Advances in high-throughput single-cell microtechnologies

Droplet Microfluidics for Advanced Single-Cell Analysis

Droplet microfluidics has emerged as a breakthrough technology that is changing our comprehension of single-cell and their associated research. By separating individual cells within tiny droplets, ranging from nanoliters to picoliters using microfluidic devices, this innovative approach has revolutionized investigations at the single-cell level. Each of these droplets serves as a distinct experimental reaction vessel, enabling thorough exploration of cellular phenotypic variations, interactions between cells or cell-microorganisms as well as genomic insights. This review paper presents a comprehensive overview of the current state-of-the-art in droplet microfluidics, which has made single-cell analysis a practical approach for biological research. The review delves into the technological advancements in single-cell encapsulation techniques within droplet microfluidics, elucidating their applications in high-throughput single-cell screening, intercellular and cell-microorganism interactions, and genomic analysis. Furthermore, it discusses the advantages and constraints of droplet microfluidic technology, shedding light on critical factors such as throughput and versatile integration. Lastly, the paper outlines the potential avenues for future research in this rapidly evolving field.

Analytical methods in studying cell force sensing: principles, current technologies and perspectives

Mechanical stimulation plays a crucial role in numerous biological activities, including tissue development, regeneration and remodeling. Understanding how cells respond to their mechanical microenvironment is vital for investigating mechanotransduction with adequate spatial and temporal resolution. Cell force sensing-also known as mechanosensation or mechanotransduction-involves force transmission through the cytoskeleton and mechanochemical signaling. Insights into cell-extracellular matrix interactions and mechanotransduction are particularly relevant for guiding biomaterial design in tissue engineering. To establish a foundation for mechanical biomedicine, this review will provide a comprehensive overview of cell mechanotransduction mechanisms, including the structural components essential for effective mechanical responses, such as cytoskeletal elements, force-sensitive ion channels, membrane receptors and key signaling pathways. It will also discuss the clutch model in force transmission, the role of mechanotransduction in both physiology and pathological contexts, and biomechanics and biomaterial design. Additionally, we outline analytical approaches for characterizing forces at cellular and subcellular levels, discussing the advantages and limitations of each method to aid researchers in selecting appropriate techniques. Finally, we summarize recent advancements in cell force sensing and identify key challenges for future research. Overall, this review should contribute to biomedical engineering by supporting the design of biomaterials that integrate precise mechanical information.

Vortex sorting of rare particles/cells in microcavities: A review

Microfluidics or lab-on-a-chip technology has shown great potential for the separation of target particles/cells from heterogeneous solutions. Among current separation methods, vortex sorting of particles/cells in microcavities is a highly effective method for trapping and isolating rare target cells, such as circulating tumor cells, from flowing samples. By utilizing fluid forces and inertial particle effects, this passive method offers advantages such as label-free operation, high throughput, and high concentration. This paper reviews the fundamental research on the mechanisms of focusing, trapping, and holding of particles in this method, designs of novel microcavities, as well as its applications. We also summarize the challenges and prospects of this technique with the hope to promote its applications in medical and biological research.

Multiplexed Near-Field Optical Trapping Exploiting Anapole States

Optical tweezers have had a major impact on bioscience research by enabling the study of biological particles with high accuracy. The focus so far has been on trapping individual particles, ranging from the cellular to the molecular level. However, biology is intrinsically heterogeneous; therefore, access to variations within the same population and species is necessary for the rigorous understanding of a biological system. Optical tweezers have demonstrated the ability of trapping multiple targets in parallel; however, the multiplexing capability becomes a challenge when moving toward the nanoscale. Here, we experimentally demonstrate a resonant metasurface that is capable of trapping a high number of nanoparticles in parallel, thereby opening up the field to large-scale multiplexed optical trapping. The unit cell of the metasurface supports an anapole state that generates a strong field enhancement for low-power near-field trapping; importantly, the anapole state is also more angle-tolerant than comparable resonant modes, which allows its excitation with a focused light beam, necessary for generating the required power density and optical forces. We use the anapole state to demonstrate the trapping of 100's of 100 nm polystyrene beads over a 10 min period, as well as the multiplexed trapping of lipid vesicles with a moderate intensity of <250 μW/μm2. This demonstration will enable studies relating to the heterogeneity of biological systems, such as viruses, extracellular vesicles, and other bioparticles at the nanoscale.

Numerical Modeling of Physical Cell Trapping in Microfluidic Chips

Microfluidic methods have proven to be effective in separation and isolation of cells for a wide range of biomedical applications. Among these methods, physical trapping is a label-free isolation approach that relies on cell size as the selective phenotype to retain target cells on-chip for follow-up analysis and imaging. In silico models have been used to optimize the design of such hydrodynamic traps and to investigate cancer cell transmigration through narrow constrictions. While most studies focus on computational fluid dynamics (CFD) analysis of flow over cells and/or pillar traps, a quantitative analysis of mechanical interaction between cells and trapping units is missing. The existing literature centers on longitudinally extended geometries (e.g., micro-vessels) to understand the biological phenomenon rather than designing an effective cell trap. In this work, we aim to make an experimentally informed prediction of the critical pressure for a cell to pass through a trapping unit as a function of cell morphology and trapping unit geometry. Our findings show that a hyperelastic material model accurately captures the stress-related softening behavior observed in cancer cells passing through micro-constrictions. These findings are used to develop a model capable of predicting and extrapolating critical pressure values. The validity of the model is assessed with experimental data. Regression analysis is used to derive a mathematical framework for critical pressure. Coupled with CFD analysis, one can use this formulation to design efficient microfluidic devices for cell trapping and potentially perform downstream analysis of trapped cells.

