Inertial-ordering-assisted droplet microfluidics for high-throughput single-cell RNA-sequencing

Droplet-based single-cell sequencing: Strategies and applications

Notable advancements in single-cell omics technologies have not only addressed longstanding challenges but also enabled unprecedented studies of cellular heterogeneity with unprecedented resolution and scale. These strides have led to groundbreaking insights into complex biological systems, paving the way for a more profound comprehension of human biology and diseases. The droplet microfluidic technology has become a crucial component in many single-cell sequencing workflows in terms of throughput, cost-effectiveness, and automation. Utilizing a microfluidic chip to encapsulate and profile individual cells within droplets has significantly improved single-cell research. Therefore, this review aims to comprehensively elaborate the droplet microfluidics-assisted omics methods from a single-cell perspective. The strategies for using droplet microfluidics in the realms of genomics, epigenomics, transcriptomics, and proteomics analyses are first introduced. On this basis, the focus then turns to the latest applications of this technology in different sequencing patterns, including mono- and multi-omics. Finally, the challenges and further perspectives of droplet-based single-cell sequencing in both foundational research and commercial applications are discussed.

On-chip dielectrophoretic single-cell manipulation

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

DropBlot: single-cell western blotting of chemically fixed cancer cells

Archived patient-derived tissue specimens play a central role in understanding disease and developing therapies. To address specificity and sensitivity shortcomings of existing single-cell resolution proteoform analysis tools, we introduce a hybrid microfluidic platform (DropBlot) designed for proteoform analyses in chemically fixed single cells. DropBlot serially integrates droplet-based encapsulation and lysis of single fixed cells, with on-chip microwell-based antigen retrieval, with single-cell western blotting of target antigens. A water-in-oil droplet formulation withstands the harsh chemical (SDS, 6 M urea) and thermal conditions (98 °C, 1-2 hr) required for effective antigen retrieval, and supports analysis of retrieved protein targets by single-cell electrophoresis. We demonstrate protein-target retrieval from unfixed, paraformaldehyde-fixed (PFA), and methanol-fixed cells. Key protein targets (HER2, GAPDH, EpCAM, Vimentin) retrieved from PFA-fixed cells were resolved and immunoreactive. Relevant to biorepositories, DropBlot profiled targets retrieved from human-derived breast tumor specimens archived for six years, offering a workflow for single-cell protein-biomarker analysis of sparing biospecimens.

Towards Design Automation of Microfluidic Mixers: Leveraging Reinforcement Learning and Artificial Neural Networks

Microfluidic mixers, a pivotal application of microfluidic technology, are primarily utilized for the rapid amalgamation of diverse samples within microscale devices. Given the intricacy of their design processes and the substantial expertise required from designers, the intelligent automation of microfluidic mixer design has garnered significant attention. This paper discusses an approach that integrates artificial neural networks (ANNs) with reinforcement learning techniques to automate the dimensional parameter design of microfluidic mixers. In this study, we selected two typical microfluidic mixer structures for testing and trained two neural network models, both highly precise and cost-efficient, as alternatives to traditional, time-consuming finite-element simulations using up to 10,000 sets of COMSOL simulation data. By defining effective state evaluation functions for the reinforcement learning agents, we utilized the trained agents to successfully validate the automated design of dimensional parameters for these mixer structures. The tests demonstrated that the first mixer model could be automatically optimized in just 0.129 s, and the second in 0.169 s, significantly reducing the time compared to manual design. The simulation results validated the potential of reinforcement learning techniques in the automated design of microfluidic mixers, offering a new solution in this field.

