Phenotypic drug profiling in droplet microfluidics for better targeting of drug-resistant tumors

Single Cell Droplet-Based Efficacy and Transcriptomic Analysis of a Novel Anti-KLRG1 Antibody for Elimination of Autoreactive T Cells

Progress in developing improvements in the treatment of autoimmune disease has been gradual, due to challenges presented by the nature of these conditions. Namely, the need to suppress a patient's immune response while maintaining the essential activity of the immune system in controlling disease. Targeted treatments to eliminate the autoreactive immune cells driving disease symptoms present a promising new option for major improvements in treatment efficacy and side effect management. Monoclonal antibody therapies can be applied to target autoreactive immune cells if the cells possess unique surface marker expression patterns. Killer cell lectin like receptor G1 (KLRG1) expression on autoreactive T cells presents an optimal target for this type of cell depleting antibody therapy. In this study, we apply a variety of in vitro screening methods to determine the efficacy of a novel anti-KLRG1 antibody at mediating specific natural killer (NK) cell mediated antibody-dependent cellular cytotoxicity (ADCC). The methods include single-cell droplet microfluidic techniques, allowing timelapse imaging and sorting based on cellular interactions. Included in this study is the development of a novel method of sorting cells using a droplet-sorting platform and a fluorescent calcium dye to separate cells based on CD16 recognition of cell-bound antibody. We applied this novel sorting method to visualize transcriptomic variation between NK cells that are or are not activated by binding the anti-KLRG1 antibody using RNA sequencing. The data in this study reveals a reliable and target-specific cytotoxicity of the cell depleting anti-KLRG1 antibody, and supports our droplet-sorting calcium assay as a novel method of sorting cells based on receptor activation.

Droplet-based microfluidics: an efficient high-throughput portable system for cell encapsulation

One of the goals of tissue engineering and regenerative medicine is restoring primary living tissue function by manufacturing a 3D microenvironment. One of the main challenges is protecting implanted non-autologous cells or tissues from the host immune system. Cell encapsulation has emerged as a promising technique for this purpose. It involves entrapping cells in biocompatible and semi-permeable microcarriers made from natural or synthetic polymers that regulate the release of cellular secretions. In recent years, droplet-based microfluidic systems have emerged as powerful tools for cell encapsulation in tissue engineering and regenerative medicine. These systems offer precise control over droplet size, composition, and functionality, allowing for creating of microenvironments that closely mimic native tissue. Droplet-based microfluidic systems have extensive applications in biotechnology, medical diagnosis, and drug discovery. This review summarises the recent developments in droplet-based microfluidic systems and cell encapsulation techniques, as well as their applications, advantages, and challenges in biology and medicine. The integration of these technologies has the potential to revolutionise tissue engineering and regenerative medicine by providing a precise and controlled microenvironment for cell growth and differentiation. By overcoming the immune system's challenges and enabling the release of cellular secretions, these technologies hold great promise for the future of regenerative medicine.

An innovative single-cell approach for phenotyping and functional genotyping of CAR NK cells

BACKGROUND

To accelerate the translation of novel immunotherapeutic treatment approaches, the development of analytic methods to assess their efficacy at early in vitro stages is necessary. Using a droplet-based microfluidic platform, we have established a method for multiparameter quantifiable phenotypic and genomic observations of immunotherapies. Chimeric antigen receptor (CAR) natural killer (NK) cells are of increased interest in the current immunotherapy landscape and thus provide an optimal model for evaluating our novel methodology.

METHODS

For this approach, NK cells transduced with a CD19 CAR were compared with non-transduced NK cells in their ability to kill a lymphoma cell line. Using our microfluidic platform, we were able to quantify the increase in cytotoxicity and synaptic contact formation of CAR NK cells over non-transduced NK cells. We then optimized our droplet sorter and successfully used it to separate NK cells based on target cell killing to perform transcriptomic analyses.

RESULTS

Our data revealed expected improvement in cytotoxicity with the CD19 CAR but more importantly, provided unique insights into the factors involved in the cytotoxic mechanisms of CAR NK cells. This demonstrates a novel, improved system for accelerating the pre-clinical screening of future immunotherapy treatments.

CONCLUSIONS

This study provides a new potential approach for enhanced early screening of immunotherapies to improve their development, with a highly relevant cell model to demonstrate. Additionally, our validation studies provided some potential insights into transcriptomic determinants influencing CAR NK cytotoxicity.

Microfluidic-based platforms for cell-to-cell communication studies

Intercellular communication is critical to the understanding of human health and disease progression. However, compared to traditional methods with inefficient analysis, microfluidic co-culture technologies developed for cell-cell communication research can reliably analyze crucial biological processes, such as cell signaling, and monitor dynamic intercellular interactions under reproducible physiological cell co-culture conditions. Moreover, microfluidic-based technologies can achieve precise spatial control of two cell types at the single-cell level with high throughput. Herein, this review focuses on recent advances in microfluidic-based 2D and 3D devices developed to confine two or more heterogeneous cells in the study of intercellular communication and decipher the advantages and limitations of these models in specific cellular research scenarios. This review will stimulate the development of more functionalized microfluidic platforms for biomedical research, inspiring broader interests across various disciplines to better comprehend cell-cell communication and other fields, such as tumor heterogeneity and drug screening.

On the synergy of biomicrofluidic technologies and real-time 3D tracking: A perspective

Particle image velocimetry and particle tracking velocimetry have played pivotal roles in flow and particle characterization, owing to their non-invasive and accurate data collection methods. However, their broader application in the biomicrofluidics field is constrained by challenges, such as intensive calibration, high post-processing costs, and optical compatibility issues, especially in settings where space is a bottleneck. This article describes recent advancements in non-iterative ray tracing that promise more streamlined post-capture calibration and highlights examples of applications and areas that merit further technological investigation. The development and adoption of these techniques may pave the way for new innovations.

