Droplet Microfluidic Platform Research Articles

Open-Channel Droplet Microfluidic Platform for Passive Generation of Human Sperm Microdroplets.

Sperm cryopreservation is important for many individuals across the globe. Recent studies show that vitrification is a valuable approach for maintaining sperm quality after freeze-thawing processes and requires sub-microliter to microliter volumes. A major challenge for the adoption of vitrification in fertility laboratories is the ability to pipette small volumes of sample. Here, we present an open droplet generator that leverages open-channel microfluidics to passively generate sub-microliter to microliter volumes of purified human sperm samples and preserves sperm kinematics. We conclude that our platform is compatible with human sperm, an important foundation for future implementation of vitrification in fertility laboratories.

Mitigation Strategies against Antibody Aggregation Induced by Oleic Acid in Liquid Formulations.

Polysorbates 20 and 80 (PS20 and PS80) are commonly used in the formulations of biologics to protect against interfacial stresses. However, these surfactants can degrade over time, releasing free fatty acids, which assemble into solid particles or liquid droplets. Here, we apply a droplet microfluidic platform to analyze the interactions between antibodies and oleic acid, the primary free fatty acid resulting from the hydrolysis of PS80. We show that antibodies adsorb within seconds to the polar oleic acid-water interface, forming a viscoelastic protein layer that leads to particle formation upon mechanical rupture. By testing two different monoclonal antibodies of pharmaceutical origin, we show that the propensity to form a rigid viscoelastic layer is protein-specific. We further demonstrate that intact PS80 is effective in preventing antibody adsorption at the oleic acid-water interface only at low antibody concentrations and low pH, where oleic acid is fully protonated. Importantly, introduction of the amino acid l-arginine prevents the formation of the interfacial layer and protein particles even at high antibody concentrations (180 mg mL-1). Overall, our findings indicate that oleic acid droplets in antibody formulations can lead to the formation of protein particles via an interface-mediated mechanism. Depending on the conditions, intact PS80 alone might not be sufficient to protect against antibody aggregation. Additional mitigation strategies include the optimization of protein physicochemical properties, pH, and the addition of arginine.

Stepwise Isolation of Diverse Metabolic Cell Populations Using Sorting by Interfacial Tension (SIFT).

We present here a passive and label-free droplet microfluidic platform to sort cells stepwise by lactate and proton secretion from glycolysis. A technology developed in our lab, Sorting by Interfacial Tension (SIFT), sorts droplets containing single cells into two populations based on pH by using interfacial tension. Cellular glycolysis lowers the pH of droplets through proton secretion, enabling passive selection based on interfacial tension and hence single-cell glycolysis. The SIFT technique is expanded here by exploiting the dynamic droplet acidification from surfactant adsorption that leads to a concurrent increase in interfacial tension. This allows multiple microfabricated rails at different downstream positions to isolate cells with distinct glycolytic levels. The device is used to correlate sorted cells with three levels of glycolysis with a conventional surface marker for T-cell activation. As glycolysis is associated with both disease and cell state, this technology facilitates the sorting and analysis of crucial cell subpopulations for applications in oncology, immunology and immunotherapy.

Passive Droplet Microfluidic Platform for High-Throughput Screening of Microbial Proteolytic Activity.

Traditional bacterial isolation methods are often costly, have limited throughput, and may not accurately reflect the true microbial community composition. Consequently, identifying rare or slow-growing taxa becomes challenging. Over the past decade, a new approach has been proposed to replace traditional flasks or multiwell plates with ultrahigh-throughput droplet microfluidic screening assays. In this study, we present a novel passive droplet-based method designed for isolating proteolytic microorganisms, which are crucial in various biotechnology industries. Following the encapsulation of single cells in gelatin microgel compartments and their subsequent clonal cultivation, microcultures are passively sorted at high throughput based on the deformability of droplets. Our novel chip design offers a 50-fold improvement in throughput compared to a previously developed deformability-based droplet sorter. This method expands an array of droplet-based microbial enrichment assays and significantly reduces the time and resources required to isolate proteolytic bacteria strains.