Single-cell HER2 quantification via instant signal amplification in microdroplets

Accurate and ultrasensitive evaluation of human epidermal growth factor receptor 2 (HER2) protein is key to early diagnosis and subtype differentiation of breast cancer. Single-cell analyses to reduce ineffective targeted therapies due to breast cancer heterogeneity and improve patient survival remain challenging. Herein, we reported a novel droplet microfluidic combined with an instant cation exchange signal amplification strategy for quantitative analysis of HER2 protein expression on single cells. In the 160 μm droplets produced by a tapered capillary bundle, abundant Immuno-CdS labeled on HER2-positive cells were replaced by Ag ⁺ to obtain Cd²⁺ that stimulated Rhod-5N fluorescence. This uniformly distributed and instantaneous fluorescence amplification strategy in droplets improves sensitivity and reduces signal fluctuation. Using HER2 modified PS microsphere to simulate single cells, we obtained a linear fitting of HER2-modified concentration and fluorescence intensity in microdroplets with the limit detection of 11.372 pg mL^-1. Moreover, the relative standard deviation (RSD) was 4.2-fold lower than the traditional immunofluorescence technique (2.89% vs 12.21%). The HER2 protein on SK-BR-3 cells encapsulated in droplets was subsequently quantified, ranging from 9862.954 pg mL^-1 and 205.26 pg mL^-1, equivalent to 9.795 × 10⁶ and 2.038 × 10⁵ protein molecules. This detection system provides a universal platform for single-cell sensitive quantitative analysis and contributes to the evaluation of HER2-positive tumors.

Spectroelectrochemical behavior of parallel arrays of single vertically oriented Pseudomonas aeruginosa cells

Pseudomonas aeruginosa is a Gram-negative opportunistic human pathogen responsible for a number of healthcare-associated infection. It is currently difficult to assess single cell behaviors of P. aeruginosa that might contribute to acquisition of antibiotic resistance, intercellular communication, biofilm development, or virulence, because mechanistic behavior is inferred from ensemble collections of cells, thus averaging effects over a population. Here, we develop and characterize a device that can capture and trap arrays of single P. aeruginosa cells in individual micropores in order to study their behaviors using spectroelectrochemistry. Focused ion beam milling is used to fabricate an array of micropores in a Au/dielectric/Au/SiO₂-containing multilayer substrate, in which individual micropores are formed with dimensions that facilitate the capture of single P. aeruginosa cells in a predominantly vertical orientation. The bottom Au ring is then used as a working electrode to explore the spectroelectrochemical behavior of parallel arrays of individual P. aeruginosa cells. Application of step-potential or swept-potential waveforms produces changes in the fluorescence emission that can be imaged and correlated with applied potential. Arrays of P. aeruginosa cells typically exhibit three characteristic fluorescence behaviors that are sensitive to nutritional stress and applied potential. The device developed here enables the study of parallel collections of single bacterial cells with well-defined orientational order and should facilitate efforts to elucidate methods of bacterial communication and multidrug resistance at the single cell level.

Recent Advances of Utilizing Artificial Intelligence in Lab on a Chip for Diagnosis and Treatment

Nowadays, artificial intelligence (AI) creates numerous promising opportunities in the life sciences. AI methods can be significantly advantageous for analyzing the massive datasets provided by biotechnology systems for biological and biomedical applications. Microfluidics, with the developments in controlled reaction chambers, high-throughput arrays, and positioning systems, generate big data that is not necessarily analyzed successfully. Integrating AI and microfluidics can pave the way for both experimental and analytical throughputs in biotechnology research. Microfluidics enhances the experimental methods and reduces the cost and scale, while AI methods significantly improve the analysis of huge datasets obtained from high-throughput and multiplexed microfluidics. This review briefly presents a survey of the role of AI and microfluidics in biotechnology. Also, the incorporation of AI with microfluidics is comprehensively investigated. Specifically, recent studies that perform flow cytometry cell classification, cell isolation, and a combination of them by gaining from both AI methods and microfluidic techniques are covered. Despite all current challenges, various fields of biotechnology can be remarkably affected by the combination of AI and microfluidic technologies. Some of these fields include point-of-care systems, precision, personalized medicine, regenerative medicine, prognostics, diagnostics, and treatment of oncology and non-oncology-related diseases.

Drug repurposing in cancer neuroscience: From the viewpoint of the autophagy-mediated innervated niche

Based on the bidirectional interactions between neurology and cancer science, the burgeoning field “cancer neuroscience” has been proposed. An important node in the communications between nerves and cancer is the innervated niche, which has physical contact with the cancer parenchyma or nerve located in the proximity of the tumor. In the innervated niche, autophagy has recently been reported to be a double-edged sword that plays a significant role in maintaining homeostasis. Therefore, regulating the innervated niche by targeting the autophagy pathway may represent a novel therapeutic strategy for cancer treatment. Drug repurposing has received considerable attention for its advantages in cost-effectiveness and safety. The utilization of existing drugs that potentially regulate the innervated niche via the autophagy pathway is therefore a promising pharmacological approach for clinical practice and treatment selection in cancer neuroscience. Herein, we present the cancer neuroscience landscape with an emphasis on the crosstalk between the innervated niche and autophagy, while also summarizing the underlying mechanisms of candidate drugs in modulating the autophagy pathway. This review provides a strong rationale for drug repurposing in cancer treatment from the viewpoint of the autophagy-mediated innervated niche.

