Dean Flow Assisted Single Cell and Bead Encapsulation for High Performance Single Cell Expression Profiling

Enhancing single-cell encapsulation in droplet microfluidics with fine-tunable on-chip sample enrichment

Single-cell encapsulation in droplet microfluidics is commonly hindered by the tradeoff between cell suspension density and on-chip focusing performance. In this study, we introduce a novel droplet microfluidic chip to overcome this challenge. The chip comprises a double spiral focusing unit, a flow resistance-based sample enrichment module with fine-tunable outlets, and a crossflow droplet generation unit. Utilizing a low-density cell/bead suspension (2 × 106 objects/mL), cells/beads are focused into a near-equidistant linear arrangement within the double spiral microchannel. The excess water phase is diverted while cells/beads remain focused and sequentially encapsulated in individual droplets. Focusing performance was assessed through numerical simulations and experiments at three flow rates (40, 60, 80 μL/min), demonstrating successful focusing at 40 and 80 μL/min for beads and cells, respectively. In addition, both simulation and experimental results revealed that the flow resistance at the sample enrichment module is adjustable by punching different outlets, allowing over 50% of the aqueous phase to be removed. YOLOv8n-based droplet detection algorithms realized the counting of cells/beads in droplets, statistically demonstrating single-cell and bead encapsulation rates of 72.2% and 79.2%, respectively. All the results indicate that this on-chip sample enrichment approach can be further developed and employed as a critical component in single-cell encapsulation in water-in-oil droplets.

The Physics and Manipulation of Dean Vortices in Single- and Two-Phase Flow in Curved Microchannels: A Review

Microchannels with curved geometries have been employed for many applications in microfluidic devices in the past decades. The Dean vortices generated in such geometries have been manipulated using different methods to enhance the performance of devices in applications such as mixing, droplet sorting, and particle/cell separation. Understanding the effect of the manipulation method on the Dean vortices in different geometries can provide crucial information to be employed in designing high-efficiency microfluidic devices. In this review, the physics of Dean vortices and the affecting parameters are summarized. Various Dean number calculation methods are collected and represented to minimize the misinterpretation of published information due to the lack of a unified defining formula for the Dean dimensionless number. Consequently, all Dean number values reported in the references are recalculated to the most common method to facilitate comprehension of the phenomena. Based on the converted information gathered from previous numerical and experimental studies, it is concluded that the length of the channel and the channel pathline, e.g., spiral, serpentine, or helix, also affect the flow state. This review also provides a detailed summery on the effect of other geometric parameters, such as cross-section shape, aspect ratio, and radius of curvature, on the Dean vortices' number and arrangement. Finally, considering the importance of droplet microfluidics, the effect of curved geometry on the shape, trajectory, and internal flow organization of the droplets passing through a curved channel has been reviewed.

Microfluidic design in single-cell sequencing and application to cancer precision medicine

Single-cell sequencing (SCS) is a crucial tool to reveal the genetic and functional heterogeneity of tumors, providing unique insights into the clonal evolution, microenvironment, drug resistance, and metastatic progression of cancers. Microfluidics is a critical component of many SCS technologies and workflows, conferring advantages in throughput, economy, and automation. Here, we review the current landscape of microfluidic architectures and sequencing techniques for single-cell omics analysis and highlight how these have enabled recent applications in oncology research. We also discuss the challenges and the promise of microfluidics-based single-cell analysis in the future of precision oncology.

