods, including fluorescence, Raman spectroscopy, mass spectroscopy and electrochemical detection, are summarized from applications. Both pros and cons for existing techniques are reviewed and discussed. The functions of microdroplets-on-chip cover cell culture, nucleic acid test and cell identification. For each field, principles/mechanisms and/or schematic images are laconically introduced. Microdroplet in microfluidics has become a major research direction in single-cell analysis. With updated methods of droplet formation such as inertial ordering and micro-vortice, microdroplets-based biochips will expect high throughput detection and high-accuracy trace detection for clinical diagnosis in the near future.

Droplet encapsulation of particles in different regimes and sorting of particle-encapsulating-droplets from empty droplets

Encapsulation of microparticles in droplets has profound applications in biochemical assays. We investigate encapsulation of rigid particles (polystyrene beads) and deformable particles (biological cells) inside aqueous droplets in various droplet generation regimes, namely, squeezing, dripping, and jetting. Our study reveals that the size of the positive (particle-encapsulating) droplets is larger or smaller compared to that of the negative (empty) droplets in the dripping and jetting regimes but no size contrast is observed in the squeezing regime. The size contrast of the positive and negative droplets in the different regimes is characterized in terms of capillary number C a and stream width ratio ω (i.e., ratio of stream width at the throat to particle diameter ω = w / d p ). While for deformable particles, the positive droplets are always larger compared to the negative droplets, for rigid particles, the positive droplets are larger in the dripping and jetting regimes for 0.50 ≤ ω ≤ 0.80 but smaller in the jetting regime for ω < 0.50 . We exploit the size contrast of positive and negative droplets for sorting across the fluid-fluid interface based on noninertial lift force (at R e ≪ 1 ), which is a strong function of droplet size. We demonstrate sorting of the positive droplets encapsulating polystyrene beads and biological cells from the negative droplets with an efficiency of ∼95% and purity of ∼65%. The proposed study will find relevance in single-cell studies, where positive droplets need to be isolated from the empty droplets prior to downstream processing.

Label-Free Metabolic Classification of Single Cells in Droplets Using the Phasor Approach to Fluorescence Lifetime Imaging Microscopy

Characterization of single cell metabolism is imperative for understanding subcellular functional and biochemical changes associated with healthy tissue development and the progression of numerous diseases. However, single-cell analysis often requires the use of fluorescent tags and cell lysis followed by genomic profiling to identify the cellular heterogeneity. Identifying individual cells in a noninvasive and label-free manner is crucial for the detection of energy metabolism which will discriminate cell types and most importantly critical for maintaining cell viability for further analysis. Here, we have developed a robust assay using the droplet microfluidic technology together with the phasor approach to fluorescence lifetime imaging microscopy to study cell heterogeneity within and among the leukemia cell lines (K-562 and Jurkat). We have extended these techniques to characterize metabolic differences between proliferating and quiescent cells-a critical step toward label-free single cancer cell dormancy research. The result suggests a droplet-based noninvasive and label-free method to distinguish individual cells based on their metabolic states, which could be used as an upstream phenotypic platform to correlate with genomic statistics. © 2018 International Society for Advancement of Cytometry.

Microfluidic diamagnetic water-in-water droplets: a biocompatible cell encapsulation and manipulation platform