Review of the role of surfactant dynamics in drop microfluidics

Surfactants are employed in microfluidic systems not just for drop stabilisation, but also to study local phenomena in industrial processes. On the scale of a single drop, these include foaming, emulsification and stability of foams and emulsions using statistically significant ensembles of bubbles or drops respectively. In addition, surfactants are often a part of a formulation in microfluidic drop reactors. In all these applications, surfactant dynamics play a crucial role and need to be accounted for. In this review, the effect of surfactant dynamics is considered on the level of standard microfluidic operations: drop formation, movement in channels and coalescence, but also on a more general level, considering the mechanisms controlling surfactant adsorption on time- and length-scales characteristic of microfluidics. Some examples of relevant calculations are provided. The advantages and challenges of the use of microfluidics to measure dynamic interfacial tension at short time-scales are discussed.

Interface Dynamics and the Influence of Gravity on Droplet Generation in a Y-microchannel

The present experimental investigation is focused on the influence of gravity upon water-droplet formation in a Y-microchannel filled with oil. The flows are in the Stokes regime, with very small capillary numbers and Ohnesorge numbers less than one. The study was performed in a square-cross-section channel, with a = 1.0 mm as the characteristic dimension and a flow rate ratio κ in a range between 0.55 and 1.8. The interface dynamics in the vicinity of breakup and the transitory plug flow regime after the detachment of the droplet were analysed. The dependence of droplet length L was correlated with the channel position against the gravity and κ parameters. The results of the work prove that, for κ=1, the droplet length L is independent of channel orientation.

Application of Microfluidics in Drug Development from Traditional Medicine

While there are many clinical drugs for prophylaxis and treatment, the search for those with low or no risk of side effects for the control of infectious and non-infectious diseases is a dilemma that cannot be solved by today's traditional drug development strategies. The need for new drug development strategies is becoming increasingly important, and the development of new drugs from traditional medicines is the most promising strategy. Many valuable clinical drugs have been developed based on traditional medicine, including drugs with single active ingredients similar to modern drugs and those developed from improved formulations of traditional drugs. However, the problems of traditional isolation and purification and drug screening methods should be addressed for successful drug development from traditional medicine. Advances in microfluidics have not only contributed significantly to classical drug development but have also solved many of the thorny problems of new strategies for developing new drugs from traditional drugs. In this review, we provide an overview of advanced microfluidics and its applications in drug development (drug compound synthesis, drug screening, drug delivery, and drug carrier fabrication) with a focus on its applications in conventional medicine, including the separation and purification of target components in complex samples and screening of active ingredients of conventional drugs. We hope that our review gives better insight into the potential of traditional medicine and the critical role of microfluidics in the drug development process. In addition, the emergence of new ideas and applications will bring about further advances in the field of drug development.

Droplet microfluidics for functional temporal analysis and cell recovery on demand using microvalves: application in immunotherapies for cancer

Most common methods of cellular analysis employ the top-down approach (investigating proteomics or genomics directly), thereby destroying the cell, which does not allow the possibility of using the same cell to correlate genomics with functional assays. Herein we describe an approach for single-cell tools that serve as a bottom-up approach. Our technology allows functional phenotyping to be conducted by observing the cytotoxicity of cells and then probe the underlying biology. We have developed a droplet microfluidic device capable of trapping droplets in the array and releasing the droplet of interest selectively using microvalves. Each droplet in the array encapsulates natural killer cells (NK cells) and tumour cells for real-time monitoring of burst kinetics and spatial coordination during killing by single NK cells. Finally, we use the microvalve actuation to selectively release droplets with the desired functional phenotype such as for fast and serial killing of target tumour cells by NK cells. From this perspective, our device allows for investigating first interactions and real-time monitoring of kinetics and later cell recovery on demand for single-cell omic analysis such as single-cell RNA sequencing (scRNA), which to date, is primarily based on in-depth analyses of the entire transcriptome of a relatively low number of cells.

Ensemble latent assimilation with deep learning surrogate model: application to drop interaction in a microfluidics device

A major challenge in the field of microfluidics is to predict and control drop interactions. This work develops an image-based data-driven model to forecast drop dynamics based on experiments performed on a microfluidics device. Reduced-order modelling techniques are applied to compress the recorded images into low-dimensional spaces and alleviate the computational cost. Recurrent neural networks are then employed to build a surrogate model of drop interactions by learning the dynamics of compressed variables in the reduced-order space. The surrogate model is integrated with real-time observations using data assimilation. In this paper we developed an ensemble-based latent assimilation algorithm scheme which shows an improvement in terms of accuracy with respect to the previous approaches. This work demonstrates the possibility to create a reliable data-driven model enabling a high fidelity prediction of drop interactions in microfluidics device. The performance of the developed system is evaluated against experimental data (i.e., recorded videos), which are excluded from the training of the surrogate model. The developed scheme is general and can be applied to other dynamical systems.

CancerCellTracker: a brightfield time-lapse microscopy framework for cancer drug sensitivity estimation

MOTIVATION

Time-lapse microscopy is a powerful technique that relies on images of live cells cultured ex vivo that are captured at regular intervals of time to describe and quantify their behavior under certain experimental conditions. This imaging method has great potential in advancing the field of precision oncology by quantifying the response of cancer cells to various therapies and identifying the most efficacious treatment for a given patient. Digital image processing algorithms developed so far require high-resolution images involving very few cells originating from homogeneous cell line populations. We propose a novel framework that tracks cancer cells to capture their behavior and quantify cell viability to inform clinical decisions in a high-throughput manner.