DUPLETS: Deformability-Assisted Dual-Particle Encapsulation Via Electrically Activated Sorting

Co-encapsulation of bead carriers and biological cells in microfluidics has become a powerful technique for various biological assays in single-cell genomics and drug screening because of its distinct capability of single-cell confinement. However, current co-encapsulation approaches exist a trade-off between cell/bead pairing rate and probability of multiple cells in individual droplets, significantly limiting the effective throughput of single-paired cell-bead droplets production. Deformability-assisted dUal-Particle encapsuLation via Electrically acTivated Sorting (DUPLETS) system is reported to overcome this problem. The DUPLETS can differentiate the encapsulated content in individual droplets and sort out targeted droplets via a combined screening of mechanical and electrical characteristics of single droplets in label-free manners and with the highest effective throughput in comparison to current commercial platforms. The DUPLETS has been demonstrated to enrich single-paired cell-bead droplets to over 80% (above eightfold higher than current co-encapsulation techniques). It eliminates multicell droplets to 0.1% whereas up to ≈24% in 10× Chromium. It is believed that merging DUPLETS into the current co-encapsulation platforms can meaningfully elevate sample quality in terms of high purity of single-paired cell-bead droplets, low fraction of multicell droplets, and high cell viability, which can benefit a multitude of biological assay applications.

Viscoelastic Particle Encapsulation Using a Hyaluronic Acid Solution in a T-Junction Microfluidic Device

The encapsulation of particles and cells in droplets is highly relevant in biomedical engineering as well as in material science. So far, however, the majority of the studies in this area have focused on the encapsulation of particles or cells suspended in Newtonian liquids. We here studied the particle encapsulation phenomenon in a T-junction microfluidic device, using a non-Newtonian viscoelastic hyaluronic acid solution in phosphate buffer saline as suspending liquid for the particles. We first studied the non-Newtonian droplet formation mechanism, finding that the data for the normalised droplet length scaled as the Newtonian ones. We then performed viscoelastic encapsulation experiments, where we exploited the fact that particles self-assembled in equally-spaced structures before approaching the encapsulation area, to then identify some experimental conditions for which the single encapsulation efficiency was larger than the stochastic limit predicted by the Poisson statistics.

Droplets microfluidics platform-A tool for single cell research

Cells are the most basic structural and functional units of living organisms. Studies of cell growth, differentiation, apoptosis, and cell-cell interactions can help scientists understand the mysteries of living systems. However, there is considerable heterogeneity among cells. Great differences between individuals can be found even within the same cell cluster. Cell heterogeneity can only be clearly expressed and distinguished at the level of single cells. The development of droplet microfluidics technology opens up a new chapter for single-cell analysis. Microfluidic chips can produce many nanoscale monodisperse droplets, which can be used as small isolated micro-laboratories for various high-throughput, precise single-cell analyses. Moreover, gel droplets with good biocompatibility can be used in single-cell cultures and coupled with biomolecules for various downstream analyses of cellular metabolites. The droplets are also maneuverable; through physical and chemical forces, droplets can be divided, fused, and sorted to realize single-cell screening and other related studies. This review describes the channel design, droplet generation, and control technology of droplet microfluidics and gives a detailed overview of the application of droplet microfluidics in single-cell culture, single-cell screening, single-cell detection, and other aspects. Moreover, we provide a recent review of the application of droplet microfluidics in tumor single-cell immunoassays, describe in detail the advantages of microfluidics in tumor research, and predict the development of droplet microfluidics at the single-cell level.

Effect of wall slip on the viscoelastic particle ordering in a microfluidic channel

The formation of a line of equally spaced particles at the centerline of a microchannel, referred as "particle ordering," is desired in several microfluidic applications. Recent experiments and simulations highlighted the capability of viscoelastic fluids to form a row of particles characterized by a preferential spacing. When dealing with non-Newtonian fluids in microfluidics, the adherence condition of the liquid at the channel wall may be violated and the liquid can slip over the surface, possibly affecting the ordering efficiency. In this work, we investigate the effect of wall slip on the ordering of particles suspended in a viscoelastic liquid by numerical simulations. The dynamics of a triplet of particles in an infinite cylindrical channel is first addressed by solving the fluid and particle governing equations. The relative velocities computed for the three-particle system are used to predict the dynamics of a train of particles flowing in a long microchannel. The distributions of the interparticle spacing evaluated at different slip coefficients, linear particle concentrations, and distances from the channel inlet show that wall slip slows down the self-assembly mechanism. For strong slipping surfaces, no significant change of the initial microstructure is observed at low particle concentrations, whereas strings of particles in contact form at higher concentrations. The detrimental effect of wall slip on viscoelastic ordering suggests care when designing microdevices, especially in case of hydrophobic surfaces that may enhance the slipping phenomenon.