Biophysical Approaches for Applying and Measuring Biological Forces

Over the past decades, increasing evidence has indicated that mechanical loads can regulate the morphogenesis, proliferation, migration, and apoptosis of living cells. Investigations of how cells sense mechanical stimuli or the mechanotransduction mechanism is an active field of biomaterials and biophysics. Gaining a further understanding of mechanical regulation and depicting the mechanotransduction network inside cells require advanced experimental techniques and new theories. In this review, the fundamental principles of various experimental approaches that have been developed to characterize various types and magnitudes of forces experienced at the cellular and subcellular levels are summarized. The broad applications of these techniques are introduced with an emphasis on the difficulties in implementing these techniques in special biological systems. The advantages and disadvantages of each technique are discussed, which can guide readers to choose the most suitable technique for their questions. A perspective on future directions in this field is also provided. It is anticipated that technical advancement can be a driving force for the development of mechanobiology.

The biophysics of cancer: emerging insights from micro- and nanoscale tools

Cancer is a complex and dynamic disease that is aberrant both biologically and physically. There is growing appreciation that physical abnormalities with both cancer cells and their microenvironment that span multiple length scales are important drivers for cancer growth and metastasis. The scope of this review is to highlight the key advancements in micro- and nano-scale tools for delineating the cause and consequences of the aberrant physical properties of tumors. We focus our review on three important physical aspects of cancer: 1) solid mechanical properties, 2) fluid mechanical properties, and 3) mechanical alterations to cancer cells. Beyond posing physical barriers to the delivery of cancer therapeutics, these properties are also known to influence numerous biological processes, including cancer cell invasion and migration leading to metastasis, and response and resistance to therapy. We comment on how micro- and nanoscale tools have transformed our fundamental understanding of the physical dynamics of cancer progression and their potential for bridging towards future applications at the interface of oncology and physical sciences.

Results of the Seventh Scientific Workshop of ECCO: Precision Medicine in IBD-What, Why, and How

Many diseases that affect modern humans fall in the category of complex diseases, thus called because they result from a combination of multiple aetiological and pathogenic factors. Regardless of the organ or system affected, complex diseases present major challenges in diagnosis, classification, and management. Current forms of therapy are usually applied in an indiscriminate fashion based on clinical information, but even the most advanced drugs only benefit a limited number of patients and to a variable and unpredictable degree. This 'one measure does not fit all' situation has spurred the notion that therapy for complex disease should be tailored to individual patients or groups of patients, giving rise to the notion of 'precision medicine' [PM]. Inflammatory bowel disease [IBD] is a prototypical complex disease where the need for PM has become increasingly clear. This prompted the European Crohn's and Colitis Organisation to focus the Seventh Scientific Workshop on this emerging theme. The articles in this special issue of the Journal address the various complementary aspects of PM in IBD, including what PM is; why it is needed and how it can be used; how PM can contribute to prediction and prevention of IBD; how IBD PM can aid in prognosis and improve response to therapy; and the challenges and future directions of PM in IBD. This first article of this series is structured on three simple concepts [what, why, and how] and addresses the definition of PM, discusses the rationale for the need of PM in IBD, and outlines the methodology required to implement PM in IBD in a correct and clinically meaningful way.

Heterofunctional Particles as Single Cell Sensors to Capture Secreted Immunoglobulins and Isolate Antigen-Specific Antibody Secreting Cells

Isolating cells based on their secreted proteins remain a challenge. The authors demonstrate a capacity for high throughput single-cell protein secretion analysis and isolation based on heterofunctional particles combined with fluorescence activated cell sorting (FACS). The workflow shows that antibody secreting cells (ASCs) specific for the H1 protein from influenza virus can be isolated from B cells. The workflow consists of incubating anti-CD27 particles with the ASCs, capturing locally secreted immunoglobulins with Protein G on the particles, and identifying immunoglobulins specific to H1 via fluorescent labeled antigens followed by FACS to enrich antigen-specific ASCs. Two particles designs, Janus and mixed, are tested with hybridoma cells. Mixed particles are found to improve antibody collection, while Janus particles are found to bind target cells more effectively. Targeted hybridoma cells in coculture with non-specific hybridoma cells are identified with a sensitivity of 96% and specificity of 98%. Heterofunctional particles are used to capture ASCs that secrete antibodies specific for influenza virus from B cells from healthy adults isolated from blood after vaccination. Positive H1-tetramer sorted ASCs are validated using single ASC cultures and identify 23/56 cells specific for H1 demonstrating 164-fold enrichment from total B cells and 14.6-fold enrichment from total ASCs.