Flexible droplet microfluidic devices for tuneable droplet generation

Droplet microfluidics is a promising technology for applications that require precise handling of minute fluid volumes. This technology has broad applications in the pharmaceutical industry, food and beverage, and material synthesis. Droplet size and frequency are the two key parameters in these applications. Current droplet microfluidic devices are rigid platforms where the geometry and dimensions of microchannels are fixed after the device fabrication. This poses a significant limitation when adjusting the droplet generation characteristics. Repetitive design, fabrication, and testing are often needed to achieve the optimal microchannel dimensions. To overcome this bottleneck, we develop a proof-of-concept stretchable microfluidic device that can control droplet size and generation frequency by precisely controlling the microchannel dimensions in real-time. Theoretical analysis, numerical modelling, and experimental characterisation were conducted to study the influence of device lateral stretching on these characteristics. We found that the lateral stretching of the device increased the droplet diameter and spacing but reduced the droplet generation frequency. Droplet diameter and spacing increased by ∼20 %, and droplet frequency decreased by ∼45 % when the device was strained up to 25 %. We believe this innovative, flexible droplet microfluidic platform will provide an alternative way to precisely control the droplet formation by modifying the channel dimensions on-site and in real-time.

Single-cell multi-modal chromatin profiles revealing epigenetic regulations of cells in hepatocellular carcinoma.

Various epigenetic regulations systematically govern gene expression in cells involving various biological processes. Dysregulation of the epigenome leads to aberrant transcriptional programs and subsequently results in diseases, such as cancer. Therefore, comprehensive profiling epigenomics is essential for exploring the mechanisms underlying gene expression regulation during development and disease. In this study, we developed single-cell chromatin proteins and accessibility tagmentation (scCPA-Tag), a multi-modal single-cell epigenetic profile capturing technique based on barcoded Tn5 transposases and a droplet microfluidics platform. scCPA-Tag enables the simultaneous capture of DNA profiles of histone modification and chromatin accessibility in the same cell. By applying scCPA-Tag to K562 cells and a hepatocellular carcinoma (HCC) sample, we found that the silence of several chromatin-accessible genes can be attributed to lysine-27-trimethylation of the histone H3 tail (H3K27me3) modification. We characterized the epigenetic features of the tumour cells and different immune cell types in the HCC tumour tissue by scCPA-Tag. Besides, a tumour cell subtype (C2) with more aggressive features was identified and characterized by high chromatin accessibility and a lower abundance of H3K27me3 on tumour-promoting genes. Our multi-modal scCPA-Tag provides a comprehensive approach for exploring the epigenetic landscapes of heterogeneous cell types and revealing the mechanisms of gene expression regulation during developmental and pathological processes at the single-cell level. scCPA-Tag offers a highly efficient and high throughput technique to simultaneously profile histone modification and chromatin accessibility within a single cell. scCPA-Tag enables to uncover multiple epigenetic modification features of cellular compositions within tumor tissues. scCPA-Tag facilitates the exploration of the epigenetic landscapes of heterogeneous cell types and provides the mechanisms governing gene expression regulation.

Environmental modulators of algae-bacteria interactions at scale

Interactions between photosynthetic and heterotrophic microbes play a key role in global primary production. Understanding phototroph-heterotroph interactions remains challenging because these microbes reside in chemically complex environments. Here, we leverage a massively parallel droplet microfluidic platform that enables us to interrogate interactions between photosynthetic algae and heterotrophic bacteria in >100,000 communities across ∼525 environmental conditions with varying pH, carbon availability, and phosphorus availability. By developing a statistical framework to dissect interactions in this complex dataset, we reveal that the dependence of algae-bacteria interactions on nutrient availability is strongly modulated by pH and buffering capacity. Furthermore, we show that the chemical identity of the available organic carbon source controls how pH, buffering capacity, and nutrient availability modulate algae-bacteria interactions. Our study reveals the previously underappreciated role of pH in modulating phototroph-heterotroph interactions and provides a framework for thinking about interactions between phototrophs and heterotrophs in more natural contexts.