Beating Poisson stochastic particle encapsulation in flow-focusing microfluidic devices using viscoelastic liquids

The encapsulation and co-encapsulation of particles in microfluidic flows is essential in applications related to single-cell analysis and material synthesis. However, the whole encapsulation process is stochastic in nature, and its efficiency is limited by the so-called Poisson limit. We here demonstrate particle encapsulation in microfluidic devices having flow-focusing geometries with efficiency up to 2-fold larger than the stochastic limit imposed by the Poisson statistics. To this aim, we exploited the recently observed phenomenon of particle train formation in viscoelastic liquids, so that particles could approach the encapsulation area with a constant frequency that was subsequently synchronised to the constant frequency of droplet formation. We also developed a simplified expression based on the experimental results that can guide optimal design of the microfluidic encapsulation system. Finally, we report the first experimental evidence of viscoelastic co-encapsulation of particles coming from different streams.

Thermo-Induced Coalescence of Dual Cores in Double Emulsions for Single-Cell RT-PCR

Single-cell reverse-transcription polymerase chain reaction (RT-PCR) has shown significant promise for transcriptional profiling of heterogeneous cells. However, currently developed microfluidic droplet-based methodologies for single-cell RT-PCR often require complex chip design to accommodate the associated multistep processes as well as customized detection platforms for high-throughput analysis. Herein, we proposed a dual-core double emulsion (DE)-based method to streamline the single-cell RT-PCR through thermo-induced coalescence of the dual cores. The dual-core DEs were produced by pairing two water-in-oil single emulsions containing a single-cell/lysis buffer and RT-PCR mix, respectively. After complete lysis of single cells in one of the cores, the dual-core DEs were merged by gentle heating, made possible by the optimized glycerol concentration present in the cores. Upon the coalescence of dual cores, the alkaline lysis buffer present in the core of the cell lysate was neutralized by the reaction buffer presented in the RT-PCR core, allowing TaqMan assay-based RT-PCR to occur effectively within the DEs. To demonstrate the potential of this streamlined dual-core platform, AKR1B10-positive A549 cells and AKR1B10-negative HEK293 cells were investigated via the TaqMan assay. Subsequently, specific transcript of AKR1B10 was readily available for quantitative profiling at the single-cell level using a commercially available flow cytometer in a high-throughput manner.

Single-cell droplet microfluidics for biomedical applications

This review focuses on the recent advances in the fundamentals of single-cell droplet microfluidics and its applications in biomedicine, providing insights into design and establishment of single-cell microsystems and their further performance.

Single-Cell Sequencing to Unveil the Mystery of Embryonic Development

Embryonic development is a fundamental physiological process that can provide tremendous insights into stem cell biology and regenerative medicine. In this process, cell fate decision is highly heterogeneous and dynamic, and investigations at the single-cell level can greatly facilitate the understanding of the molecular roadmap of embryonic development. Rapid advances in the technology of single-cell sequencing offer a perfectly useful tool to fulfill this purpose. Despite its great promise, single-cell sequencing is highly interdisciplinary, and successful applications in specific biological contexts require a general understanding of its diversity as well as the advantage versus limitations for each of its variants. Here, the technological principles of single-cell sequencing are consolidated and its applications in the study of embryonic development are summarized. First, the technology basics are presented and the available tools for each step including cell isolation, library construction, sequencing, and data analysis are discussed. Then, the works that employed single-cell sequencing are reviewed to investigate the specific processes of embryonic development, including preimplantation, peri-implantation, gastrulation, and organogenesis. Further, insights are provided on existing challenges and future research directions.