Generation of Genetic Tools for Gauging Multiple-Gene Expression at the Single-Cell Level

Key microbial processes in many bacterial species are heterogeneously expressed in single cells of bacterial populations. However, the paucity of adequate molecular tools for live, real-time monitoring of multiple-gene expression at the single-cell level has limited the understanding of phenotypic heterogeneity. To investigate phenotypic heterogeneity in the ubiquitous opportunistic pathogen Pseudomonas aeruginosa, a genetic tool that allows gauging multiple-gene expression at the single-cell level has been generated. This tool, named pRGC, consists of a promoter-probe vector for transcriptional fusions that carries three reporter genes coding for the fluorescent proteins mCherry, green fluorescent protein (GFP), and cyan fluorescent protein (CFP). The pRGC vector has been characterized and validated via single-cell gene expression analysis of both constitutive and iron-regulated promoters, showing clear discrimination of the three fluorescence signals in single cells of a P. aeruginosa population without the need for image processing for spectral cross talk correction. In addition, two pRGC variants have been generated for either (i) integration of the reporter gene cassette into a single neutral site of P. aeruginosa chromosome that is suitable for long-term experiments in the absence of antibiotic selection or (ii) replication in bacterial genera other than Pseudomonas The easy-to-use genetic tools generated in this study will allow rapid and cost-effective investigation of multiple-gene expression in populations of environmental and pathogenic bacteria, hopefully advancing the understanding of microbial phenotypic heterogeneity.IMPORTANCE Within a bacterial population, single cells can differently express some genes, even though they are genetically identical and experience the same chemical and physical stimuli. This phenomenon, known as phenotypic heterogeneity, is mainly driven by gene expression noise and results in the emergence of bacterial subpopulations with distinct phenotypes. The analysis of gene expression at the single-cell level has shown that phenotypic heterogeneity is associated with key bacterial processes, including competence, sporulation, and persistence. In this study, new genetic tools have been generated that allow easy cloning of up to three promoters upstream of distinct fluorescent genes, making it possible to gauge multiple-gene expression at the single-cell level by fluorescence microscopy without the need for advanced image-processing procedures. A proof of concept has been provided by investigating iron uptake and iron storage gene expression in response to iron availability in P. aeruginosa.

Unraveling the mechanobiology of immune cells

Immune cells can sense and respond to biophysical cues - from dynamic forces to spatial features - during their development, activation, differentiation and expansion. These biophysical signals regulate a variety of immune cell functions such as leukocyte extravasation, macrophage polarization, T cell selection and T cell activation. Recent studies have advanced our understanding on immune responses to biophysical cues and the underlying mechanisms of mechanotransduction, which provides rational basis for the design and development of immune-modulatory therapeutics. This review discusses the recent progress in mechanosensing and mechanotransduction of immune cells, particularly monocytes/macrophages and T lymphocytes, and features new biomaterial designs and biomedical devices that translate these findings into biomedical applications.

Positional dependence of particles and cells in microfluidic electrical impedance flow cytometry: origin, challenges and opportunities

Microfluidic electrical impedance flow cytometry is now a well-known and established method for single-cell analysis. Given the richness of the information provided by impedance measurements, this non-invasive and label-free approach can be used in a wide field of applications ranging from simple cell counting to disease diagnostics. One of its major limitations is the variation of the impedance signal with the position of the cell in the sensing area. Indeed, identical particles traveling along different trajectories do not result in the same data. The positional dependence can be considered as a challenge for the accuracy of microfluidic impedance cytometers. On the other hand, it has recently been regarded by several groups as an opportunity to estimate the position of particles in the microchannel and thus take a further step in the logic of integrating sensors in so-called "Lab-on-a-chip" devices. This review provides a comprehensive overview of the physical grounds of the positional dependence of impedance measurements. Then, both the developed strategies to reduce position influence in impedance-based assays and the recent reported technologies exploiting that dependence for the integration of position detection in microfluidic devices are reviewed.

Rapid and easy-to-use ES cell manipulation device with a small groove near culturing wells

Objective

Production of genetically modified mice including Knock-out (KO) or Knock-in (KI) mice is necessary for organism-level phenotype analysis. Embryonic stem cell (ESC)-based technologies can produce many genetically modified mice with less time without crossing. However, a complicated manual operation is required to increase the number of ESC colonies. Here, the objective of this study was to design and demonstrate a new device to easily find colonies and carry them to microwells.

Results

We developed a polydimethylsiloxane-based device for easy manipulation and isolation of ESC colonies. By introducing ESC colonies into the groove placed near culturing microwells, users can easily find, pick up and carry ESC colonies to microwells. By hydrophilic treatment using bovine serum albumin, 2-μL droplets including colonies reached the microwell bottom. Operation time using this device was shortened for both beginners (2.3-fold) and experts (1.5-fold) compared to the conventional colony picking operation. Isolated ESC colonies were confirmed to have maintained pluripotency. This device is expected to promote research by shortening the isolation procedure for ESC colonies or other large cells (e.g. eggs or embryos) and shortening training time for beginners as a simple sorter.

Emerging technologies for profiling extracellular vesicle heterogeneity

Extracellular vesicles (EVs) are membrane-bound vesicles secreted by most cell types and exist in virtually all bodily fluids. They carry on a wealth of proteomic and genetic information including proteins, lipids, miRNAs, mRNA, non-coding RNA and other molecules from parental cells. Increasing evidence shows that within populations of EVs, their biogenesis, physical characteristics (e.g. size, density, morphology) and cargos (e.g. protein, lipid content, nucleic acids) may vary substantially, which accordingly change their biological properties. To fully exploit the potential of EVs, it requires qualified methods to profile EV heterogeneity. In this review, we survey recent approaches for EV isolation with innovative discoveries in heterogeneity. The main challenges in EV heterogeneity research are identified, and the roles of single cell EV profiling and single EV imaging are highlighted. We further discuss promising opportunities for resolving the underlying complexity of EV heterogeneity.