Advanced Microfluidic Platform for Tumor Spheroid Formation and Cultivation Fabricated from OSTE+ Polymer

In the evolving landscape of cancer research, 3D cell cultures, particularly tumor cell spheroids, are increasingly preferred in drug screening due to their enhanced mimicry of in vivo tumor environments, especially in drug resistance aspects. However, the consistent formation of uniform spheroids and their precise manipulation remain complex challenges. Among various methodologies, droplet microfluidics emerges as a highly effective approach for tumor spheroid formation. This paper introduces a novel, multifaceted microfluidic system that streamlines the entire spheroid cultivation process: (i) generating tumor spheroids from cell suspensions within individual droplets, (ii) merging these droplets into a continuous aqueous phase once spheroid formation is complete, and (iii) transferring the spheroids to a specialized cultivation area within the chip, equipped with trapping elements for extended cultivation in perfusion mode. Remarkably, this process requires no hydrogel encapsulation or external handling, as all operations are conducted within the microfluidic chip. Fabricated from the innovative OSTE+ (off-stoichiometry thiol-ene epoxy) polymer, the chip is designed for repeated use. To show its efficacy, we successfully formed spheroids from MCF-7, GAMG, and U87 cell lines in our system and compared them with spheroids prepared by a traditional agarose microwell method. Additionally, our methodology has successfully enabled the in-chip release of spheroids from droplets, followed by their effective trapping for subsequent cultivation, a process we have exemplified with MCF-7 spheroids. To our knowledge, this research represents the first instance of a fully integrated droplet microfluidic platform achieving scaffoldless tumor spheroid formation and handling. Our method holds promise for improving high-throughput, automated procedures in the formation, transfer, and cultivation of tumor cell spheroids.Graphical abstract

Optimization of a tunable process for rapid production of calcium phosphate microparticles using a droplet-based microfluidic platform.

Calcium phosphate (CaP) biomaterials are amongst the most widely used synthetic bone graft substitutes, owing to their chemical similarities to the mineral part of bone matrix and off-the-shelf availability. However, their ability to regenerate bone in critical-sized bone defects has remained inferior to the gold standard autologous bone. Hence, there is a need for methods that can be employed to efficiently produce CaPs with different properties, enabling the screening and consequent fine-tuning of the properties of CaPs towards effective bone regeneration. To this end, we propose the use of droplet microfluidics for rapid production of a variety of CaP microparticles. Particularly, this study aims to optimize the steps of a droplet microfluidic-based production process, including droplet generation, in-droplet CaP synthesis, purification and sintering, in order to obtain a library of CaP microparticles with fine-tuned properties. The results showed that size-controlled, monodisperse water-in-oil microdroplets containing calcium- and phosphate-rich solutions can be produced using a flow-focusing droplet-generator microfluidic chip. We optimized synthesis protocols based on in-droplet mineralization to obtain a range of CaP microparticles without and with inorganic additives. This was achieved by adjusting synthesis parameters, such as precursor concentration, pH value, and aging time, and applying heat treatment. In addition, our results indicated that the synthesis and fabrication parameters of CaPs in this method can alter the microstructure and the degradation behavior of CaPs. Overall, the results highlight the potential of the droplet microfluidic platform for engineering CaP microparticle biomaterials with fine-tuned properties.

Microfluidic Approach to Resolve Simultaneous and Sequential Cytokine Secretion of Individual Polyfunctional Cells.

Infections, autoimmune diseases, desired and adverse immunological responses to treatment can lead to a complex and dynamic cytokine response in vivo. This response involves numerous immune cells secreting various cytokines to orchestrate the immune reaction. However, the secretion dynamics, amounts, and co-occurrence of the different cytokines by various cell subtypes remain poorly understood due to a lack of appropriate tools to study them. Here, we describe a protocol using a microfluidic droplet platform that allows the time-resolved quantitative measurement of secretion dynamics for several cytokines in parallel on the single-cell level. This is enabled by the encapsulation of individual cells into microfluidic droplets together with a multiplexed immunoassay for parallel quantification of cytokine concentrations, their immobilization for dynamic fluorescent imaging, and the analysis of the respective images to derive secreted quantities and dynamics. The protocol describes the preparation of functionalized magnetic nanoparticles, calibration experiments, cell preparation, and the encapsulation of the cells and nanoparticles into droplets for fluorescent imaging and subsequent image and data analysis using the example of lipopolysaccharide-stimulated human peripheral blood mononuclear cells. The presented platform identified distinct cytokine secretion behavior for single and co-secreting cells, characterizing the expected phenotypic heterogeneity in the measured cell sample. Furthermore, the modular nature of the assay allows its adaptation and application to study a variety of proteins, cytokines, and cell samples, potentially leading to a deeper understanding of the interplay between different immune cell types and the role of the different cytokines secreted dynamically to shape the tightly regulated immune response. These new insights could be particularly interesting in the studies of immune dysregulations or in identifying target populations in therapy and drug development.