Influence of Sphericity on Surface Termination of Icosahedral Colloidal Clusters

Colloids self-organize into icosahedral clusters composed of a Mackay core and an anti-Mackay shell under spherical confinement to minimize the free energy. This study explores the variation of surface arrangements of colloids in icosahedral clusters, focusing on the determining factors behind the surface arrangement. To efficiently assemble particles in emulsion droplets, droplet-to-droplet osmotic extraction from particle-laden droplets to salt-containing droplets is used, where the droplets are microfluidically prepared to guarantee a high size uniformity. The icosahedral clusters are optimally produced during a 24-h consolidation period at a 0.04 m salt concentration. The findings reveal an increase in the number of particle layers from 10 to 15 in the icosahedral clusters as the average number of particles increases from 3300 to 11 000. Intriguingly, the number of layers in the anti-Mackay shells, or surface termination, appears to more strongly depend on the sphericity of the clusters than on the deviation in the particle count from an ideal icosahedral cluster. This result suggests that the sphericity of the outermost layer, formed by the late-stage rearrangement of particles to form an anti-Mackay shell near the droplet interface, may play a pivotal role in determining the surface morphology to accommodate a spherical interface.

Numerical investigation of heterogeneous soft particle pairs in inertial microfluidics

The formation of pairs of particles or cells of different types in microfluidic channels can be desired or detrimental in healthcare applications. It is still unclear what role softness heterogeneity plays in the formation of these particle pairs. We use an in-house lattice-Boltzmann-immersed-boundary-finite-element solver to simulate a pair of particles with different softness flowing through a straight channel with a rectangular cross-section under initial conditions representative of a dilute suspension. We find that softness heterogeneity significantly affects the pair dynamics, determining whether a pair will form or not, and determining the lateral and inter-particle equilibrium behaviour in the pair. We also observe close matches between the transient deformation of particles in a linear pair and single particles in isolation. These results further our understanding of pair behaviour, providing a foundation for understanding particle train formation, and open up the potential to develop reduced-order models for particle pair formation based upon the behaviour of single particles.

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.

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.

Deep learning with microfluidics for on-chip droplet generation, control, and analysis

Droplet microfluidics has gained widespread attention in recent years due to its advantages of high throughput, high integration, high sensitivity and low power consumption in droplet-based micro-reaction. Meanwhile, with the rapid development of computer technology over the past decade, deep learning architectures have been able to process vast amounts of data from various research fields. Nowadays, interdisciplinarity plays an increasingly important role in modern research, and deep learning has contributed greatly to the advancement of many professions. Consequently, intelligent microfluidics has emerged as the times require, and possesses broad prospects in the development of automated and intelligent devices for integrating the merits of microfluidic technology and artificial intelligence. In this article, we provide a general review of the evolution of intelligent microfluidics and some applications related to deep learning, mainly in droplet generation, control, and analysis. We also present the challenges and emerging opportunities in this field.

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

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

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.

Inertial microfluidics: current status, challenges, and future opportunities

Inertial microfluidics uses the hydrodynamic effects induced at finite Reynolds numbers to achieve passive manipulation of particles, cells, or fluids and offers the advantages of high-throughput processing, simple channel geometry, and label-free and external field-free operation. Since its proposal in 2007, inertial microfluidics has attracted increasing interest and is currently widely employed as an important sample preparation protocol for single-cell detection and analysis. Although great success has been achieved in the inertial microfluidics field, its performance and outcome can be further improved. From this perspective, herein, we reviewed the current status, challenges, and opportunities of inertial microfluidics concerning the underlying physical mechanisms, available simulation tools, channel innovation, multistage, multiplexing, or multifunction integration, rapid prototyping, and commercial instrument development. With an improved understanding of the physical mechanisms and the development of novel channels, integration strategies, and commercial instruments, improved inertial microfluidic platforms may represent a new foundation for advancing biomedical research and disease diagnosis.

Negative Magnetophoresis Focusing Microchips Online-Coupled with ICP-MS for High-Throughput Single-Cell Analysis

