Applications In Single-cell Analysis Research Articles

Single-cell measurement of microbial growth rate with Raman microspectroscopy.

Rates of microbial growth are fundamental to understanding environmental geochemistry and ecology. However, measuring the heterogeneity of microbial activity at the single-cell level, especially within complex populations and environmental matrices, remains a forefront challenge. Stable isotope probing (SIP) is a method for assessing microbial growth and involves measuring the incorporation of an isotopic label into microbial biomass. Here, we assess Raman microspectroscopy as a SIP technique, specifically focusing on the measurement of deuterium (2H), a tracer of microbial biomass production. We correlatively measured cells grown in varying concentrations of deuterated water with both Raman spectroscopy and nanoscale secondary ion mass spectrometry (nanoSIMS), generating isotopic calibrations of microbial 2H. Relative to Raman, we find that nanoSIMS measurements of 2H are subject to substantial dilution due to rapid exchange of H during sample washing. We apply our Raman-derived calibration to a numerical model of microbial growth, explicitly parameterizing the factors controlling growth rate quantification and demonstrating that Raman-SIP can sensitively measure the growth of microorganisms with doubling times ranging from hours to years. The measurement of single-cell growth with Raman spectroscopy, a rapid, nondestructive technique, represents an important step toward application of single-cell analysis into complex sample matrices or cellular assemblages.

Addressing variability in cell electrorotation through holographic imaging and correction factors

This study addresses the variations observed in electrorotation measurements due to cell positioning and movement. Electrorotation provides a non-disruptive method for inferring the electrical properties of individual cells. However, its widespread adoption is hindered by significant variation in the observed speed. By mitigating the impact of positional dependencies and other influencing factors, our methodology opens avenues for broader applications of electrorotation in single-cell analysis without the need for complex setups to trap and retain the cell in place. Our novel approach combines multi-plane imaging with mathematical treatment of rotation data. This method uses a conventional quadrupole chip and lens-free imaging to track cell movement, resulting in a simpler design and set-up. Through numerical simulations incorporating cell coordinates, chip design, and experimental parameters, we calculate the variation in torque for each position. These values serve as the basis for the correction factors. Validation experiments with T-lymphocytes and fibroblasts show that the correction factors reduce electrorotation speed variation due to cell movement, with an average reduction to 21% and 18%, respectively. These corrections also revealed previously concealed changes in cell properties, in response to external stimuli, thereby enhancing the reliability of measurements and enabling broader applications in single-cell analysis.

Confinement effect on the microcapillary flow and shape of red blood cells.

The ability to change shape is essential for the proper functioning of red blood cells (RBCs) within the microvasculature. The shape of RBCs significantly influences blood flow and has been employed in microfluidic lab-on-a-chip devices, serving as a diagnostic biomarker for specific pathologies and enabling the assessment of RBC deformability. While external flow conditions, such as the vessel size and the flow velocity, are known to impact microscale RBC flow, our comprehensive understanding of how their shape-adapting ability is influenced by channel confinement in biomedical applications remains incomplete. This study explores the impact of various rectangular and square channels, each with different confinement and aspect ratios, on the in vitro RBC flow behavior and characteristic shapes. We demonstrate that rectangular microchannels, with a height similar to the RBC diameter in combination with a confinement ratio exceeding 0.9, are required to generate distinctive well-defined croissant and slipper-like RBC shapes. These shapes are characterized by their equilibrium positions in the channel cross section, and we observe a strong elongation of both stable shapes in response to the shear rate across the different channels. Less confined channel configurations lead to the emergence of unstable other shape types that display rich shape dynamics. Our work establishes an experimental framework to understand the influence of channel size on the single-cell flow behavior of RBCs, providing valuable insights for the design of biomicrofluidic single-cell analysis applications.

Microfluidic device for the high-throughput and selective encapsulation of single target cells.