RESULTS

The brightfield microscopy images a large number of patient-derived cells in an ex vivo reconstruction of the tumor microenvironment treated with 31 drugs for up to 6 days. We developed a robust and user-friendly pipeline CancerCellTracker that detects cells in co-culture, tracks these cells across time and identifies cell death events using changes in cell attributes. We validated our computational pipeline by comparing the timing of cell death estimates by CancerCellTracker from brightfield images and a fluorescent channel featuring ethidium homodimer. We benchmarked our results using a state-of-the-art algorithm implemented in ImageJ and previously published in the literature. We highlighted CancerCellTracker's efficiency in estimating the percentage of live cells in the presence of bone marrow stromal cells.

AVAILABILITY AND IMPLEMENTATION

https://github.com/compbiolabucf/CancerCellTracker.

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

Machine learning phenomics (MLP) combining deep learning with time-lapse-microscopy for monitoring colorectal adenocarcinoma cells gene expression and drug-response

High-throughput phenotyping is becoming increasingly available thanks to analytical and bioinformatics approaches that enable the use of very high-dimensional data and to the availability of dynamic models that link phenomena across levels: from genes to cells, from cells to organs, and through the whole organism. The combination of phenomics, deep learning, and machine learning represents a strong potential for the phenotypical investigation, leading the way to a more embracing approach, called machine learning phenomics (MLP). In particular, in this work we present a novel MLP platform for phenomics investigation of cancer-cells response to therapy, exploiting and combining the potential of time-lapse microscopy for cell behavior data acquisition and robust deep learning software architectures for the latent phenotypes extraction. A two-step proof of concepts is designed. First, we demonstrate a strict correlation among gene expression and cell phenotype with the aim to identify new biomarkers and targets for tailored therapy in human colorectal cancer onset and progression. Experiments were conducted on human colorectal adenocarcinoma cells (DLD-1) and their profile was compared with an isogenic line in which the expression of LOX-1 transcript was knocked down. In addition, we also evaluate the phenotypic impact of the administration of different doses of an antineoplastic drug over DLD-1 cells. Under the omics paradigm, proteomics results are used to confirm the findings of the experiments.

Inkjet-Patterned Microdroplets as Individual Microenvironments for Adherent Single Cell Culture

Adhesion of single cells is the foundation of manifold cellular behaviors and life processes. However, investigating the function of a specific cell is still challenging due to deficiency of adhesion or interference from surrounding cells. Herein, an open microfluidic system is reported for culturing adherent single cells, implemented by a micrometer-scale droplet matrix on an inkjet-printed polylysine template. The target cells are isolated from any cell from other droplets, and their adhesion strength is determined to be comparable to conventional petri dishes via an in-situ investigation with a microfluidic extractor. On this proposed platform, isolated single cells are observed to display an entirely distinct spreading behavior featuring total absence of elongation, indicating drastic cell behavior change from their "singleness." This system has high versatility and compatibility for various assaying methods, assuring a promising potential in detailed single cell behavior and cell heterogeneity studies.

Cell Culture in Microfluidic Droplets

Cell manipulation in droplets has emerged as one of the great successes of microfluidic technologies, with the development of single-cell screening. However, the droplet format has also served to go beyond single-cell studies, namely by considering the interactions between different cells or between cells and their physical or chemical environment. These studies pose specific challenges linked to the need for long-term culture of adherent cells or the diverse types of measurements associated with complex biological phenomena. Here we review the emergence of droplet microfluidic methods for culturing cells and studying their interactions. We begin by characterizing the quantitative aspects that determine the ability to encapsulate cells, transport molecules, and provide sufficient nutrients within the droplets. This is followed by an evaluation of the biological constraints such as the control of the biochemical environment and promoting the anchorage of adherent cells. This first part ends with a description of measurement methods that have been developed. The second part of the manuscript focuses on applications of these technologies for cancer studies, immunology, and stem cells while paying special attention to the biological relevance of the cellular assays and providing guidelines on improving this relevance.

Application of Microfluidic Systems for Breast Cancer Research

Cancer is a disease in which cells in the body grow out of control; breast cancer is the most common cancer in women in the United States. Due to early screening and advancements in therapeutic interventions, deaths from breast cancer have declined over time, although breast cancer remains the second leading cause of cancer death among women. Most deaths are due to metastasis, as cancer cells from the primary tumor in the breast form secondary tumors in remote sites in distant organs. Over many years, the basic biological mechanisms of breast cancer initiation and progression, as well as the subsequent metastatic cascade, have been studied using cell cultures and animal models. These models, although extremely useful for delineating cellular mechanisms, are poor predictors of physiological responses, primarily due to lack of proper microenvironments. In the last decade, microfluidics has emerged as a technology that could lead to a paradigm shift in breast cancer research. With the introduction of the organ-on-a-chip concept, microfluidic-based systems have been developed to reconstitute the dominant functions of several organs. These systems enable the construction of 3D cellular co-cultures mimicking in vivo tissue-level microenvironments, including that of breast cancer. Several reviews have been presented focusing on breast cancer formation, growth and metastasis, including invasion, intravasation, and extravasation. In this review, realizing that breast cancer can recur decades following post-treatment disease-free survival, we expand the discussion to account for microfluidic applications in the important areas of breast cancer detection, dormancy, and therapeutic development. It appears that, in the future, the role of microfluidics will only increase in the effort to eradicate breast cancer.

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.

Microfluidic technology for multiple single-cell capture

Microfluidic devices are widely used in single-cell capture and for pairing single cells or groups of cells for cell-cell interaction analysis; these advances have improved drug screening and cell signal transduction analysis. The complex in vivo environment involves interactions between two cells and among multiple cells of the same or different phenotypes. This study reviewed the core principles and performance of several microfluidic multiple- and single-cell capture methods, namely, the microwell, valve, trap, and droplet methods. The advantages and disadvantages of the methods were compared, and suggestions regarding their application to multiple-cell capture were provided. The results may serve as a reference for research on microfluidic multiple single-cell coculture technology.