High-throughput single-cell analysis is critical to elucidate the cell heterogeneity. Recently, droplet microchips using oil/gas phases to generate single-cell encapsulated droplets have been combined with inductively coupled plasma-mass spectrometry (ICP-MS) for determination of trace elements in single cells with a throughput of dozens of cells per min. To improve the sample throughput and avoid the oil phase introduced into ICP-MS, herein, a negative magnetophoresis focusing microchip was established and online-coupled to ICP-MS for single-cell analysis. MCF-7 cells in the paramagnetic salt solution were introduced into the designed focusing microchannel, in which they were focused into a single stream under both the magnetic repulsion force and inertial lift force, and then were introduced into ICP-MS for online single-cell analysis. The important parameters including the chip design, the concentration of the paramagnetic salt solution, flow rate, cell density, and dwell time were optimized. Under the optimal conditions, a high sample throughput of 1390 cells min^-1 was obtained. The established online analytical system was applied to study the uptake behaviors of MCF-7 cells for Zn²⁺ and ZnO nanoparticles (NPs) at a single-cell level. The single-cell analysis results indicate that MCF-7 cells displayed more remarkable heterogeneity when they were treated with ZnO NPs, and the uptake content of ZnO NPs by MCF-7 cells was less than that of Zn²⁺. Compared with other droplet microdevice-ICP-MS analysis systems, the developed system has the advantages of simple design and fabrication, no organic phase, a high throughput, and a low sample consumption (only 5 μL).

Numerical investigation of the formation and stability of homogeneous pairs of soft particles in inertial microfluidics

We investigate the formation and stability of a pair of identical soft capsules in channel flow under mild inertia. We employ a combination of the lattice Boltzmann, finite element and immersed boundary methods to simulate the elastic particles in flow. Validation tests show excellent agreement with numerical results obtained by other research groups. Our results reveal new trajectory types that have not been observed for pairs of rigid particles. While particle softness increases the likelihood of a stable pair forming, the pair stability is determined by the lateral position of the particles. A key finding is that stabilisation of the axial distance occurs after lateral migration of the particles. During the later phase of pair formation, particles undergo damped oscillations that are independent of initial conditions. These damped oscillations are driven by a strong hydrodynamic coupling of the particle dynamics, particle inertia and viscous dissipation. While the frequency and damping coefficient of the oscillations depend on particle softness, the pair formation time is largely determined by the initial particle positions: the time to form a stable pair grows exponentially with the initial axial distance. Our results demonstrate that particle softness has a strong impact on the behaviour of particle pairs. The findings could have significant ramifications for microfluidic applications where a constant and reliable axial distance between particles is required, such as flow cytometry.

Micro and nanofluidics for high throughput drug screening

In this book chapter, we elaborate on the state-of-the-art technology developments in high throughput screening, microfluidics and nanofluidics. This book chapter further elaborated on the application of microfluidics and nanofluidics for high throughput drug screening with respect to communicable diseases and non-communicable diseases such as cancer. As a future perspective, there is tremendous potential for microfluidics and nanofluidics to be applied in high throughput drug screening which could be applied for various biotechnology applications such as in cancer precision medicine, point-of-care diagnostics and imaging. With the integration of Fourth industrial revolution (4IR) technologies with micro and nanofluidics technologies, it envisioned that such integration along with digital health would enable next generation technology development in medical field.

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.

A Portrait of Intratumoral Genomic and Transcriptomic Heterogeneity at Single-Cell Level in Colorectal Cancer

In the study of cancer, omics technologies are supporting the transition from traditional clinical approaches to precision medicine. Intra-tumoral heterogeneity (ITH) is detectable within a single tumor in which cancer cell subpopulations with different genome features coexist in a patient in different tumor areas or may evolve/differ over time. Colorectal carcinoma (CRC) is characterized by heterogeneous features involving genomic, epigenomic, and transcriptomic alterations. The study of ITH is a promising new frontier to lay the foundation towards successful CRC diagnosis and treatment. Genome and transcriptome sequencing together with editing technologies are revolutionizing biomedical research, representing the most promising tools for overcoming unmet clinical and research challenges. Rapid advances in both bulk and single-cell next-generation sequencing (NGS) are identifying primary and metastatic intratumoral genomic and transcriptional heterogeneity. They provide critical insight in the origin and spatiotemporal evolution of genomic clones responsible for early and late therapeutic resistance and relapse. Single-cell technologies can be used to define subpopulations within a known cell type by searching for differential gene expression within the cell population of interest and/or effectively isolating signal from rare cell populations that would not be detectable by other methods. Each single-cell sequencing analysis is driven by clustering of cells based on their differentially expressed genes. Genes that drive clustering can be used as unique markers for a specific cell population. In this review we analyzed, starting from published data, the possible achievement of a transition from clinical CRC research to precision medicine with an emphasis on new single-cell based techniques; at the same time, we focused on all approaches and issues related to this promising technology. This transition might enable noninvasive screening for early diagnosis, individualized prediction of therapeutic response, and discovery of additional novel drug targets.