How single-cell immunology is benefiting from microfluidic technologies

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

Label-free on chip quality assessment of cellular blood products using real-time deformability cytometry

Without cellular blood products such as platelet concentrates (PC), red blood cell concentrates (RCC), and hematopoietic stem cells (HPSC) modern treatments in medicine would not be possible. An unresolved challenge is the assessment of their quality with minimal cell manipulation. Minor changes in production, storage conditions, or blood bag composition may impact cell function, which can have important consequences on product integrity. This is especially relevant for personalized medicine, such as autologous T-cell therapy. Today a robust methodology that globally determines cell status directly before transfusion or transplantation is lacking. We demonstrate that measuring viscoelastic characteristics of peripheral blood cells using real-time deformability cytometry (RT-DC) provides comprehensive information on product quality, which is not accessible using conventional quality control tests. In addition, RT-DC requires few cells, a minimal sample volume and has a rapid turnaround time. We compared RT-DC to standard in vitro quality assays assessing: i) PC after storage at 4 °C and room temperature; ii) magnetic nanoparticle labeled platelets; iii) RCC stored in blood bags with different plasticizers; iv) RCC after gamma irradiation; and v) HPSC after cryopreservation with 5% or 10% dimethyl sulfoxide, respectively. Additionally, we evaluated the engraftment time of patients' platelets and leukocytes after transplantation of HPSC products. Our results demonstrate that label-free mechano-phenotyping can be used as a potential biomarker for quality assessment of cell-based pharmaceutical products.

High-throughput cell and spheroid mechanics in virtual fluidic channels

Microfluidics by soft lithography has proven to be of key importance for biophysics and life science research. While being based on replicating structures of a master mold using benchtop devices, design modifications are time consuming and require sophisticated cleanroom equipment. Here, we introduce virtual fluidic channels as a flexible and robust alternative to microfluidic devices made by soft lithography. Virtual channels are liquid-bound fluidic systems that can be created in glass cuvettes and tailored in three dimensions within seconds for rheological studies on a wide size range of biological samples. We demonstrate that the liquid-liquid interface imposes a hydrodynamic stress on confined samples, and the resulting strain can be used to calculate rheological parameters from simple linear models. In proof-of-principle experiments, we perform high-throughput rheology inside a flow cytometer cuvette and show the Young's modulus of isolated cells exceeds the one of the corresponding tissue by one order of magnitude.

Microfluidic systems for hydrodynamic trapping of cells and clusters

Microfluidic devices have been widely applied to trapping and isolation of cells and clusters for controllable intercellular environments and high-throughput analysis, triggering numerous advances in disease diagnosis and single-cell analysis. Passive hydrodynamic cell trapping is one of the simple and effective methods that has been gaining attention in recent years. Our aim here is to review the existing passive microfluidic trapping approaches, including microposts, microfiltration, microwells, and trapping chambers, with emphasis on design principles and performance. We summarize the remarkable advances that hydrodynamic trapping methods offer, as well as the existing challenges and prospects for development. Finally, we hope that an improved understanding of hydrodynamic trapping approaches can lead to sophisticated and useful platforms to advance medical and biological research.

Microfluidic platforms for the dynamic characterisation of synthetic circuitry

Generating novel functionality from well characterised synthetic parts and modules lies at the heart of synthetic biology. Ideally, circuitry is rationally designed in silico with quantitatively predictive models to predetermined design specifications. Synthetic circuits are intrinsically stochastic, often dynamically modulated and set in a dynamic fluctuating environment within a living cell. To build more complex circuits and to gain insight into context effects, intrinsic noise and transient performance, characterisation techniques that resolve both heterogeneity and dynamics are required. Here we review recent advances in both in vitro and in vivo microfluidic technologies that are suitable for the characterisation of synthetic circuitry, modules and parts.

Dynamical analysis of bacteria in microscopy movies

Recent advances in microscopy, computing power and image processing have enabled the analysis of ever larger datasets of movies of microorganisms to study their behaviour. However, techniques for analysing the dynamics of individual cells from such datasets are not yet widely available in the public domain. We recently demonstrated significant phenotypic heterogeneity in the adhesion of Escherichia coli bacteria to glass surfaces using a new method for the high-throughput analysis of video microscopy data. Here, we present an in-depth analysis of this method and its limitations, and make public our algorithms for following the positions and orientations of individual rod-shaped bacteria from time-series of 2D images to reconstruct their trajectories and characterise their dynamics. We demonstrate in detail how to use these algorithms to identify different types of adhesive dynamics within a clonal population of bacteria sedimenting onto a surface. The effects of measurement errors in cell positions and of limited trajectory durations on our results are discussed.