Droplet-based microfluidic technologies for encapsulating single cells have rapidly evolved into powerful tools for single-cell analysis. In conventional passive single-cell encapsulation techniques, because cells arrive randomly at the droplet generation section, to encapsulate only a single cell with high precision, the average number of cells per droplet has to be decreased by reducing the average frequency at which cells arrive relative to the droplet generation rate. Therefore, the encapsulation efficiency for a given droplet generation rate is very low. Additionally, cell sorting operations are required prior to the encapsulation of target cells for specific cell type analysis. To address these challenges, we developed a cell encapsulation technology with a cell sorting function using a microfluidic chip. The microfluidic chip is equipped with an optical detection section to detect the optical information of cells and a sorting section to encapsulate cells into droplets by controlling a piezo element, enabling active encapsulation of only the single target cells. For a particle population including both targeted and non-targeted particles arriving at an average frequency of up to 6000 particles per s, with an average number of particles per droplet of 0.45, our device maintained a high purity above 97.9% for the single-target-particle droplets and achieved an outstanding throughput, encapsulating up to 2900 single target particles per s. The proposed encapsulation technology surpasses the encapsulation efficiency of conventional techniques, provides high efficiency and flexibility for single-cell research, and shows excellent potential for various applications in single-cell analysis.

Exploring New Dimensions of Tumor Heterogeneity: The Application of Single Cell Analysis to Organoid-Based 3D In Vitro Models.

Modeling the heterogeneity of the tumor microenvironment (TME) in vitro is essential to investigating fundamental cancer biology and developing novel treatment strategies that holistically address the factors affecting tumor progression and therapeutic response. Thus, the development of new tools for both in vitro modeling, such as patient-derived organoids (PDOs) and complex 3D in vitro models, and single cell omics analysis, such as single-cell RNA-sequencing, represents a new frontier for investigating tumor heterogeneity. Specifically, the integration of PDO-based 3D in vitro models and single cell analysis offers a unique opportunity to explore the intersecting effects of interpatient, microenvironmental, and tumor cell heterogeneity on cell phenotypes in the TME. In this review, the current use of PDOs in complex 3D in vitro models of the TME is discussed and the emerging directions in the development of these models are highlighted. Next, work that has successfully applied single cell analysis to PDO-based models is examined and important experimental considerations are identified for this approach. Finally, open questions are highlighted that may be amenable to exploration using the integration of PDO-based models and single cell analysis. Ultimately, such investigations may facilitate the identification of novel therapeutic targets for cancer that address the significant influence of tumor-TME interactions.

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.

Combining atomic force microscopy with complementary techniques for multidimensional single-cell analysis.

The advent of atomic force microscopy (AFM) provides an amazing instrument for characterising the structures and properties of living biological systems under aqueous conditions with unprecedented spatiotemporal resolution. In addition to its own unique capabilities for applications in life sciences, AFM is highly compatible and has been widely integrated with various complementary techniques to simultaneously sense the multidimensional (biological, chemical and physical) properties of biological systems, offering novel possibilities for comprehensively revealing the underlying mechanisms guiding life activities particularly in the studies of single cells. Herein, typical combinations of AFM and complementary techniques (including optical microscopy, ultrasound, infrared spectroscopy, Raman spectroscopy, fluidic force microscopy and traction force microscopy) and their applications in single-cell analysis are reviewed. The future perspectives are also provided.

Acousto-dielectric tweezers for size-insensitive manipulation and biophysical characterization of single cells

The intrinsic biophysical properties of cells, such as mechanical, acoustic, and electrical properties, are valuable indicators of a cell’s function and state. However, traditional single-cell biophysical characterization methods are hindered by limited measurable properties, time-consuming procedures, and complex system setups. This study presents acousto-dielectric tweezers that leverage the balance between controllable acoustophoretic and dielectrophoretic forces applied on cells through surface acoustic waves and alternating current electric fields, respectively. Particularly, the balanced acoustophoretic and dielectrophoretic forces can trap cells at equilibrium positions independent of the cell size to differentiate between various cell-intrinsic mechanical, acoustic, and electrical properties. Experimental results show our mechanism has the potential for applications in single-cell analysis, size-insensitive cell separation, and cell phenotyping, which are all primarily based on cells’ intrinsic biophysical properties. Our results also show the measured equilibrium position of a cell can inversely determine multiple biophysical properties, including membrane capacitance, cytoplasm conductivity, and acoustic contrast factor. With these features, our acousto-dielectric tweezing mechanism is a valuable addition to the resources available for biophysical property-based biological and medical research.