Acoustofluidic Droplet Sorter Based on Single Phase Focused Transducers

Droplet microfluidics has revolutionized the biomedical and drug development fields by allowing for independent microenvironments to conduct drug screening at the single cell level. However, current microfluidic sorting devices suffer from drawbacks such as high voltage requirements (e.g., >200 Vpp), low biocompatibility, and/or low throughput. In this article, a single-phase focused transducer (SPFT)-based acoustofluidic chip is introduced, which outperforms many microfluidic droplet sorting devices through high energy transmission efficiency, high accuracy, and high biocompatibility. The SPFT-based sorter can be driven with an input power lower than 20 Vpp and maintain a postsorting cell viability of 93.5%. The SPFT sorter can achieve a throughput over 1000 events per second and a sorting purity up to 99.2%. The SPFT sorter is utilized here for the screening of doxorubicin cytotoxicity on cancer and noncancer cells, proving its drug screening capability. Overall, the SPFT droplet sorting device shows great potential for fast, precise, and biocompatible drug screening.

Investigation of Different Free Image Analysis Software for High-Throughput Droplet Detection

Droplet microfluidics has revealed innovative strategies in biology and chemistry. This advancement has delivered novel quantification methods, such as droplet digital polymerase chain reaction (ddPCR) and an antibiotic heteroresistance analysis tool. For droplet analysis, researchers often use image-based detection techniques. Unfortunately, the analysis of images may require specific tools or programming skills to produce the expected results. In order to address the issue, we explore the potential use of standalone freely available software to perform image-based droplet detection. We select the four most popular software and classify them into rule-based and machine learning-based types after assessing the software's modules. We test and evaluate the software's (i) ability to detect droplets, (ii) accuracy and precision, and (iii) overall components and supporting material. In our experimental setting, we find that the rule-based type of software is better suited for image-based droplet detection. The rule-based type of software also has a simpler workflow or pipeline, especially aimed for non-experienced users. In our case, CellProfiler (CP) offers the most user-friendly experience for both single image and batch processing analyses.

Microengineered 3D Tumor Models for Anti-Cancer Drug Discovery in Female-Related Cancers

The burden of cancer continues to increase in society and negatively impacts the lives of numerous patients. Due to the high cost of current treatment strategies, there is a crucial unmet need to develop inexpensive preclinical platforms to accelerate the process of anti-cancer drug discovery to improve outcomes in cancer patients, most especially in female patients. Many current methods employ expensive animal models which not only present ethical concerns but also do not often accurately predict human physiology and the outcomes of anti-cancer drug responsiveness. Conventional treatment approaches for cancer generally include systemic therapy after a surgical procedure. Although this treatment technique is effective, the outcome is not always positive due to various complex factors such as intratumor heterogeneity and confounding factors within the tumor microenvironment (TME). Patients who develop metastatic disease still have poor prognosis. To that end, recent efforts have attempted to use 3D microengineered platforms to enhance the predictive power and efficacy of anti-cancer drug screening, ultimately to develop personalized therapies. Fascinating features of microengineered assays, such as microfluidics, have led to the advancement in the development of the tumor-on-chip technology platforms, which have shown tremendous potential for meaningful and physiologically relevant anti-cancer drug discovery and screening. Three dimensional microscale models provide unprecedented ability to unveil the biological complexities of cancer and shed light into the mechanism of anti-cancer drug resistance in a timely and resource efficient manner. In this review, we discuss recent advances in the development of microengineered tumor models for anti-cancer drug discovery and screening in female-related cancers. We specifically focus on female-related cancers to draw attention to the various approaches being taken to improve the survival rate of women diagnosed with cancers caused by sex disparities. We also briefly discuss other cancer types like colon adenocarcinomas and glioblastoma due to their high rate of occurrence in females, as well as the high likelihood of sex-biased mutations which complicate current treatment strategies for women. We highlight recent advances in the development of 3D microscale platforms including 3D tumor spheroids, microfluidic platforms as well as bioprinted models, and discuss how they have been utilized to address major challenges in the process of drug discovery, such as chemoresistance, intratumor heterogeneity, drug toxicity, etc. We also present the potential of these platform technologies for use in high-throughput drug screening approaches as a replacements of conventional assays. Within each section, we will provide our perspectives on advantages of the discussed platform technologies.

Phenotype-related drug sensitivity analysis of single CTCs for medicine evaluation

Due to the heterogeneous and variable drug sensitivity of tumor cells, real-time monitoring of a patient's drug response is desirable for implementing personalized and dynamic therapy. Although considerable efforts have been directed at drug screening in living cells, performing repeated drug sensitivity analysis using patient-derived primary tumor cells at the single-cell level remains challenging. Here, we present an efficient approach to assess phenotype-related drug sensitivity at the single-cell level using patient-derived circulating tumor cells (CTCs) based on a drug sensitivity microfluidic chip (DS-Chip). The DS-Chip consists of a drug gradient generator and parallel cell traps, achieving continuous single CTC capture, drug gradient distributions, drug stimulation, fluorescent probe labeling and three-color fluorescence imaging. Based on the established DS-Chip, we investigated the drug sensitivity of single cells by simultaneously monitoring epithelial–mesenchymal transition (EMT) biomarkers and apoptosis in living cells, and verified the correlation between EMT gradients and drug sensitivity. Using the new approach, we further tested the optimal drug response dose in individual CTCs isolated from 5 cancer patients through fluorescence analysis of EMT and apoptosis. The DS-Chip allows noninvasive and real-time measurements of the drug sensitivity of a patient's tumor cells during therapy. This developed approach has practical significance and can effectively guide drug selection and therapeutic evaluation for personalized medicine.

Due to the heterogeneous and variable drug sensitivity of tumor cells, real-time monitoring of a patient's drug response is desirable for implementing personalized and dynamic therapy.

