Manipulating Femtoliter to Picoliter Droplets by Pins for Single Cell Analysis and Quantitative Biological Assay

Precise Capture and Dynamic Release of Circulating Liver Cancer Cells with Dual-Histidine-Based Cell Imprinted Hydrogels

Circulating tumor cells (CTCs) detection presents significant advantages in diagnosing liver cancer due to its noninvasiveness, real-time monitoring, and dynamic tracking. However, the clinical application of CTCs-based diagnosis is largely limited by the challenges of capturing low-abundance CTCs within a complex blood environment while ensuring them alive. Here, an ultrastrong ligand, l-histidine-l-histidine (HH), specifically targeting sialylated glycans on the surface of CTCs, is designed. Furthermore, HH is integrated into a cell-imprinted polymer, constructing a hydrogel with precise CTCs imprinting, high elasticity, satisfactory blood compatibility, and robust anti-interference capacities. These features endow the hydrogel with excellent capture efficiency (>95%) for CTCs in peripheral blood, as well as the ability to release CTCs controllably and alive. Clinical tests substantiate the accurate differentiation between liver cancer, cirrhosis, and healthy groups using this method. The remarkable diagnostic accuracy (94%), lossless release of CTCs, material reversibility, and cost-effectiveness ($6.68 per sample) make the HH-based hydrogel a potentially revolutionary technology for liver cancer diagnosis and single-cell analysis.

Microfluidics Coupled Mass Spectrometry for Single Cell Multi-Omics

Population-level analysis masks significant heterogeneity between individual cells, making it difficult to accurately reflect the true intricacies of life activities. Microfluidics is a technique that can manipulate individual cells effectively and is commonly coupled with a variety of analytical methods for single-cell analysis. Single-cell omics provides abundant molecular information at the single-cell level, fundamentally revealing differences in cell types and biological states among cell individuals, leading to a deeper understanding of cellular phenotypes and life activities. Herein, this work summarizes the microfluidic chips designed for single-cell isolation, manipulation, trapping, screening, and sorting, including droplet microfluidic chips, microwell arrays, hydrodynamic microfluidic chips, and microchips with microvalves. This work further reviews the studies on single-cell proteomics, metabolomics, lipidomics, and multi-omics based on microfluidics and mass spectrometry. Finally, the challenges and future application of single-cell multi-omics are discussed.

Microarray fabrication techniques for multiplexed bioassay applications

Microarrays are powerful tools for high-throughput bioassays that can extract information from tens of thousands of micro-spots consisting of biomolecules. This information is invaluable to many applications, such as drug discovery and disease diagnostics. Different applications of these microarrays need spots of different shapes, sizes, and chemistries to achieve their goals. Micro/nano-fabrication techniques are used to make microarrays with different feature structures and array densities for required assay procedures. Understanding these fabrication methods is essential to creating an effective microarray. The purpose of this article is to critically review fabrication methods used in recent microarray-based bioassay studies. We summarized commonly used microarray fabrication techniques and filled the gap in recent literature on relevant topics. We discussed recent examples of how microarrays were fabricated and used in a variety of bioassays. Specifically, we examined microarray printing, various microlithography techniques, and microfluidics-based microarray fabrication. We evaluated how their application shaped the fabrication methods and compared their performance based on different applications. In the end, we discussed current challenges and outlined potential future directions. This review addressed the gap in literature and provided important insights for choosing appropriate fabrication techniques towards different applications.

Visualization of the Dynamics of Photoinduced Crawling Motion of 4-(Methylamino)Azobenzene Crystals via Diffracted X-ray Tracking

The photoinduced crawling motion of crystals is a continuous motion that azobenzene molecular crystals exhibit under light irradiation. Such motion enables object manipulation at the microscale with a simple setup of fixed LED light sources. Transportation of nano-/micromaterials using photoinduced crawling motion has recently been reported. However, the details of the motion mechanism have not been revealed so far. Herein, we report visualization of the dynamics of fine particles in 4-(methylamino)azobenzene (4-MAAB) crystals under light irradiation via diffracted X-ray tracking (DXT). Continuously repeated melting and recrystallization of 4-MAAB crystals under light irradiation results in the flow of liquid 4-MAAB. Zinc oxide (ZnO) particles were introduced inside the 4-MAAB crystals to detect diffracted X-rays. The ZnO particles rotate with the flow of liquid 4-MAAB. By using white X-rays with a wide energy width, the rotation of each zinc oxide nanoparticle was detected as the movement of a bright spot in the X-ray diffraction pattern. It was clearly shown that the ZnO particles rotated increasingly as the irradiation light intensity increased. Furthermore, we also found anisotropy in the rotational direction of ZnO particles that occurred during the crawling motion of 4-MAAB crystals. It has become clear that the flow perpendicular to the supporting film of 4-MAAB crystals is enhanced inside the crystal during the crawling motion. DXT provides a unique means to elucidate the mechanism of photoinduced crawling motion of crystals.