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.

Controlled viscoelastic particle encapsulation in microfluidic devices

The encapsulation of particles in droplets using microfluidic devices finds application across several fields ranging from biomedical engineering to materials science. The encapsulation process, however, is often affected by poor single encapsulation efficiency, quantified by the Poisson statistics, with droplets containing more than one particle or with several empty droplets. We here demonstrate that viscoelastic aqueous solutions of xanthan gum enable controlled single particle encapsulation in microfluidic devices with a single encapsulation efficiency up to 2-fold larger than the one predicted by the Poisson statistics. We achieved such a result by identifying viscoelastic xanthan gum aqueous solutions that could drive particle ordering before approaching the encapsulation area and simultaneously form uniform droplets. This is the first experimental evidence of viscoelastic encapsulation in microfluidic devices, the existing literature on the subject being focused on Newtonian suspending liquids. We first studied the process of viscoelastic droplet formation, and found that the droplet length normalised by the channel diameter scaled as predicted for Newtonian solutions. At variance with Newtonian solutions, we observed that the droplet formation mechanism became unstable above critical values of the Weissenberg number, which quantifies the elasticity of the xanthan gum solutions carrying the particles. In terms of controlled encapsulation, we discovered that the single encapsulation efficiency was larger than the Poisson values in a specific range of xanthan gum mass concentrations. Finally, we introduced an empirical formula that can help the design of controlled viscoelastic encapsulation systems.

Microfluidic recapitulation of circulating tumor cell-neutrophil clusters via double spiral channel-induced deterministic encapsulation

Circulating tumor cell (CTC)-neutrophil clusters are highly potent precursors of cancer metastasis. However, their rarity in patients' blood has restricted research thus far, and moreover, studies on in vitro methods for mimicking cell clusters have generally neglected in vivo conditions. Here, we introduce an inertial-force-assisted droplet microfluidic chip that allows the recapitulation of CTC-neutrophil clusters in terms of physical as well as biochemical features. The deterministic encapsulation of cells via double spiral channels facilitates the pairing of neutrophils and cancer cells with ratios of interest (from 1 : 1 to 1 : 3). The encapsulated cells are spontaneously associated to form clusters, achieving the physical emulation of CTC-neutrophil clusters. Furthermore, the molecular signatures of CTC-neutrophil clusters (e.g., their E-cadherin, VCAM-1, and mRNA expressions) were well defined. Our novel microfluidic platform for exploring CTC-neutrophil clusters can therefore play a promising role in cancer-metastasis studies.

Dual dean entrainment with volume ratio modulation for efficient droplet co-encapsulation: extreme single-cell indexing

The future of single cell diversity screens involves ever-larger sample sizes, dictating the need for higher throughput methods with low analytical noise to accurately describe the nature of the cellular system. Current approaches are limited by the Poisson statistic, requiring dilute cell suspensions and associated losses in throughput. In this contribution, we apply Dean entrainment to both cell and bead inputs, defining different volume packets to effect efficient co-encapsulation. Volume ratio scaling was explored to identify optimal conditions. This enabled the co-encapsulation of single cells with reporter beads at rates of ∼1 million cells per hour, while increasing assay signal-to-noise with cell multiplet rates of ∼2.5% and capturing ∼70% of cells. The method, called Pirouette coupling, extends our capacity to investigate biological systems.

Microfluidic formation of crystal-like structures

Crystal-like structures find application in several fields ranging from biomedical engineering to material science. For instance, droplet crystals are critical for high throughput assays and material synthesis, while particle crystals are important for particles and cell encapsulation, Drop-seq technologies, and single-cell analysis. Formation of crystal-like structures relies entirely on the possibility of manipulating with great accuracy the micrometer-size objects forming the crystal. In this context, microfluidic devices offer versatile tools for the precise manipulation of droplets and particles, thus enabling fabrication of crystal-like structures that form due to hydrodynamic interactions among droplets or particles. In this review, we aim at providing an holistic representation of crystal-like structure formation mediated by hydrodynamic interactions in microfluidic devices. We also discuss the physical origin of these hydrodynamic interactions and their relation to parameters such as device geometry, fluid properties, and flow conditions.