Recent advances in single cell manipulation and biochemical analysis on microfluidics

Single cell analysis has become of great interest with unprecedented capabilities for the systematic investigation of cell-to-cell variation in large populations. Rapid and multi-parametric analysis of intercellular biomolecules at the single-cell level is imperative for the improvement of early disease diagnosis and personalized medicine. However, the small size of cells and the low concentration levels of target biomolecules are critical challenges for single cell analysis. In recent years, microfluidic platforms capable of handling small-volume fluid have been demonstrated to be powerful tools for single cell analysis. In addition, microfluidic techniques allow for precise control of the localized microenvironment, which yield more accurate outcomes. Many different microfluidic techniques have been greatly improved for highly efficient single-cell manipulation and highly sensitive detection over the past few decades. To date, microfluidics-based single cell analysis has become the hot research topic in this field. In this review, we particularly highlight the advances in this field during the past three years in the following three aspects: (1) microfluidic single cell manipulation based on microwells, micropatterns, droplets, traps and flow cytometric methods; (2) detection methods based on fluorescence, mass spectrometry, electrochemical, and polymerase chain reaction-based analysis; (3) applications in the fields of small molecule detection, protein analysis, multidrug resistance analysis, and single cell sequencing with droplet microfluidics. We also discuss future research opportunities by focusing on key performances of throughput, multiparametric target detection and data processing.

Recent advances in optical microscopic methods for single-particle tracking in biological samples

With the rapid development of optical microscopic techniques, explorations on the chemical and biological properties of target objects in biological samples at single-molecule/particle level have received great attention recently. In the past decades, various powerful techniques have been developed for single-particle tracking (SPT) in biological samples. In this review, we summarize the commonly used optical microscopic methods for SPT, such as total internal reflection fluorescence microscopy (TIRFM), super-resolution fluorescence microscopy (SRM), dark-field optical microscopy (DFM), total internal reflection scattering microscopy (TIRSM), and differential interference contrast microscopy (DICM). We then discuss the image processing and data analysis methods, including particle localization, trajectory reconstruction, and diffusion behavior analysis. The application of SPT on the cell membrane, within the cell, and the cellular invading process of viruses are introduced. Finally, the challenges and prospects of optical microscopic technologies for SPT are delineated.

Advances in Micropipette Aspiration: Applications in Cell Biomechanics, Models, and Extended Studies

With five decades of sustained application, micropipette aspiration has enabled a wide range of biomechanical studies in the field of cell mechanics. Here, we provide an update on the use of the technique, with a focus on recent developments in the analysis of the experiments, innovative microaspiration-based approaches, and applications in a broad variety of cell types. We first recapitulate experimental variations of the technique. We then discuss analysis models focusing on important limitations of widely used biomechanical models, which underpin the urge to adopt the appropriate ones to avoid misleading conclusions. The possibilities of performing different studies on the same cell are also considered.

High throughput screening of complex biological samples with mass spectrometry – from bulk measurements to single cell analysis

We review the state of the art in HTS using mass spectrometry with minimal sample preparation from complex biological matrices. We focus on industrial and biotechnological applications.

Estimation methods for heterogeneous cell population models in systems biology

Heterogeneity among individual cells is a characteristic and relevant feature of living systems. A range of experimental techniques to investigate this heterogeneity is available, and multiple modelling frameworks have been developed to describe and simulate the dynamics of heterogeneous populations. Measurement data are used to adjust computational models, which results in parameter and state estimation problems. Methods to solve these estimation problems need to take the specific properties of data and models into account. The aim of this review is to give an overview on the state of the art in estimation methods for heterogeneous cell population data and models. The focus is on models based on the population balance equation, but stochastic and individual-based models are also discussed. It starts with a brief discussion of common experimental approaches and types of measurement data that can be obtained in this context. The second part describes computational modelling frameworks for heterogeneous populations and the types of estimation problems occurring for these models. The third part starts with a discussion of observability and identifiability properties, after which the computational methods to solve the various estimation problems are described.

Recent Progress in the Development of Microfluidic Vascular Models

The blood vessel is part of the circulatory system, and systemic circulation provides the blood supply to all tissues. Arteries are pathways through which the blood is carried, and the capillaries have a key role in material exchange to maintain the tissue environment. Blood vessels have structures appropriate for their functions, and their sizes and cell types are different. In this review, we introduced recent studies of the microfluidic vascular models. The model structures are classified mainly as poly(dimethylsiloxane) and hydrogel microchannels and self-assembled networks. Basic phenomena and functions were realized in vascular models, including fluid shear stress, cell strain, interstitial flow, endothelial permeation, angiogenesis, and thrombosis. In some models, endothelial cells were co-cultured with smooth muscle cells, pericytes, and fibroblasts in an extracellular matrix. Examples of vascular models involving the brain, lung, liver, kidney, placenta, and cancer were also introduced.

Particle-Templated Emulsification for Microfluidics-Free Digital Biology

The compartmentalization of reactions in monodispersed droplets is valuable for applications across biology. However, the requirement of microfluidics to partition the sample into monodispersed droplets is a significant barrier that impedes implementation. Here, we introduce particle-templated emulsification, a method to encapsulate samples in monodispersed emulsions without microfluidics. By vortexing a mixture of hydrogel particles and sample solution, we encapsulate the sample in monodispersed emulsions that are useful for most droplet applications. We illustrate the method with ddPCR and single cell culture. The ability to encapsulate samples in monodispersed droplets without microfluidics should facilitate the implementation of compartmentalized reactions in biology.

Opportunities and Challenges in Implementation of Multiparameter Single Cell Analysis Platforms for Clinical Translation

The high-content interrogation of single cells with platforms optimized for the multiparameter characterization of cells in liquid and solid biopsy samples can enable characterization of heterogeneous populations of cells ex vivo. Doing so will advance the diagnosis, prognosis, and treatment of cancer and other diseases. However, it is important to understand the unique issues in resolving heterogeneity and variability at the single cell level before navigating the validation and regulatory requirements in order for these technologies to impact patient care. Since 2013, leading experts representing industry, academia, and government have been brought together as part of the Foundation for the National Institutes of Health (FNIH) Biomarkers Consortium to foster the potential of high-content data integration for clinical translation.