Droplet microfluidic platform for extracellular vesicle isolation based on magnetic bead handling

Extracellular vesicles (EVs) are rapidly gaining in popularity as biomarkers of various diseases, acting as cargoes of valuable information from the cell of origin. Despite their important value, their current use in clinical practice is still limited. One of the most limiting factors is their isolation. In fact, conventional approaches are characterized by low purity and throughput, or poor reproducibility. Here, we present a droplet microfluidic platform specifically developed for EV isolation by affinity capture with magnetic beads. This platform is capable of processing large sample volumes (2 mL) in a relatively short time (4.5 hours), with considerable automation. In detail, EVs and magnetic beads are co-encapsulated within the same droplet, which acts promoting their mixing due to the spontaneous recirculation; this continuous agitation prevents any loss usually caused by bead sedimentation and promotes the EV capturing. Our droplet microfluidic protocol is compared to a commercially available method, showing a shorter required incubation time (about 2.5 times) and a higher capture efficiency (2.5-folds). The microfluidic approach is therefore positively evaluated in terms of protein content, EV quantification and microRNA cargo analysis.

XPORT ENTRAP: A droplet microfluidic platform for enhanced DNA transfer between microbial species

A significant hurdle for the widespread implementation and use of synthetic biology is the challenge of highly efficient introduction of DNA into microorganisms. This is especially a barrier for the utilization of non-model organisms and/or novel chassis species for a variety of applications, ranging from molecular biology to biotechnology and biomanufacturing applications. Common approaches to episomal and chromosomal gene editing, which employ techniques such as chemical competence and electroporation, are typically only amenable to a small subset of microbial species while leaving the vast majority of microorganisms in nature genetically inaccessible. To address this challenge, we have employed the previously described B. subtilis broad-host conjugation strain, XPORT, which was modularly designed for loading DNA cargo and conjugating such DNA into recalcitrant microbes. In this current work, we have leveraged and adapted the XPORT strain for use in a droplet microfluidic platform to enable increased efficiency of conjugation-based DNA transfer. The system named DNA ENTRAP (DNA ENhanced TRAnsfer Platform) utilizes cell-encapsulated water-in-oil emulsion droplets as pico-liter-volume bioreactors that allows controlled contacts between the donor and receiver cells within the emulsion bioreactor. This allowed enhanced XPORT-mediated genetic transfer over the current benchtop XPORT process, demonstrated using two different Bacillus subtilis strains (donor and receiver), as well as increased throughput (e.g., number of successfully conjugated cells) due to the automated assay steps inherent to microfluidic lab-on-a-chip systems. DNA ENTRAP paves the way for a streamlined automation of culturing and XPORT-mediated genetic transfer processes as well as future high-throughput cell engineering and screening applications.

Pan-Cancer Single-Nucleus Total RNA Sequencing Using snHH-Seq.

Tumor heterogeneity and its drivers impair tumor progression and cancer therapy. Single-cell RNA sequencing is used to investigate the heterogeneity of tumor ecosystems. However, most methods of scRNA-seq amplify the termini of polyadenylated transcripts, making it challenging to perform total RNA analysis and somatic mutation analysis.Therefore, a high-throughput and high-sensitivity method called snHH-seq is developed, which combines random primers and a preindex strategy in the droplet microfluidic platform. This innovative method allows for the detection of total RNA in single nuclei from clinically frozen samples. A robust pipeline to facilitate the analysis of full-length RNA-seq data is also established. snHH-seq is applied to more than 730000 single nuclei from 32 patients with various tumor types. The pan-cancer study enables it to comprehensively profile data on the tumor transcriptome, including expression levels, mutations, splicing patterns, clone dynamics, etc. New malignant cell subclusters and exploring their specific function across cancers are identified. Furthermore, the malignant status of epithelial cells is investigated among different cancer types with respect to mutation and splicing patterns. The ability to detect full-length RNA at the single-nucleus level provides a powerful tool for studying complex biological systems and has broad implications for understanding tumor pathology.