Nanoliter-Scale Droplet-Droplet Microfluidic Microextraction Coupled with MALDI-TOF Mass Spectrometry for Metabolite Analysis of Cell Droplets

The further miniaturization of liquid-phase microextraction (LPME) systems has important significance and major challenges for microscale sample analysis. Herein, we developed a rapid and flexible droplet-droplet microfluidic microextraction approach to perform nanoliter-scale miniaturized sample pretreatment, by combining droplet-based microfluidics, robotic liquid handling, and LPME techniques. Differing from the previous microextraction methods, both the extractant and sample volumes were decreased from the microliter scale or even milliliter scale to the nanoliter scale. We utilized the ability of a liquid-handling robot to manipulate nanoliter-scale droplets and micrometer-scale positioning to overcome the scaling effect difficulties in performing liquid-liquid extraction of nanoliter-volume samples in microsystems. Two microextraction modes, droplet-in-droplet microfluidic microextraction and droplet-on-droplet microfluidic microextraction, were developed according to the different solubility properties of the extractants. Various factors affecting the microextraction process were investigated, including the extraction time, recovery method of the extractant droplet, static and dynamic extraction mode, and cross-contamination. To demonstrate the validity and adaptability of the pretreatment and analysis of droplet samples with complex matrices, the present microextraction system coupled with MALDI-TOF mass spectrometry (MS) detection was applied to the quantitative determination of 7-ethyl-10-hydroxylcamptothecin (SN-38), an active metabolite of the anticancer drug irinotecan, in 800-nL droplets containing HepG2 cells. A linear relationship (y = 0.0305x + 0.376, R² = 0.984) was obtained in the range of 4-100 ng/mL, with the limits of detection and quantitation being 2.2 and 4.5 ng/mL for SN-38, respectively.

Machine learning-aided quantification of antibody-based cancer immunotherapy by natural killer cells in microfluidic droplets

Natural killer (NK) cells have emerged as an effective alternative option to T cell-based immunotherapies, particularly against liquid (hematologic) tumors. However, the effectiveness of NK cell therapy has been less than optimal for solid tumors, partly due to the heterogeneity in target interaction leading to variable anti-tumor cytotoxicity. This paper describes a microfluidic droplet-based cytotoxicity assay for quantitative comparison of immunotherapeutic NK-92 cell interaction with various types of target cells. Machine learning algorithms were developed to assess the dynamics of individual effector-target cell pair conjugation and target death in droplets in a semi-automated manner. Our results showed that while short contacts were sufficient to induce potent killing of hematological cancer cells, long-lasting stable conjugation with NK-92 cells was unable to kill HER2+ solid tumor cells (SKOV3, SKBR3) significantly. NK-92 cells that were engineered to express FcγRIII (CD16) mediated antibody-dependent cellular cytotoxicity (ADCC) selectively against HER2+ cells upon addition of Herceptin (trastuzumab). The requirement of CD16, Herceptin and specific pre-incubation temperature served as three inputs to generate a molecular logic function with HER2+ cell death as the output. Mass proteomic analysis of the two effector cell lines suggested differential changes in adhesion, exocytosis, metabolism, transport and activation of upstream regulators and cytotoxicity mediators, which can be utilized to regulate specific functionalities of NK-92 cells in future. These results suggest that this semi-automated single cell assay can reveal the variability and functional potency of NK cells and may be used to optimize immunotherapeutic efficacy for preclinical analyses.

Detection of Small Subsets of CD4+ Lymphocytes with SmartFlare Nanoprobes

SmartFlare technology allows detection of mRNA in single living cells. We studied the possibility of using SmartFlare nanoprobes for detection of small subsets of CD4⁺ lymphocytes. It was found that SmartFlare allows detection of transcriptional master regulators of major CD4⁺T helper subsets in living human lymphocytes. Nanoprobes labeled with Cy5 fluorophore were better detected by flow cytometry than nanoprobes labeled with Cy3. Appropriate time of lymphocyte incubation with SmartFlare probes was 24 h.

Dendronized fluorosurfactant for highly stable water-in-fluorinated oil emulsions with minimal inter-droplet transfer of small molecules

Fluorosurfactant-stabilized microfluidic droplets are widely used as pico- to nanoliter volume reactors in chemistry and biology. However, current surfactants cannot completely prevent inter-droplet transfer of small organic molecules encapsulated or produced inside the droplets. In addition, the microdroplets typically coalesce at temperatures higher than 80 °C. Therefore, the use of droplet-based platforms for ultrahigh-throughput combination drug screening and polymerase chain reaction (PCR)-based rare mutation detection has been limited. Here, we provide insights into designing surfactants that form robust microdroplets with improved stability and resistance to inter-droplet transfer. We used a panel of dendritic oligo-glycerol-based surfactants to demonstrate that a high degree of inter- and intramolecular hydrogen bonding, as well as the dendritic architecture, contribute to high droplet stability in PCR thermal cycling and minimize inter-droplet transfer of the water-soluble fluorescent dye sodium fluorescein salt and the drug doxycycline.

Microdroplets are used as chemical and biological reactors; however, stability and inter-droplet transfer are major issues. Here, the authors report on the development of dendritic glycerol-based surfactants for the creation of stable microdroplets and demonstrate application for PCR, minimal emulsion, and cell encapsulation.