Recent advances in the use of microfluidic technologies for single cell analysis

The inherent heterogeneity in cell populations has become of great interest and importance as analytical techniques have improved over the past decades. With the advent of personalized medicine, understanding the impact of this heterogeneity has become an important challenge for the research community. Many different microfluidic approaches with varying levels of throughput and resolution exist to study single cell activity. In this review, we take a broad view of the recent microfluidic developments in single cell analysis based on microwell, microchamber, and droplet platforms. We cover physical, chemical, and molecular biology approaches for cellular and molecular analysis including newly emerging genome-wide analysis.

Functional and Biomimetic Materials for Engineering of the Three-Dimensional Cell Microenvironment

The cell microenvironment has emerged as a key determinant of cell behavior and function in development, physiology, and pathophysiology. The extracellular matrix (ECM) within the cell microenvironment serves not only as a structural foundation for cells but also as a source of three-dimensional (3D) biochemical and biophysical cues that trigger and regulate cell behaviors. Increasing evidence suggests that the 3D character of the microenvironment is required for development of many critical cell responses observed in vivo, fueling a surge in the development of functional and biomimetic materials for engineering the 3D cell microenvironment. Progress in the design of such materials has improved control of cell behaviors in 3D and advanced the fields of tissue regeneration, in vitro tissue models, large-scale cell differentiation, immunotherapy, and gene therapy. However, the field is still in its infancy, and discoveries about the nature of cell-microenvironment interactions continue to overturn much early progress in the field. Key challenges continue to be dissecting the roles of chemistry, structure, mechanics, and electrophysiology in the cell microenvironment, and understanding and harnessing the roles of periodicity and drift in these factors. This review encapsulates where recent advances appear to leave the ever-shifting state of the art, and it highlights areas in which substantial potential and uncertainty remain.

A microfluidic flow cytometer enabling absolute quantification of single-cell intracellular proteins

Quantification of single-cell proteomics provides key insights into cellular heterogeneity while conventional flow cytometry cannot provide absolute quantification of intracellular proteins of single cells due to the lack of calibration approaches. This paper presents a constriction channel (with a cross sectional area smaller than cells) based microfluidic flow cytometer, capable of collecting copy numbers of specific intracellular proteins. In this platform, single cells stained with fluorescence labelled antibodies were forced to squeeze through the constriction channel with the fluorescence intensities quantified and since cells fully filled the constriction channel during the squeezing process, solutions with fluorescence labelled antibodies were flushed into the constriction channel to obtain calibration curves. By combining raw fluorescence data and calibration curves, absolute quantification of intracellular proteins was realized. As a demonstration, copy numbers of beta-actin of single tumour cells were quantified to be 0.90 ± 0.30 μM (A549, n_cell = 14 228), 2.34 ± 0.70 μM (MCF 10A, n_cell = 2455), and 0.98 ± 0.65 μM (Hep G2, n_cell = 6945). The travelling time for individual cells was quantified to be roughly 10 ms and thus a throughput of 100 cells per s can be achieved. This microfluidic system can be used to quantify the copy numbers of intracellular proteins in a high-throughput manner, which may function as an enabling technique in the field of single-cell proteomics.

Microtechnologies for Cell Microenvironment Control and Monitoring

A great breadth of questions remains in cellular biology. Some questions cannot be answered using traditional analytical techniques and so demand the development of new tools for research. In the near future, the development of highly integrated microfluidic analytical platforms will enable the acquisition of unknown biological data. These microfluidic systems must allow cell culture under controlled microenvironment and high throughput analysis. For this purpose, the integration of a variable number of newly developed micro- and nano-technologies, which enable control of topography and surface chemistry, soluble factors, mechanical forces and cell–cell contacts, as well as technology for monitoring cell phenotype and genotype with high spatial and temporal resolution will be necessary. These multifunctional devices must be accompanied by appropriate data analysis and management of the expected large datasets generated. The knowledge gained with these platforms has the potential to improve predictive models of the behavior of cells, impacting directly in better therapies for disease treatment. In this review, we give an overview of the microtechnology toolbox available for the design of high throughput microfluidic platforms for cell analysis. We discuss current microtechnologies for cell microenvironment control, different methodologies to create large arrays of cellular systems and finally techniques for monitoring cells in microfluidic devices.

Next-generation Sequencing (NGS) Analysis on Single Circulating Tumor Cells (CTCs) with No Need of Whole-genome Amplification (WGA)

BACKGROUND

Isolation and genotyping of circulating tumor cells (CTCs) is gaining an increasing interest by clinical researchers in oncology not only for investigative purposes, but also for concrete application in clinical practice in terms of diagnosis, prognosis and decision treatment with targeted therapies. For the mutational analysis of single CTCs, the most advanced biotechnology methodology currently available includes the combination of whole genome amplification (WGA) followed by next-generation sequencing (NGS). However, the sequence of these molecular techniques is time-consuming and may also favor operator-dependent errors, related to the procedures themselves that, as in the case of the WGA technique, might affect downstream molecular analyses.