Ultra-high-throughput screening of Trichoderma reesei strains capable of carbon catabolite repression release and cellulase hyper-production using a microfluidic droplet platform.

Trichoderma reesei is the most well-known cellulase producer in the biorefinery industry. Its cellulase biosynthesis is repressed by glucose via carbon catabolite repression (CCR), making CCR-releasing strains with cellulase hyper-production desirable. Here, we employed a microfluidic droplet platform to culture and screen T. reesei mutants capable of CCR release and cellulase overproduction from extensive mutagenesis libraries. With three mutagenesis rounds, about 6.20×103 droplets were sorted from a population of 1.51×106 droplets in a period of 4.4 h; 76 recovery mutants were screened on flask fermentation, and two glucose uptake retarded mutants, MG-9-3 and MG-9-3-30, were eventually isolated. We also generated a hyper-cellulase producer, M-5, with CCR release via a single mutagenesis round. The hyphal morphology and molecular mechanisms in the mutants were analyzed. This versatile approach combined with a comprehensive understanding of CCR release mechanisms will provide innovative and effective strategies for low-cost cellulase production.

Droplet microfluidic technologies for next-generation high-throughput screening

Droplet microfluidics has evolved into a promising platform for high-throughput screening (HTS), allowing for rapid and precise analysis of thousands of samples encapsulated within droplets. Droplet microfluidic platform offers versatility, high-throughput, and the ability to compartmentalize reactions for a wide range of applications including pharmaceutics, cell analysis, and combinatorial chemical analysis. While droplet-based microfluidics has made considerable advances in automating basic laboratory tasks, for instance, manipulation, storage, and analysis, there has been comparatively little advancement toward HTS applications. The complexity of the technology, the lack of standardization, and the challenges associated with screening large numbers of samples are all factors that have contributed to the limited adoption of droplet-based microfluidics in HTS. In this perspective, we provide a comprehensive overview of the progress of droplet microfluidics as a potential platform for next-generation HTS, specifically in the domain of droplet separation and library generation. We hope that this perspective will inspire further research in relevant academic fields and contribute to the development of innovative HTS strategies based on droplet microfluidic technologies.

Microfluidically-generated Encapsulated Spheroids (μ-GELS): An All-Aqueous Droplet Microfluidics Platform for Multicellular Spheroids Generation.

Spheroids are three-dimensional clusters of cells that serve as in vitro tumor models to recapitulate in vivo morphology. A limitation of many existing on-chip platforms for spheroid formation is the use of cytotoxic organic solvents as the continuous phase in droplet generation processes. All-aqueous methods do not contain cytotoxic organic solvents but have so far been unable to achieve complete hydrogel gelation on chip. Here, we describe an enhanced droplet microfluidic platform that achieves on-chip gelation of all-aqueous hydrogel multicellular spheroids (MCSs). Specifically, we generate dextran-alginate droplets containing MCF-7 breast cancer cells, surrounded by polyethylene glycol, at a flow-focusing junction. Droplets then travel to a second flow-focusing junction where they interact with calcium chloride and gel on chip to form hydrogel MCSs. On-chip gelation of the MCSs is possible here because of an embedded capillary at the second junction that delays the droplet gelation, which prevents channel clogging problems that would otherwise exist. In drug-free experiments, we demonstrate that MCSs remain viable for 6 days. We also confirm the applicability of this system for cancer drug testing by observing that dose-dependent cell death is achievable using doxorubicin.