Inertial focusing of microparticles, bacteria, and blood in serpentine glass channels

Early detection of pathogenic microorganisms is pivotal to diagnosis and prevention of health and safety crises. Standard methods for pathogen detection often rely on lengthy culturing procedures, confirmed by biochemical assays, leading to >24 h for a diagnosis. The main challenge for pathogen detection is their low concentration within complex matrices. Detection of blood-borne pathogens via techniques such as PCR requires an initial positive blood culture and removal of inhibitory blood components, reducing its potential as a diagnostic tool. Among different label-free microfluidic techniques, inertial focusing on microscale channels holds great promise for automation, parallelization, and passive continuous separation of particles and cells. This work presents inertial microfluidic manipulation of small particles and cells (1-10 μm) in curved serpentine glass channels etched at different depths (deep and shallow designs) that can be exploited for (1) bacteria preconcentration from biological samples and (2) bacteria-blood cell separation. In our shallow device, the ability to focus Escherichia coli into the channel side streams with high recovery (89% at 2.2× preconcentration factor) could be applied for bacteria preconcentration in urine for diagnosis of urinary tract infections. Relying on differential equilibrium positions of red blood cells and E. coli inside the deep device, 97% red blood cells were depleted from 1:50 diluted blood with 54% E. coli recovered at a throughput of 0.7 mL/min. Parallelization of such devices could process relevant volumes of 7 mL whole blood in 10 min, allowing faster sample preparation for downstream molecular diagnostics of bacteria present in bloodstream.

Methods and platforms for analysis of nucleic acids from single-cell based on microfluidics

Single-cell nucleic acid analysis aims at discovering the genetic differences between individual cells which is well known as the cellular heterogeneity. This technology facilitates cancer diagnosis, stem cell research, immune system analysis, and other life science applications. The conventional platforms for single-cell nucleic acid analysis more rely on manual operation or bulky devices. Recently, the emerging microfluidic technology has provided a perfect platform for single-cell nucleic acid analysis with the characteristic of accurate and automatic single-cell manipulation. In this review, we briefly summarized the procedure of single-cell nucleic acid analysis including single-cell isolation, single-cell lysis, nucleic acid amplification, and genetic analysis. And then, three representative microfluidic platforms for single-cell nucleic acid analysis are concluded as valve-, microwell-, and droplet-based platforms. Furthermore, we described the state-of-the-art integrated single-cell nucleic acid analysis systems based on the three platforms. Finally, the future development and challenges of microfluidics-based single-cell nucleic acid analysis are discussed as well.

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.

The up-to-date strategies for the isolation and manipulation of single cells

Due to the large cellular heterogeneity, the strategies for the isolation and manipulation of single cells have been pronounced indispensable in the fields of disease diagnostics, drug delivery, and cancer biology at the single-cell resolution. Herein, an overview of the up-to-date techniques for precise manipulation/separation and analysis of single-cell is accomplished, these include the various approaches for the isolation and detection of individual cells in flow cytometry, microfluidic systems, micromodule systems, and others. In addition, the advanced application of these protocols is discussed. In particular, a few designs are highlighted for visualization, non-invasion, and intelligentization in single cell analysis, i.e., imaging flow cytometry, label-free microfluidic platform, single-cell capillary probe, and other related techniques. At the present, the main barriers in the various schemes for single cell manipulation which limited their practical applications are their cumbersome construction and single-functionality. The future opportunities and outstanding challenges in the isolation/manipulation of single cells are depicted.