MATERIALS AND METHODS

A preliminary approach of molecular analysis by NGS on a model of CTCs without previous WGA procedural step was performed. We set-up an artificial sample obtained by spiking the SK-MEL-28 melanoma cell line in normal donor peripheral whole blood. Melanoma cells were first enriched using an AutoMACS® (Miltenyi) cell separator and then isolated as single and pooled CTCs by DEPArray™ System (Silicon Biosystems). NGS analysis, using the Ion AmpliSeq™ Cancer Hotspot Panel v2 (Life Technologies) with the Ion Torrent PGM™ system (Life Technologies), was performed on the SK-MEL-28 cell pellet, a single CTC previously processed with WGA and on 1, 2, 4 and 8 recovered CTCs without WGA pre-amplification.

RESULTS

NGS directly carried out on CTCs without WGA showed the same mutations identified in SK-MEL-28 cell line pellet, with a considerable efficiency and avoiding the errors induced by the WGA procedure.

CONCLUSION

We identified a cost-effective, time-saving and reliable methodological approach that could improve the analytical accuracy of the liquid biopsy and appears promising in studying CTCs from cancer patients for both research and clinical purposes.

Advances in digital polymerase chain reaction (dPCR) and its emerging biomedical applications

Since the invention of polymerase chain reaction (PCR) in 1985, PCR has played a significant role in molecular diagnostics for genetic diseases, pathogens, oncogenes and forensic identification. In the past three decades, PCR has evolved from end-point PCR, through real-time PCR, to its current version, which is the absolute quantitive digital PCR (dPCR). In this review, we first discuss the principles of all key steps of dPCR, i.e., sample dispersion, amplification, and quantification, covering commercialized apparatuses and other devices still under lab development. We highlight the advantages and disadvantages of different technologies based on these steps, and discuss the emerging biomedical applications of dPCR. Finally, we provide a glimpse of the existing challenges and future perspectives for dPCR.

A Microfluidic System with Surface Patterning for Investigating Cavitation Bubble(s)-Cell Interaction and the Resultant Bioeffects at the Single-cell Level

In this manuscript, we first describe the fabrication protocol of a microfluidic chip, with gold dots and fibronectin-coated regions on the same glass substrate, that precisely controls the generation of tandem bubbles and individual cells patterned nearby with well-defined locations and shapes. We then demonstrate the generation of tandem bubbles by using two pulsed lasers illuminating a pair of gold dots with a few-microsecond time delay. We visualize the bubble-bubble interaction and jet formation by high-speed imaging and characterize the resultant flow field using particle image velocimetry (PIV). Finally, we present some applications of this technique for single cell analysis, including cell membrane poration with macromolecule uptake, localized membrane deformation determined by the displacements of attached integrin-binding beads, and intracellular calcium response from ratiometric imaging. Our results show that a fast and directional jetting flow is produced by the tandem bubble interaction, which can impose a highly localized shear stress on the surface of a cell grown in close proximity. Furthermore, different bioeffects can be induced by altering the strength of the jetting flow by adjusting the standoff distance from the cell to the tandem bubbles.

A Microfluidic Chip for Cell Patterning Utilizing Paired Microwells and Protein Patterns

Cell patterning has been widely used in research on fundamental cell biology and in applications such as tissue engineering, neuron network formation, cell based biosensor and drug screening. Although various methods have been developed, cell patterning in an enclosed microfluidic device at single cell level remains challenging. This paper describes a microfluidic device with microwells and protein patterns paired together in a single microchannel for an easy cell patterning. Cells captured in the microwells were positioned directly onto the protein patterns within 5 min and the patterning performance was successfully demonstrated using HeLa cells and human gallbladder carcinoma cells (SGC-996). Cells survived for 6 days in the microchannel. Cell attachment, migration, proliferation and cell colony formation were observed. Our device is free of topographic constraint for the patterned cells and no complex chemical modification to the substrate is needed, offering a simple, fast, and easy-to-operate way of patterning cells at single cell level in an enclosed microfluidic channel.

A fluidic circuit based, high-efficiency and large-scale single cell trap

Single cell traps have important applications in biological cell manipulation and analysis. This paper describes a novel single cell trap design and device with a matrix of cell trap units inspired by an equivalent resistive electric circuit. This fluidic device follows the least flow resistance path principle of such devices allowing deterministic single cell trapping with high efficiency and flexibility for large scale cell patterning.

Synchronizing stochastic circadian oscillators in single cells of Neurospora crassa

The synchronization of stochastic coupled oscillators is a central problem in physics and an emerging problem in biology, particularly in the context of circadian rhythms. Most measurements on the biological clock are made at the macroscopic level of millions of cells. Here measurements are made on the oscillators in single cells of the model fungal system, Neurospora crassa, with droplet microfluidics and the use of a fluorescent recorder hooked up to a promoter on a clock controlled gene-2 (ccg-2). The oscillators of individual cells are stochastic with a period near 21 hours (h), and using a stochastic clock network ensemble fitted by Markov Chain Monte Carlo implemented on general-purpose graphical processing units (or GPGPUs) we estimated that >94% of the variation in ccg-2 expression was stochastic (as opposed to experimental error). To overcome this stochasticity at the macroscopic level, cells must synchronize their oscillators. Using a classic measure of similarity in cell trajectories within droplets, the intraclass correlation (ICC), the synchronization surface ICC is measured on >25,000 cells as a function of the number of neighboring cells within a droplet and of time. The synchronization surface provides evidence that cells communicate, and synchronization varies with genotype.