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.

Inertial microfluidics for high-throughput cell analysis and detection: a review

Since it was first proposed in 2007, inertial microfluidics has been extensively studied in terms of theory, design, fabrication, and application. In recent years, with the rapid development of microfabrication technologies, a variety of channel structures that can focus, concentrate, separate, and capture bioparticles or fluids have been designed and manufactured to extend the range of potential biomedical applications of inertial microfluidics. Due to the advantages of high throughput, simplicity, and low device cost, inertial microfluidics is a promising candidate for rapid sample processing, especially for large-volume samples with low-abundance targets. As an approach to cellular sample pretreatment, inertial microfluidics has been widely employed to ensure downstream cell analysis and detection. In this review, a comprehensive summary of the application of inertial microfluidics for high-throughput cell analysis and detection is presented. According to application areas, the recent advances can be sorted into label-free cell mechanical phenotyping, sheathless flow cytometric counting, electrical impedance cytometer, high-throughput cellular image analysis, and other methods. Finally, the challenges and prospects of inertial microfluidics for cell analysis and detection are summarized.

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.

Single Cell Metabolite Detection Using Inertial Microfluidics-Assisted Ion Mobility Mass Spectrometry

Single-cell metabolite measurement remains highly challenging due to difficulties related to single cell isolation, metabolite detection, and identification of low levels of metabolites. Here, as a first step of the technological development, we propose a novel strategy integrating spiral inertial microfluidics and ion mobility mass spectrometry (IM-MS) for single-cell metabolite detection and identification. Cells in methanol suspension are inertially focused into a single stream in the spiral microchannel. This stream of separated cells is delivered to the nanoelectrospray needle to be lysed and ionized and subsequently analyzed in real time by IM-MS. This analytical system enables six to eight single-cell metabolic fingerprints to be collected per minute, including gas-phase collisional cross section (CCS) measurements as an additional molecular descriptor, giving increased confidence in metabolite identification. As a proof of concept, the metabolic profiles of three types of cancer cells (U2OS, HepG2, and HepG2.215) were successfully screened, and 19 distinct lipids species were identified with CCS value filtering. Furthermore, principal component analysis (PCA) showed differentiation of the three cancer cell lines, mainly due to cellular surface phospholipids. Taken together, our technology platform offers a simple and efficient method for single-cell lipid profiling, with additional ion mobility separation of lipids significantly improving the confidence toward identification of metabolites.

Single-Cell Sequencing Methodologies: From Transcriptome to Multi-Dimensional Measurement

Cells are the basic building blocks of biological systems, with inherent unique molecular features and development trajectories. The study of single cells facilitates in-depth understanding of cellular diversity, disease processes, and organization of multicellular organisms. Single-cell RNA sequencing (scRNA-seq) technologies have become essential tools for the interrogation of gene expression patterns and the dynamics of single cells, allowing cellular heterogeneity to be dissected at unprecedented resolution. Nevertheless, measuring at only transcriptome level or 1D is incomplete; the cellular heterogeneity reflects in multiple dimensions, including the genome, epigenome, transcriptome, spatial, and even temporal dimensions. Hence, integrative single cell analysis is highly desired. In addition, the way to interpret sequencing data by virtue of bioinformatic tools also exerts critical roles in revealing differential gene expression. Here, a comprehensive review that summarizes the cutting-edge single-cell transcriptome sequencing methodologies, including scRNA-seq, spatial and temporal transcriptome profiling, multi-omics sequencing and computational methods developed for scRNA-seq data analysis is provided. Finally, the challenges and perspectives of this field are discussed.

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.