Applications of single-cell analysis in blood research

Single-cell analysis encompasses analyses at the single-cell level. Specifically, DNA sequences, RNA and protein expression levels, and epigenome modifications are currently analyzed at the single-cell level. In recent years, single-cell sequencing technologies have been incorporated into numerous blood studies. This paper introduces an overview of single-cell technologies and further explains achievements in blood research using single-cell analysis.

A Simple 3-D Microelectrode Fabrication Process and Its Application in Microfluidic Impedance Cytometry

Microfluidic impedance cytometry (MIC) has wide applications in single-cell analysis. However, the complex microelectrode fabrication process seriously restricts the miniaturization and commercialization of MIC devices. Common microelectrode configurations such as a coplanar electrode, a symmetric electrode, and a liquid electrode have difficulties in meeting the requirements of high detection accuracy and simple fabrication at the same time. Hence, a simple 3-D symmetric microelectrode fabrication process is developed in this article. We design a microchip containing both a microfluidic channel and a microelectrode channel. The alloy with high surface tension and low melting point is used to fabricate the 3-D microelectrodes by injecting the melted alloy into the microelectrode channel with a properly controlled driving pressure. The melted alloy flows into the microelectrode channel and automatically stops at the end of the microelectrode channel due to the effect of surface tension. This process intrinsically provides a high-precision alignment for the 3-D microelectrodes. The fabricated MIC chip is experimentally tested, and the results show that it can effectively count and classify microspheres of different sizes. This study can facilitate the development and commercialization of MIC devices.

Pressure-Regulated Single-Entity Electrochemistry Inside Carbon Nanopipettes.

Conductive nanopipettes have been widely used as a multifunctional platform for emerging sensing applications in small spaces, although the electrochemical processes involved are not well controlled and fully quantified. Herein, we use an external pressure to precisely control the solution volume and regulate the electrochemical signals in carbon nanopipettes. In addition to polarizing the redox concentration profile, the pressure is found to generate a convective flow to control the transport processes of redox molecules and nanoparticles as well, and their quantitative correlation is established by a numerical simulation. The elucidated pressure-regulated electrochemistry in conductive nanopipettes would reveal the fundamental charge transport processes at the nanoscale and promote better usage of conductive nanopipettes for delivery and sensing applications in single-cell analysis.

A design and optimization of a high throughput valve based microfluidic device for single cell compartmentalization and analysis

The need for high throughput single cell screening platforms has been increasing with advancements in genomics and proteomics to identify heterogeneity, unique cell subsets or super mutants from thousands of cells within a population. For real-time monitoring of enzyme kinetics and protein expression profiling, valve-based microfluidics or pneumatic valving that can compartmentalize single cells is advantageous by providing on-demand fluid exchange capability for several steps in assay protocol and on-chip culturing. However, this technique is throughput limited by the number of compartments in the array. Thus, one big challenge lies in increasing the number of microvalves to several thousand that can be actuated in the microfluidic device to confine enzymes and substrates in picoliter volumes. This work explores the design and optimizations done on a microfluidic platform to achieve high-throughput single cell compartmentalization as applied to single-cell enzymatic assay for protein expression quantification. Design modeling through COMSOL Multiphysics was utilized to determine the circular microvalve’s optimized parameters, which can close thousands of microchambers in an array at lower sealing pressure. Multiphysical modeling results demonstrated the relationships of geometry, valve dimensions, and sealing pressure, which were applied in the fabrication of a microfluidic device comprising of up to 5000 hydrodynamic traps and corresponding microvalves. Comparing the effects of geometry, actuation media and fabrication technique, a sealing pressure as low as 0.04 MPa was achieved. Applying to single cell enzymatic assay, variations in granzyme B activity in Jurkat and human PBMC cells were observed. Improvement in the microfluidic chip’s throughput is significant in single cell analysis applications, especially in drug discovery and treatment personalization.

Immunotherapy in the Treatment of Urothelial Bladder Cancer: Insights From Single-Cell Analysis.