Recent advances in microfluidic platforms for single-cell analysis in cancer biology, diagnosis and therapy

Understanding molecular, cellular, genetic and functional heterogeneity of tumors at the single-cell level has become a major challenge for cancer research. The microfluidic technique has emerged as an important tool that offers advantages in analyzing single-cells with the capability to integrate time-consuming and labour-intensive experimental procedures such as single-cell capture into a single microdevice at ease and in a high-throughput fashion. Single-cell manipulation and analysis can be implemented within a multi-functional microfluidic device for various applications in cancer research. Here, we present recent advances of microfluidic devices for single-cell analysis pertaining to cancer biology, diagnostics, and therapeutics. We first concisely introduce various microfluidic platforms used for single-cell analysis, followed with different microfluidic techniques for single-cell manipulation. Then, we highlight their various applications in cancer research, with an emphasis on cancer biology, diagnosis, and therapy. Current limitations and prospective trends of microfluidic single-cell analysis are discussed at the end.

Coupling Microfluidic Platforms, Microfabrication, and Tissue Engineered Scaffolds to Investigate Tumor Cells Mechanobiology

The tumor microenvironment (TME) is composed of dynamic and complex networks composed of matrix substrates, extracellular matrix (ECM), non-malignant cells, and tumor cells. The TME is in constant evolution during the disease progression, most notably through gradual stiffening of the stroma. Within the tumor, increased ECM stiffness drives tumor growth and metastatic events. However, classic in vitro strategies to study the TME in cancer lack the complexity to fully replicate the TME. The quest to understand how the mechanical, geometrical, and biochemical environment of cells impacts their behavior and fate has been a major force driving the recent development of new technologies in cell biology research. Despite rapid advances in this field, many challenges remain in order to bridge the gap between the classical culture dish and the biological reality of actual tissue. Microfabrication coupled with microfluidic approaches aim to engineer the actual complexity of the TME. Moreover, TME bioengineering allows artificial modulations with single or multiple cues to study different phenomena occurring in vivo. Some innovative cutting-edge tools and new microfluidic approaches could have an important impact on the fields of biology and medicine by bringing deeper understanding of the TME, cell behavior, and drug effects.

Microdroplets-on-chip: A review

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

On-chip anticancer drug screening - Recent progress in microfluidic platforms to address challenges in chemotherapy

There is an increasing need for advanced and inexpensive preclinical models to accelerate the development of anticancer drugs. While costly animal models fail to predict human clinical outcomes, in vitro models such as microfluidic chips ('tumor-on-chip') are showing tremendous promise at predicting and providing meaningful preclinical drug screening outcomes. Research on 'tumor-on-chips' has grown enormously worldwide and is being widely accepted by pharmaceutical companies as a drug development tool. In light of this shift in philosophy, it is important to review the recent literature on microfluidic devices to determine how rapidly the technology has progressed as a promising model for drug screening and aiding cancer therapy. We review the past five years of successful developments and capabilities in microdevice technology (cancer models) for use in anticancer drug screening. Microfluidic devices that are being designed to address current challenges in chemotherapy, such as drug resistance, combinatorial drug therapy, personalized medicine, and cancer metastasis are also reviewed in detail. We provide a perspective on how personalized 'tumor-on-chip', as well as high-throughput microfluidic platforms based on patient-specific tumor cells, can potentially replace the more expensive and 'non-human' animal models in preclinical anticancer drug development.

Application of microfluidic chip technology in pharmaceutical analysis: A review

The development of pharmaceutical analytical methods represents one of the most significant aspects of drug development. Recent advances in microfabrication and microfluidics could provide new approaches for drug analysis, including drug screening, active testing and the study of metabolism. Microfluidic chip technologies, such as lab-on-a-chip technology, three-dimensional (3D) cell culture, organs-on-chip and droplet techniques, have all been developed rapidly. Microfluidic chips coupled with various kinds of detection techniques are suitable for the high-throughput screening, detection and mechanistic study of drugs. This review highlights the latest (2010–2018) microfluidic technology for drug analysis and discusses the potential future development in this field.

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

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

Static droplet array for culturing single live adherent cells in an isolated chemical microenvironment

We present here a new method to easily and reliably generate an array of hundreds of dispersed nanoliter-volume semi-droplets for single-cells culture and analysis. The liquid segmentation step occurs directly in indexed traps by a tweezer-like mechanism and is stabilized by spatial confinement. Unlike common droplet-based techniques, the semi-droplet wets its surrounding trap walls thus supporting the culturing of both adherent and non-adherent cells. To eliminate cross-droplet cell migration and chemical cross-talk each semi-droplet is separated from a nearby trap by an ∼80 pL air plug. The overall setup and injection procedure takes less than 10 minutes, is insensitive to fabrication defects and supports cell recovery for downstream analysis. The method offers a new approach to easily capture, image and culture single cells in a chemically isolated microenvironment as a preliminary step towards high-throughput single-cell assays.

Microfluidic Devices for Drug Delivery Systems and Drug Screening

Microfluidic devices present unique advantages for the development of efficient drug carrier particles, cell-free protein synthesis systems, and rapid techniques for direct drug screening. Compared to bulk methods, by efficiently controlling the geometries of the fabricated chip and the flow rates of multiphase fluids, microfluidic technology enables the generation of highly stable, uniform, monodispersed particles with higher encapsulation efficiency. Since the existing preclinical models are inefficient drug screens for predicting clinical outcomes, microfluidic platforms might offer a more rapid and cost-effective alternative. Compared to 2D cell culture systems and in vivo animal models, microfluidic 3D platforms mimic the in vivo cell systems in a simple, inexpensive manner, which allows high throughput and multiplexed drug screening at the cell, organ, and whole-body levels. In this review, the generation of appropriate drug or gene carriers including different particle types using different configurations of microfluidic devices is highlighted. Additionally, this paper discusses the emergence of fabricated microfluidic cell-free protein synthesis systems for potential use at point of care as well as cell-, organ-, and human-on-a-chip models as smart, sensitive, and reproducible platforms, allowing the investigation of the effects of drugs under conditions imitating the biological system.