Synchronous control of magnetic particles and magnetized cells in a tri-axial magnetic field

Precise manipulation of single particles is one of the main goals in the lab-on-a-chip field. Here, we present a microfluidic platform with "T" and "I" shaped magnetic tracks on the substrate to transport magnetic particles and magnetized cells in a tri-axial time-varying magnetic field. The driving magnetic field is composed of a vertical field bias and an in-plane rotating field component, with the advantage of lowering the attraction tendency and cluster formation between the particles compared to the traditional magnetophoretic circuits. We demonstrate three fundamental achievements. First, all the particle movements are synced with the external rotating field to achieve precise control over individual particles. Second, single-particle and single living cell transport in a controlled fashion is achieved for a large number of them in parallel, without the need for a complicated control system to send signals to individual particles. We carefully study the proposed design and introduce proper operating parameters. Finally, in addition to moving the particles along straight tracks, transporting them using a ∼60° bend is demonstrated. The proposed chip has direct applications in the fields of lab-on-a-chip, single-cell biology, and drug screening, where precise control over single particles is needed.

Anti-bias training for (sc)RNA-seq: experimental and computational approaches to improve precision

RNA-seq, including single cell RNA-seq (scRNA-seq), is plagued by insufficient sensitivity and lack of precision. As a result, the full potential of (sc)RNA-seq is limited. Major factors in this respect are the presence of global bias in most datasets, which affects detection and quantitation of RNA in a length-dependent fashion. In particular, scRNA-seq is affected by technical noise and a high rate of dropouts, where the vast majority of original transcripts is not converted into sequencing reads. We discuss these biases origins and implications, bioinformatics approaches to correct for them, and how biases can be exploited to infer characteristics of the sample preparation process, which in turn can be used to improve library preparation.

The Present and Future Role of Microfluidics for Protein and Peptide-Based Therapeutics and Diagnostics

The implementation of peptide-based molecules within the medical field has vast potential, owing to their unique nature and predictable physicochemical profiles. However, peptide therapeutic usage is hindered by delivery-related challenges, meaning that their formulations must be altered to overcome these limitations. This process could be propelled by applying microfluidics (MFs) due to its highly controllable and adaptable attributes; however, therapeutic research within this field is extremely limited. Peptides possess multifunctional roles within therapeutic formulations, ranging from enhancing target specificity to acting as the active component of the medicine. Diagnostically, MFs are well explored in the field of peptides, as MFs provide an unsullied platform to provide fast yet accurate examinations. The capacity to add attributes, such as integrated sensors and microwells, to the MF chip, only enhances the attractiveness of MFs as a diagnostic platform. The structural individuality of peptides makes them prime candidates for diagnostic purposes, for example, antigen detection and isolation. Therefore, this review provides a useful insight into the current applications of MFs for peptide-based therapy and diagnostics and highlights potential gaps in the field that are yet to be explored or optimized.

Novel Technologies in Studying Brain Immune Response

Over the past few decades, the immune system, including both the adaptive and innate immune systems, proved to be essential and critical to brain damage and recovery in the pathogenesis of several diseases, opening a new avenue for developing new immunomodulatory therapies and novel treatments for many neurological diseases. However, due to the specificity and structural complexity of the central nervous system (CNS), and the limit of the related technologies, the biology of the immune response in the brain is still poorly understood. Here, we discuss the application of novel technologies in studying the brain immune response, including single-cell RNA analysis, cytometry by time-of-flight, and whole-genome transcriptomic and proteomic analysis. We believe that advancements in technology related to immune research will provide an optimistic future for brain repair.

Debugging: putting the synthetic yeast chromosome to work

Synthetic genomics aims to de novo synthesize a functional genome redesigned from natural sequences with custom features. Designed genomes provide new toolkits for better understanding organisms, evolution and the construction of cellular factories. Currently maintaining the fitness of cells with synthetic genomes is particularly challenging as defective designs and unanticipated assembly errors frequently occur. Mapping and correcting bugs that arise during the synthetic process are imperative for the successful construction of a synthetic genome that can sustain a desired cellular function. Here, we review recently developed methods used to map and fix various bugs which arise during yeast genome synthesis with the hope of providing guidance for putting the synthetic yeast chromosome to work.