Urothelial bladder cancer (UBC) is a global challenge of public health with limited therapeutic options. Although the emergence of cancer immunotherapy, most notably immune checkpoint inhibitors, represents a major breakthrough in the past decade, many patients still suffer from unsatisfactory clinical outcome. A thorough understanding of the fundamental cellular and molecular mechanisms responsible for antitumor immunity may lead to optimized treatment guidelines and new immunotherapeutic strategies. With technological developments and protocol refinements, single-cell approaches have become powerful tools that provide unprecedented insights into the kaleidoscopic tumor microenvironment and intricate cell-cell communications. In this review, we summarize recent applications of single-cell analysis in characterizing the UBC multicellular ecosystem, and discuss how to leverage the high-resolution information for more effective immune-based therapies.

Single-cell sequencing in translational cancer research and challenges to meet clinical diagnostic needs.

The ability to capture alterations in the genome or transcriptome by next-generation sequencing has provided critical insight into molecular changes and programs underlying cancer biology. With the rapid technological development in single-cell sequencing, it has become possible to study individual cells at the transcriptional, genetic, epigenetic, and protein level. Using single-cell analysis, an increased resolution of fundamental processes underlying cancer development is obtained, providing comprehensive insights otherwise lost by sequencing of entire (bulk) samples, in which molecular signatures of individual cells are averaged across the entire cell population. Here, we provide a concise overview on the application of single-cell analysis of different modalities within cancer research by highlighting key articles of their respective fields. We furthermore examine the potential of existing technologies to meet clinical diagnostic needs and discuss current challenges associated with this translation.

Dual Intramolecular Electron Transfer for In Situ Coreactant‐Embedded Electrochemiluminescence Microimaging of Membrane Protein

AbstractThe demand for transporting coreactant to emitter and short lifetime of the radicals in electrochemiluminescence (ECL) emission inhibit greatly its application in cytosensing and microscopic imaging. Herein we designed a dual intramolecular electron transfer strategy and tertiary amine conjugated polymer dots (TEA‐Pdots) to develop a coreactant‐embedded ECL mechanism and microimaging system. The TEA‐Pdots could produce ECL emission at +1.2 V without need of coreactant in test solution. The superstructure and intramolecular electron transfer led to unprecedented ECL strength, which was 132 and 45 times stronger than those from the mixture of Pdots with TEA at equivalent and 62.5 times higher amounts, respectively. The ECL efficiency was even higher than that of typical [Ru(bpy)3]2+ system. Therefore, this strategy and coreactant‐embedded ECL system could be used for in situ ECL microimaging of membrane protein on single living cells without additional permeable treatment for transporting coreactant. The feasibility and validity were demonstrated by evaluating the specific protein expression on cell surface. This work opens new avenues for ECL applications in single cell analysis and dynamic study of biological events.

Dual Intramolecular Electron Transfer for In Situ Coreactant-Embedded Electrochemiluminescence Microimaging of Membrane Protein.

The demand for transporting coreactant to emitter and short lifetime of the radicals in electrochemiluminescence (ECL) emission inhibit greatly its application in cytosensing and microscopic imaging. Herein we designed a dual intramolecular electron transfer strategy and tertiary amine conjugated polymer dots (TEA-Pdots) to develop a coreactant-embedded ECL mechanism and microimaging system. The TEA-Pdots could produce ECL emission at +1.2 V without need of coreactant in test solution. The superstructure and intramolecular electron transfer led to unprecedented ECL strength, which was 132 and 45 times stronger than those from the mixture of Pdots with TEA at equivalent and 62.5 times higher amounts, respectively. The ECL efficiency was even higher than that of typical [Ru(bpy)3 ]2+ system. Therefore, this strategy and coreactant-embedded ECL system could be used for in situ ECL microimaging of membrane protein on single living cells without additional permeable treatment for transporting coreactant. The feasibility and validity were demonstrated by evaluating the specific protein expression on cell surface. This work opens new avenues for ECL applications in single cell analysis and dynamic study of biological events.

Single-cell patterning technology for biological applications.