Droplet microfluidics enables cellular encapsulation for biomedical applications such as single-cell analysis, which is an important tool used by biologists to study cells on a single-cell level, and understand cellular heterogeneity in cell populations. However, most cell encapsulation strategies in microfluidics rely on random encapsulation processes, resulting in large numbers of empty droplets. Therefore, post-sorting of droplets is necessary to obtain samples of purely cell-encapsulating droplets. With the recent advent of aqueous two-phase systems (ATPS) as a biocompatible alternative of the conventional water-in-oil droplet systems for cellular encapsulation, there has also been a focus on integrating ATPS with droplet microfluidics. In this paper, we describe a new technique that combines ATPS-based water-in-water droplets with diamagnetic manipulation to isolate single-cell encapsulating water-in-water droplets, and achieve a purity of 100% in a single pass. We exploit the selective partitioning of ferrofluid in an ATPS of polyethylene glycol-polypropylene glycol-polyethylene glycol triblock copolymer (PEG-PPG-PEG) and dextran (DEX), to achieve diamagnetic manipulation of water-in-water droplets. A cell-triggered Rayleigh-Plateau instability in the dispersed phase thread results in a size distinction between the cell-encapsulating and empty droplets, enabling diamagnetic separation and sorting of the cell-encapsulating droplets from empty droplets. This is a simple and biocompatible all-aqueous platform for single-cell encapsulation and droplet manipulation, with applications in single-cell analysis.

Quantifying phenotypes in single cells using droplet microfluidics

This book chapter describes the use of droplet microfluidics to phenotype single cells. The basic process flow includes the encapsulation of single cells with a specific probe into aqueous micro-droplets suspended in a biocompatible oil. The probe is chosen to measure the phenotype of interest. After incubation, the encapsulated cell turns the probe fluorescent and renders the entire droplet fluorescent. Enumerating drops that are fluorescent quantifies the concentration of cells possessing the phenotype of interest. Examining the distribution of fluorescence further allows one to quantify the heterogeneity among the cell population.

Lipoplex-Mediated Single-Cell Transfection via Droplet Microfluidics

While lipoplex (cationic lipid-nucleic acid complex)-mediated intracellular delivery is widely adopted in mammalian cell transfection, its transfection efficiency for suspension cells, e.g., lymphatic and hematopoietic cells, is reported at only ≈5% or even lower. Here, efficient and consistent lipoplex-mediated transfection is demonstrated for hard-to-transfect suspension cells via a single-cell, droplet-microfluidics approach. In these microdroplets, monodisperse lipoplexes for effective gene delivery are generated via chaotic mixing induced by the serpentine microchannel and co-confined with single cells. Moreover, the cell membrane permeability increases due to the shear stress exerted on the single cells when they pass through the droplet pinch-off junction. The transfection efficiency, examined by the delivery of the pcDNA3-EGFP plasmid, improves from ≈5% to ≈50% for all three tested suspension cell lines, i.e., K562, THP-1, Jurkat, and with significantly reduced cell-to-cell variation, compared to the bulk method. Efficient targeted knockout of the TP53BP1 gene for K562 cells via the CRISPR (clustered regularly interspaced short palindromic repeats)-CAS9 (CRISPR-associated nuclease 9) mechanism is also achieved using this platform. Lipoplex-mediated single-cell transfection via droplet microfluidics is expected to have broad applications in gene therapy and regenerative medicine by providing high transfection efficiency and low cell-to-cell variation for hard-to-transfect suspension cells.

A Microfluidic Strategy for Controllable Generation of Water-in-Water Droplets as Biocompatible Microcarriers

Droplet microfluidics has been widely applied in functional microparticles fabricating, tissue engineering, and drug screening due to its high throughput and great controllability. However, most of the current droplet microfluidics are dependent on water-in-oil (W/O) systems, which involve organic reagents, thus limiting their broader biological applications. In this work, a new microfluidic strategy is described for controllable and high-throughput generation of monodispersed water-in-water (W/W) droplets. Solutions of polyethylene glycol and dextran are used as continuous and dispersed phases, respectively, without any organic reagents or surfactants. The size of W/W droplets can be precisely adjusted by changing the flow rate of dispersed and continuous phases and the valve switch cycle. In addition, uniform cell-laden microgels are fabricated by introducing the alginate component and rat pancreatic islet (β-TC6) cell suspension to the dispersed phase. The encapsulated islet cells retain high viability and the function of insulin secretion after cultivation for 7 days. The high-throughput droplet microfluidic system with high biocompatibility is stable, controllable, and flexible, which can boost various chemical and biological applications, such as bio-oriented microparticles synthesizing, microcarriers fabricating, tissue engineering, etc.