Dynamic Analysis of Human Natural Killer Cell Response at Single-Cell Resolution in B-Cell Non-Hodgkin Lymphoma

Natural killer (NK) cells are phenotypically and functionally diverse lymphocytes that recognize and kill cancer cells. The susceptibility of target cancer cells to NK cell-mediated cytotoxicity depends on the strength and balance of regulatory (activating/inhibitory) ligands expressed on target cell surface. We performed gene expression arrays to determine patterns of NK cell ligands associated with B-cell non-Hodgkin lymphoma (b-NHL). Microarray analyses revealed significant upregulation of a multitude of NK-activating and costimulatory ligands across varied b-NHL cell lines and primary lymphoma cells, including ULBP1, CD72, CD48, and SLAMF6. To correlate genetic signatures with functional anti-lymphoma activity, we developed a dynamic and quantitative cytotoxicity assay in an integrated microfluidic droplet generation and docking array. Individual NK cells and target lymphoma cells were co-encapsulated in picoliter-volume droplets to facilitate monitoring of transient cellular interactions and NK cell effector outcomes at single-cell level. We identified significant variability in NK-lymphoma cell contact duration, frequency, and subsequent cytolysis. Death of lymphoma cells undergoing single contact with NK cells occurred faster than cells that made multiple short contacts. NK cells also killed target cells in droplets via contact-independent mechanisms that partially relied on calcium-dependent processes and perforin secretion, but not on cytokines (interferon-γ or tumor necrosis factor-α). We extended this technique to characterize functional heterogeneity in cytolysis of primary cells from b-NHL patients. Tumor cells from two diffuse large B-cell lymphoma patients showed similar contact durations with NK cells; primary Burkitt lymphoma cells made longer contacts and were lysed at later times. We also tested the cytotoxic efficacy of NK-92, a continuously growing NK cell line being investigated as an antitumor therapy, using our droplet-based bioassay. NK-92 cells were found to be more efficient in killing b-NHL cells compared with primary NK cells, requiring shorter contacts for faster killing activity. Taken together, our combined genetic and microfluidic analysis demonstrate b-NHL cell sensitivity to NK cell-based cytotoxicity, which was associated with significant heterogeneity in the dynamic interaction at single-cell level.

A droplet-merging platform for comparative functional analysis of m1 and m2 macrophages in response to e. coli-induced stimuli

Microfluidic droplets are used to isolate cell pairs and prevent crosstalk with neighboring cells, while permitting free motility and interaction within the confined space. Dynamic analysis of cellular heterogeneity in droplets has provided insights in various biological processes. Droplet manipulation methods such as fusion and fission make it possible to precisely regulate the localized environment of a cell in a droplet and deliver reagents as required. Droplet fusion strategies achieved by passive mechanisms preserve cell viability and are easier to fabricate and operate. Here, we present a simple and effective method for the co-encapsulation of polarized M1 and M2 macrophages with Escherichia coli (E. coli) by passive merging in an integrated droplet generation, merging, and docking platform. This approach facilitated live cell profiling of effector immune functions in situ and quantitative functional analysis of macrophage heterogeneity. Biotechnol. Bioeng. 2017;114: 705-709. © 2016 Wiley Periodicals, Inc.

Microfluidic cell isolation technology for drug testing of single tumor cells and their clusters

Drug assays with patient-derived cells such as circulating tumor cells requires manipulating small sample volumes without loss of rare disease-causing cells. Here, we report an effective technology for isolating and analyzing individual tumor cells and their clusters from minute sample volumes using an optimized microfluidic device integrated with pipettes. The method involves using hand pipetting to create an array of cell-laden nanoliter-sized droplets immobilized in a microfluidic device without loss of tumor cells during the pipetting process. Using this technology, we demonstrate single-cell analysis of tumor cell response to the chemotherapy drug doxorubicin. We find that even though individual tumor cells display diverse uptake profiles of the drug, the onset of apoptosis is determined by accumulation of a critical intracellular concentration of doxorubicin. Experiments with clusters of tumor cells compartmentalized in microfluidic drops reveal that cells within a cluster have higher viability than their single-cell counterparts when exposed to doxorubicin. This result suggests that circulating tumor cell clusters might be able to better survive chemotherapy drug treatment. Our technology is a promising tool for understanding tumor cell-drug interactions in patient-derived samples including rare cells.

Droplet-based microtumor model to assess cell-ECM interactions and drug resistance of gastric cancer cells

Gastric cancer (GC) is a common aggressive malignant tumor with high incidence and mortality worldwide. GC is classified into intestinal and diffuse types according to the histo-morphological features. Because of distinctly different clinico-pathological features, new cancer therapy strategies and in vitro preclinical models for the two pathological variants of GC is necessary. Since extracellular matrix (ECM) influence the biological behavior of tumor cells, we hypothesized that GC might be more similarly modeled in 3D with matrix rather than in 2D. Herein, we developed a microfluidic-based a three-dimensional (3D) in vitro gastric cancer model, with subsequent drug resistance assay. AGS (intestinal type) and Hs746T (diffuse type) gastric cancer cell lines were encapsulated in collagen beads with high cellular viability. AGS exhibited an aggregation pattern with expansive growth, whereas Hs746T showed single-cell-level infiltration. Importantly, in microtumor models, epithelial-mesenchymal transition (EMT) and metastatic genes were upregulated, whereas E-cadherin was downregulated. Expression of ß-catenin was decreased in drug-resistant cells, and chemosensitivity toward the anticancer drug (5-FU) was observed in microtumors. These results suggest that in vitro microtumor models may represent a biologically relevant platform for studying gastric cancer cell biology and tumorigenesis, and for accelerating the development of novel therapeutic targets.