Inertial Microfluidics Enabling Clinical Research

Fast and accurate interrogation of complex samples containing diseased cells or pathogens is important to make informed decisions on clinical and public health issues. Inertial microfluidics has been increasingly employed for such investigations to isolate target bioparticles from liquid samples with size and/or deformability-based manipulation. This phenomenon is especially useful for the clinic, owing to its rapid, label-free nature of target enrichment that enables further downstream assays. Inertial microfluidics leverages the principle of inertial focusing, which relies on the balance of inertial and viscous forces on particles to align them into size-dependent laminar streamlines. Several distinct microfluidic channel geometries (e.g., straight, curved, spiral, contraction-expansion array) have been optimized to achieve inertial focusing for a variety of purposes, including particle purification and enrichment, solution exchange, and particle alignment for on-chip assays. In this review, we will discuss how inertial microfluidics technology has contributed to improving accuracy of various assays to provide clinically relevant information. This comprehensive review expands upon studies examining both endogenous and exogenous targets from real-world samples, highlights notable hybrid devices with dual functions, and comments on the evolving outlook of the field.

Dynamic pneumatic rails enabled microdroplet manipulation

This study presented a convenient method of gathering, splitting, merging, and sorting microdroplets by dynamic pneumatic rails in double-layered microfluidic devices. In these devices, the pneumatic rails were placed below the droplet channel, with a thin elastic polydimethylsiloxane (PDMS) film between them. The PDMS film would sag down to the rail channel, forming a groove pattern at the bottom of the droplet channel, when the fluid pressure in the droplet channel was higher than the air pressure in the rail channel. The groove could capture the flattened droplets and guide the flow path of them due to the lowered surface energy when they extended into the groove. We have designed different components consisting of pneumatic rails to split, merge and sort droplets, and demonstrated that the components maintained good performance in manipulating droplets only by controlling the air pressure. Furthermore, a pneumatic rail-based sorter has been successfully used to sort out single-cell droplets. The pneumatic rail can be integrated into pneumatic valve-based microfluidic devices to be a flexible tool for droplet-based biological and chemical analysis.

Channel innovations for inertial microfluidics

Inertial microfluidics has gained significant attention since first being proposed in 2007 owing to the advantages of simplicity, high throughput, precise manipulation, and freedom from an external field. Superior performance in particle focusing, filtering, concentrating, and separating has been demonstrated. As a passive technology, inertial microfluidics technology relies on the unconventional use of fluid inertia in an intermediate Reynolds number range to induce inertial migration and secondary flow, which depend directly on the channel structure, leading to particle migration to the lateral equilibrium position or trapping in a specific cavity. With the advances in micromachining technology, many channel structures have been designed and fabricated in the past decade to explore the fundamentals and applications of inertial microfluidics. However, the channel innovations for inertial microfluidics have not been discussed comprehensively. In this review, the inertial particle manipulations and underlying physics in conventional channels, including straight, spiral, sinusoidal, and expansion-contraction channels, are briefly described. Then, recent innovations in channel structure for inertial microfluidics, especially channel pattern modification and unconventional cross-sectional shape, are reviewed. Finally, the prospects for future channel innovations in inertial microfluidic chips are also discussed. The purpose of this review is to provide guidance for the continued study of innovative channel designs to improve further the accuracy and throughput of inertial microfluidics.

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

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

Microfluidic droplet application for bacterial surveillance in fresh-cut produce wash waters