Single-cell patterning technology has revealed significant contributions of single cells to conduct basic and applied biological studies in vitro such as the understanding of basic cell functions, neuronal network formation, and drug screening. Unlike traditional population-based cell patterning approaches, single-cell patterning is an effective technology of fully understanding cell heterogeneity by precisely controlling the positions of individual cells. Therefore, much attention is currently being paid to this technology, leading to the development of various micro-nanofabrication methodologies that have been applied to locate cells at the single-cell level. In recent years, various methods have been continuously improved and innovated on the basis of existing ones, overcoming the deficiencies and promoting the progress in biomedicine. In particular, microfluidics with the advantages of high throughput, small sample volume, and the ability to combine with other technologies has a wide range of applications in single-cell analysis. Here, we present an overview of the recent advances in single-cell patterning technology, with a special focus on current physical and physicochemical methods including stencil patterning, trap- and droplet-based microfluidics, and chemical modification on surfaces via photolithography, microcontact printing, and scanning probe lithography. Meanwhile, the methods applied to biological studies and the development trends of single-cell patterning technology in biological applications are also described.

Interfacial Nanoinjection-Based Nanoliter Single-Cell Analysis.

Single-cell analysis offers unprecedented resolution for the investigation of cellular heterogeneity and the capture of rare cells from large populations. Here, described is a simple method named interfacial nanoinjection (INJ), which can miniaturize various single-cell assays to be performed in nanoliter water-in-oil droplets on standard microwell plates. The INJ droplet handler can adjust droplet volumes for multistep reactions on demand with high precision and excellent monodispersity, and consequently enables a wide range of single-cell assays. Importantly, INJ can be coupled with fluorescence-activated cell sorting (FACS), which is currently the most effective and accurate single-cell sorting and isolation method. FACS-INJ pipelines for high-throughput plate well-based single-cell analyses, including single-cell proliferation, drug-resistance testing, polymerase chain reaction (PCR), reverse-transcription PCR, and whole-genome sequencing are introduced. This FACS-INJ pipeline is compatible with a wide range of samples and can be extended to various single-cell analysis applications in microbiology, cell biology, and biomedical diagnostics.

Graphene quantum dots enhanced ToF-SIMS for single-cell imaging.

Time-of-flight secondary ion mass spectrometry (ToF-SIMS) has shown promising applications in single-cell analysis owing to its high spatial resolution molecular imaging capability. One of the main drawbacks hindering progress in this field is the relatively low ionization efficiency for biological systems. The complex chemical micro-environment in single cells typically causes severe matrix effects, leading to significant signal suppression of biomolecules. In this work, we investigated the signal enhancement effect of graphene quantum dots (GE QDs) in ToF-SIMS analysis. A × 160 magnification of ToF-SIMS signal for amiodarone casted on glass slide was observed by adding amino-functionalized GE QDs (amino-GE QDs), which was significantly higher than adding previously reported signal enhancement materials and hydroxyl group-functionalized GE QDs (hydroxyl-GE QDs). A possible mechanism for GE QD-induced signal enhancement was proposed. Further, effects of amino-GE QDs and hydroxyl-GE QDs on amiodarone-treated breast cancer cells were compared. A significant signal improvement for lipids and amiodarone was achieved using both types of GE QDs, especially for amino-GE QDs. In addition, ToF-SIMS chemical mapping of single cells with better quality was obtained after signal enhancement. Our strategy for effective ToF-SIMS signal enhancement holds great potential for further investigation of drug metabolism pathways and the interactions between the cell and micro-environment.

A Novel Controllable Cell Array Printing Technique on Microfluidic Chips.

The construction of single-cell array is known as the challenging technology to manipulate cell position and number and accomplish cell analysis in biomedical engineering. We put forward a novel controllable cell printing technique for rapid, precise, convenient, high cell viability, multicellular, and high-throughput printing. We also proposed a novel microfluidic device to verify the effectiveness of the printing and study the migration ability and anti-cancer drug responses of cancer cell as important applications. This technique offered a minimum process time of 5min, a maximum positional accuracy of 10μm, 0.1nL liquid volume level per droplet, above 87% cell viability after seven days and the ability to print different multicellular arrays. We found that the cell compared to cell culture in petri dish after 48h. In addition, there was a significant different inhibition on cancer cells migration ability and cell drug activities with different concentrations of paclitaxel. This novel controllable cell array printing technique on the microfluidic platforms provides a useful method with high-quality printing and cell viability for the applications of single-cell analysis and high-throughput drug screening. The controllable cell printing technique could apply in many biological processes and biomedical engineering applications, such as cell analysis, cancer development, and drug screening and metabolism. Combined with the microfluidic chips, tissue engineering, and sensors, this technique will be widely used for the construction and analysis of biological and biomedical model.