Microfluidic Platform for Parallel Single Cell Analysis for Diagnostic Applications

Cell populations are heterogeneous: they can comprise different cell types or even cells at different stages of the cell cycle and/or of biological processes. Furthermore, molecular processes taking place in cells are stochastic in nature. Therefore, cellular analysis must be brought down to the single cell level to get useful insight into biological processes, and to access essential molecular information that would be lost when using a cell population analysis approach. Furthermore, to fully characterize a cell population, ideally, information both at the single cell level and on the whole cell population is required, which calls for analyzing each individual cell in a population in a parallel manner. This single cell level analysis approach is particularly important for diagnostic applications to unravel molecular perturbations at the onset of a disease, to identify biomarkers, and for personalized medicine, not only because of the heterogeneity of the cell sample, but also due to the availability of a reduced amount of cells, or even unique cells. This chapter presents a versatile platform meant for the parallel analysis of individual cells, with a particular focus on diagnostic applications and the analysis of cancer cells. We first describe one essential step of this parallel single cell analysis protocol, which is the trapping of individual cells in dedicated structures. Following this, we report different steps of a whole analytical process, including on-chip cell staining and imaging, cell membrane permeabilization and/or lysis using either chemical or physical means, and retrieval of the cell molecular content in dedicated channels for further analysis. This series of experiments illustrates the versatility of the herein-presented platform and its suitability for various analysis schemes and different analytical purposes.

Microdroplet chain array for cell migration assays

Establishing cell migration assays in multiple different microenvironments is important in the study of tissue repair and regeneration, cancer progression, atherosclerosis, and arthritis. In this work, we developed a miniaturized and massive parallel microfluidic platform for multiple cell migration assays combining the traditional membrane-based cell migration technique and the droplet-based microfluidic technique. Nanoliter-scale droplets are flexibly assembled as building blocks based on a porous membrane to form microdroplet chains with diverse configurations for different assay modes. Multiple operations including in-droplet 2D/3D cell culture, cell co-culture and cell migration induced by a chemoattractant concentration gradient in droplet chains could be flexibly performed with reagent consumption in the nanoliter range for each assay and an assay scale-up to 81 assays in parallel in one microchip. We have applied the present platform to multiple modes of cell migration assays including the accurate cell migration assay, competitive cell migration assay, biomimetic chemotaxis assay, and multifactor cell migration assay based on the organ-on-a-chip concept, for demonstrating its versatility, applicability, and potential in cell migration-related research.

Construction of single-cell arrays and assay of cell drug resistance in an integrated microfluidic platform

The cellular heterogeneity of tumors has played important roles in various tumor-related research areas and applications such as the cellular biology, metastasis and clinical diagnosis of tumors. Although several microfluidics-based single-cell separation and analysis techniques have been used in research into the cellular heterogeneity of tumors, further investigation is still required for studying the effect of the biomechanical (e.g., size and deformability) heterogeneity of cells on their biological characteristics (e.g., drug resistance and tumor-initiating features). Here, we established an integrated microfluidic platform for the construction of single-cell arrays and analysis of drug resistance. Using this device, high-throughput single-cell arrays could be easily obtained according to the biomechanical (size and deformability) heterogeneity of cells. To demonstrate the capability of the microfluidic platform, a proof-of-concept experiment was implemented by determining the vincristine resistance of single glioblastoma cells with different biomechanical properties. The results indicated that the biomechanics of tumor cells had significant implications for cell drug resistance; that is, small and/or more deformable tumor cells had higher drug resistance than large and/or less deformable tumor cells. This device provides a new approach for the isolation of single cells according to the different biomechanical properties of cells. Also, it possesses practical potential for studies of tumors on a single-cell level.

Dynamic analysis of immune and cancer cell interactions at single cell level in microfluidic droplets

Cell-cell communication mediates immune responses to physiological stimuli at local and systemic levels. Intercellular communication occurs via a direct contact between cells as well as by secretory contact-independent mechanisms. However, there are few existing methods that allow quantitative resolution of contact-dependent and independent cellular processes in a rapid, precisely controlled, and dynamic format. This study utilizes a high-throughput microfluidic droplet array platform to analyze cell-cell interaction and effector functions at single cell level. Controlled encapsulation of distinct heterotypic cell pairs was achieved in a single-step cell loading process. Dynamic analysis of dendritic cell (DC)-T cell interactions demonstrated marked heterogeneity in the type of contact and duration. Non-stimulated DCs and T cells interacted less frequently and more transiently while antigen and chemokine-loaded DCs and T cells depicted highly stable interactions in addition to transient and sequential contact. The effector function of CD8⁺ T cells was assessed via cytolysis of multiple myeloma cell line. Variable cell conjugation periods and killing time were detected irrespective of the activation of T cells, although activated T cells delivered significantly higher cytotoxicity. T cell alloreactivity against the target cells was partially mediated by secretion of interferon gamma, which was abrogated by the addition of a neutralizing antibody. These results suggest that the droplet array-based microfluidic platform is a powerful technique for dynamic phenotypic screening and potentially applicable for evaluation of novel cell-based immunotherapeutic agents.

Innovative Tools and Technology for Analysis of Single Cells and Cell-Cell Interaction

Heterogeneity in single-cell responses and intercellular interactions results from complex regulation of cell-intrinsic and environmental factors. Single-cell analysis allows not only detection of individual cellular characteristics but also correlation of genetic content with phenotypic traits in the same cell. Technological advances in micro- and nanofabrication have benefited single-cell analysis by allowing precise control of the localized microenvironment, cell manipulation, and sensitive detection capabilities. Additionally, microscale techniques permit rapid, high-throughput, multiparametric screening that has become essential for -omics research. This review highlights innovative applications of microscale platforms in genetic, proteomic, and metabolic detection in single cells; cell sorting strategies; and heterotypic cell-cell interaction. We discuss key design aspects of single-cell localization and isolation in microfluidic systems, dynamic and endpoint analyses, and approaches that integrate highly multiplexed detection of various intracellular species.