Foodborne contamination and associated illness in the United States is responsible for an estimated 48 million cases per year. Increased food demand, global commerce of perishable foods, and the growing threat of antibiotic resistance are driving factors elevating concern for food safety. Foodborne illness is often associated with fresh-cut, ready-to-eat produce commodities due to the perishable nature of the product and relatively minimal processing from farm to the consumer. The research presented here optimizes and evaluates the utility of microfluidic droplets, also termed ultra-miniaturized bioreactors, for rapid detection of viable Salmonella enterica ser. Typhimurium in a shredded lettuce wash water acquired from a major Mid-Atlantic produce processing facility (denoted as Producer) in the U.S. Using a fluorescently-labeled anti-S. Typhimurium antibody and relative fluorescence intensities, paired with in-droplet incubation, S. Typhimurium was detected and identified with 100% specificity in less than 5 h. In initial optimization experiments using S. Typhimurium-spiked sterile water, the relative fluorescence intensity of S. Typhimurium was approximately two times that of the observed relative intensities of five non-S. Typhimurium negative controls at 4-h incubation in droplets containing Rappaport-Vasiliadis (RV) broth at 37°C: relative fluorescence intensity for S. Typhimurium = 2.36 (95% CI: 2.15-2.58), Enterobacter aerogens 1.12 (95% CI: 1.09-1.16), Escherichia coli 700609 = 1.13 (95% CI: 1.09-1.17), E. coli 13706 1.13 (95% CI: 1.07-1.19), E. coli 700891 1.05 (95% CI: 1.03-1.07) and Citrobacter freundii 1.04 (95% CI: 1.03-1.05). S. Typhimurium- and E. aerogens-spiked shredded lettuce wash waters acquired from the Producer were then incubated 4 h in-droplet at 37°C with RV broth. The observed relative fluorescence of S. Typhimurium was significantly higher than that of E. aerogens, 1.56 (95% CI: 1.42-1.71) and 1.10 (95% CI: 1.08-1.12), respectively. While further optimization focusing on compatible concentration methodologies for highly-dilute produce water samples is needed, this application of droplet microfluidics shows great promise in dramatically shortening the time necessary-from days to hours-to confirm viable bacterial contamination in ready-to-eat produce wash waters used throughout the domestic and international food industry.

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.

Single-Cell RNA Sequencing and Its Combination with Protein and DNA Analyses

Heterogeneity in cell populations poses a significant challenge for understanding complex cell biological processes. The analysis of cells at the single-cell level, especially single-cell RNA sequencing (scRNA-seq), has made it possible to comprehensively dissect cellular heterogeneity and access unobtainable biological information from bulk analysis. Recent efforts have combined scRNA-seq profiles with genomic or proteomic data, and show added value in describing complex cellular heterogeneity than transcriptome measurements alone. With the rising demand for scRNA-seq for biomedical and clinical applications, there is a strong need for a timely and comprehensive review on the scRNA-seq technologies and their potential biomedical applications. In this review, we first discuss the latest state of development by detailing each scRNA-seq technology, including both conventional and microfluidic technologies. We then summarize their advantages and limitations along with their biomedical applications. The efforts of integrating the transcriptome profile with highly multiplexed proteomic and genomic data are thoroughly reviewed with results showing the integrated data being more informative than transcriptome data alone. Lastly, the latest progress toward commercialization, the remaining challenges, and future perspectives on the development of scRNA-seq technologies are briefly discussed.

Versatile Movements of Liquid Metal Droplet under Electrostatic Actuation in Alkaline Solutions

The gallium-based eutectic liquid metal alloys exhibit unique properties of deformability, excellent electrical conductivity and low vapour pressure. The liquid metal-based circuits' element or actuator have drawn considerable attention in stretchable electronics and microelectromechanical (MEMS) actuators. Yet, the motion of the liquid metal within the electrolyte needs to be precisely regulated to satisfy application requirements. Herein, we investigated the locomotion of liquid metal within the alkaline aqueous solution under electrostatic actuation. The relationship between the travelling speed of the liquid metal slug and the relative influential parameters, such as the voltage amplitude and frequencies of the applied electric field, electrolyte concentration, electrodes distance and the liquid metal volume, were experimentally characterized. A travelling speed up to 20.33 mm/s was obtained at the applied voltage of 4 Vpp at 150 Hz at 6 V DC offset. Finally, the frequency-dependent liquid metal marble movements were demonstrated, namely oscillation and forward locomotion while oscillating. The oscillation frequency was determined by the frequency of the applied alternate current (AC) signal. The remarkable transportation and oscillating characteristic of the liquid metal marble under the electrostatic actuation may present potentials towards the development of flexible electronics and reconfigurable structures.