A home-made pipette droplet microfluidics rapid prototyping and training kit for digital PCR, microorganism/cell encapsulation and controlled microgel synthesis

Droplet microfluidics offers a platform from which new digital molecular assay, disease screening, wound healing and material synthesis technologies have been proposed. However, the current commercial droplet generation, assembly and imaging technologies are too expensive and rigid to permit rapid and broad-range tuning of droplet features/cargoes. This rapid prototyping bottleneck has limited further expansion of its application. Herein, an inexpensive home-made pipette droplet microfluidics kit is introduced. This kit includes elliptical pipette tips that can be fabricated with a simple DIY (Do-It-Yourself) tool, a unique tape-based or 3D printed shallow-center imaging chip that allows rapid monolayer droplet assembly/immobilization and imaging with a smart-phone camera or miniature microscope. The droplets are generated by manual or automatic pipetting without expensive and lab-bound microfluidic pumps. The droplet size and fluid viscosity/surface tension can be varied significantly because of our particular droplet generation, assembly and imaging designs. The versatility of this rapid prototyping kit is demonstrated with three representative applications that can benefit from a droplet microfluidic platform: (1) Droplets as microreactors for PCR reaction with reverse transcription to detect and quantify target RNAs. (2) Droplets as microcompartments for spirulina culturing and the optical color/turbidity changes in droplets with spirulina confirm successful photosynthetic culturing. (3) Droplets as templates/molds for controlled synthesis of gold-capped polyacrylamide/gold composite Janus microgels. The easily fabricated and user-friendly portable kit is hence ideally suited for design, training and educational labs.

Simple droplet microfluidics platform for drug screening on cancer spheroids.

3D in vitro biological systems are progressively replacing 2D systems to increase the physiological relevance of cellular studies. Microfluidics-based approaches can be powerful tools towards such biomimetic systems, but often require high-end complicated and expensive processes and equipment for microfabrication. Herein, a drug screening platform is proposed, minimizing technicality and manufacturing steps. It provides an alternate way of spheroid generation in droplets in tubes. Droplet microfluidics then elicit multiple droplets merging events at programmable times, to submit sequentially the spheroids to chemotherapy and to reagents for cytotoxicity screening. After a comprehensive study of tumorogenesis within the droplets, the system is validated for drug screening (IC50) with chemotherapies in cancer cell lines as well as cells from a patient-derived-xenografts (PDX). As compared to microtiter plates methods, our system reduces the initial number of cells up to 10 times and opens new avenues towards primary tumors drug screening approaches.

Biomolecular condensate phase diagrams with a combinatorial microdroplet platform

The assembly of biomolecules into condensates is a fundamental process underlying the organisation of the intracellular space and the regulation of many cellular functions. Mapping and characterising phase behaviour of biomolecules is essential to understand the mechanisms of condensate assembly, and to develop therapeutic strategies targeting biomolecular condensate systems. A central concept for characterising phase-separating systems is the phase diagram. Phase diagrams are typically built from numerous individual measurements sampling different parts of the parameter space. However, even when performed in microwell plate format, this process is slow, low throughput and requires significant sample consumption. To address this challenge, we present here a combinatorial droplet microfluidic platform, termed PhaseScan, for rapid and high-resolution acquisition of multidimensional biomolecular phase diagrams. Using this platform, we characterise the phase behaviour of a wide range of systems under a variety of conditions and demonstrate that this approach allows the quantitative characterisation of the effect of small molecules on biomolecular phase transitions.

A Microfluidic Approach for Probing Heterogeneity in Cytotoxic T-Cells by Cell Pairing in Hydrogel Droplets.

Cytotoxic T-cells (CTLs) exhibit strong effector functions to leverage antigen-specific anti-tumoral and anti-viral immunity. When naïve CTLs are activated by antigen-presenting cells (APCs) they display various levels of functional heterogeneity. To investigate this, we developed a single-cell droplet microfluidics platform that allows for deciphering single CTL activation profiles by multi-parameter analysis. We identified and correlated functional heterogeneity based on secretion profiles of IFNγ, TNFα, IL-2, and CD69 and CD25 surface marker expression levels. Furthermore, we strengthened our approach by incorporating low-melting agarose to encapsulate pairs of single CTLs and artificial APCs in hydrogel droplets, thereby preserving spatial information over cell pairs. This approach provides a robust tool for high-throughput and single-cell analysis of CTLs compatible with flow cytometry for subsequent analysis and sorting. The ability to score CTL quality, combined with various potential downstream analyses, could pave the way for the selection of potent CTLs for cell-based therapeutic strategies.