Inertial-Force-Assisted, High-Throughput, Droplet-Free, Single-Cell Sampling Coupled with ICP-MS for Real-Time Cell Analysis

Single-cell analysis facilitates perception into the most essential processes in life's mysteries. While it is highly challenging to quantify them at the single-cell level, where precise single-cell sampling is the prerequisite. Herein, a real-time single-cell quantitative platform was established for high-throughput droplet-free single-cell sampling into time-resolved (TRA) ICP-MS and real-time quantification of intracellular target elements. The concentrated cells (2 × 10⁶ cells mL^-1) were spontaneously and orderly aligned in a spiral microchannel with 104 periodic dimensional confined micropillars. The quantification is conducted simultaneously by internal standard inducing from another branch channel in the chip. The flow-rate-independent feature of single-cell focusing into an aligned stream within a wide range of fluidic velocities (100-800 μL min^-1) facilitates high-throughput, oil-free, single-cell introduction into TRA-ICP-MS. The system was used for real-time exploration of intracellular antagonism of Cu²⁺ against Cd²⁺. an obvious antagonistic effect was observed for the MCF-7 cell by culturing for 3, 6, 9, and 12 h with 100 μg L^-1 Cd²⁺ and 100 μg L^-1 Cu²⁺, and a rivalry rate of 12.8% was achieved at 12 h. At identical experimental conditions, however, limited antagonistic effect was encountered for a bEnd3 cell within the same incubation time period, with a rivalry rate of 4.81%. On the contrary, an antagonistic effect was not observed for the HepG2 cell by culturing for 6 h, while an obvious antagonistic effect was found by further culturing to 12 h, with a rivalry rate of 10.43%. For all three cell lines, significant heterogeneity was observed among individual cells.

Microfluidic Single-Cell Omics Analysis

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

Microfluidic on-demand engineering of longitudinal dynamic self-assembly of particles

A viscoelasticity-induced self-assembling microfluidic system is proposed to increase the manoeuvrability and orderliness of longitudinal dynamic self-assembly of particles, achieving control of interparticle spacing's and particle frequency.

Microfluidic Passive Valve with Ultra-Low Threshold Pressure for High-Throughput Liquid Delivery

The microvalve for accurate flow control under low fluidic pressure is vital in cost-effective and miniaturized microfluidic devices. This paper proposes a novel microfluidic passive valve comprising of a liquid chamber, an elastic membrane, and an ellipsoidal control chamber, which actualizes a high flow rate control under an ultra-low threshold pressure. A prototype of the microvalve was fabricated by 3D printing and UV laser-cutting technologies and was tested under static and time-dependent pressure conditions. The prototype microvalve showed a nearly constant flow rate of 4.03 mL/min, with a variation of ~4.22% under the inlet liquid pressures varied from 6 kPa to 12 kPa. In addition, the microvalve could stabilize the flow rate of liquid under the time-varying sinusoidal pressures or the square wave pressures. To validate the functionality of the microvalve, the prototype microvalve was applied in a gas-driven flow system which employed an air blower or human mouth blowing as the low-cost gas source. The microvalve was demonstrated to successfully regulate the steady flow delivery in the system under the low driving pressures produced by the above gas sources. We believe that this new microfluidic passive valve will be suitable for controlling fluid flow in portable microfluidic devices or systems of wider applications.

Droplet Combinations: A Scalable Microfluidic Platform for Biochemical Assays

Droplet-based microfluidics holds enormous potential for transforming high-throughput drug screening. Miniaturization through droplets in combination with automation contributes to reduce reagent use and analysis time as well as minimizing or eliminating labor-intensive steps leading to associated reductions in cost. In this paper, we demonstrate the potential of automated and cost-effective microfluidic droplet-generating technology in the context of an enzymatic activity assay for screening collagenase inhibitors. Experimental results show reproducible and accurate creation and mixing of droplet combinations resulting in biochemical data comparable to data produced by an industry standard instrument. This microfluidic platform that can generate and combine multiple droplets represents a promising tool for high-throughput drug screening.