In-depth analysis of biocatalysts by microfluidics: An emerging source of data for machine learning

Nowadays, the vastly increasing demand for novel biotechnological products is supported by the continuous development of biocatalytic applications which provide sustainable green alternatives to chemical processes. The success of a biocatalytic application is critically dependent on how quickly we can identify and characterize enzyme variants fitting the conditions of industrial processes. While miniaturization and parallelization have dramatically increased the throughput of next-generation sequencing systems, the subsequent characterization of the obtained candidates is still a limiting process in identifying the desired biocatalysts. Only a few commercial microfluidic systems for enzyme analysis are currently available, and the transformation of numerous published prototypes into commercial platforms is still to be streamlined. This review presents the state-of-the-art, recent trends, and perspectives in applying microfluidic tools in the functional and structural analysis of biocatalysts. We discuss the advantages and disadvantages of available technologies, their reproducibility and robustness, and readiness for routine laboratory use. We also highlight the unexplored potential of microfluidics to leverage the power of machine learning for biocatalyst development.

Emerging platforms for high-throughput enzymatic bioassays

Enzymes have essential roles in catalyzing biological reactions and maintaining metabolic systems. Many in vitro enzymatic bioassays have been developed for use in industrial and research fields, such as cell biology, enzyme engineering, drug screening, and biofuel production. Of note, many of these require the use of high-throughput platforms. Although the microtiter plate remains the standard for high-throughput enzymatic bioassays, microfluidic arrays and droplet microfluidics represent emerging methods. Each has seen significant advances and offers distinct advantages; however, drawbacks in key performance metrics, including reagent consumption, reaction manipulation, reaction recovery, real-time measurement, concentration gradient range, and multiplexity, remain. Herein, we compare recent high-throughput platforms using the aforementioned metrics as criteria and provide insights into remaining challenges and future research trends.

Non-adhesive contrast substrate for single-cell trapping and Raman spectroscopic analysis

Droplet splitting by exploiting tailored surface wettability is emerging as an important pathway to creating ultralow volumes of samples that can have applications in bioassays, tissue engineering, protein chips, and material synthesis. Reduction of droplet volumes enables the encapsulation of single biological cells which allows high throughput screening. In this work, we demonstrate a facile fabrication approach to create a non-adhesive contrast quartz substrate that allows droplet splitting under gravitational force and its utilization to trap single biological cells for Raman spectroscopic studies. The non-adhesive contrast surface is created by low-power continuous-wave laser-assisted removal of the region of interest from a biocompatible non-adhesive silicone oil grafted quartz substrate. For a given laser spot dimension, the hydrophilic zone dimension is controlled via irradiation with varying laser powers. The fabricated non-adhesive contrast surface can split a microliter droplet into pico- and sub-picolitre daughter droplets. By using the substrate, the trapping of a single polystyrene bead is demonstrated and the recording of Raman spectra is carried out. Additionally, the Raman spectra of two biological cells, yeast cells and human mononuclear cells (MNCs), from a daughter droplet are recorded independently and from a mixture of the solutions. This single-cell Raman analysis could find applications in cell identification and type discrimination, biochemical imaging, metabolic and functional characterization, and clinical and toxicity studies.

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.

The Intriguing Landscape of Single-Cell Protein Analysis

Profiling protein expression at single-cell resolution is essential for fundamental biological research (such as cell differentiation and tumor microenvironmental examination) and clinical precision medicine where only a limited number of primary cells are permitted. With the recent advances in engineering, chemistry, and biology, single-cell protein analysis methods are developed rapidly, which enable high-throughput and multiplexed protein measurements in thousands of individual cells. In combination with single cell RNA sequencing and mass spectrometry, single-cell multi-omics analysis can simultaneously measure multiple modalities including mRNAs, proteins, and metabolites in single cells, and obtain a more comprehensive exploration of cellular signaling processes, such as DNA modifications, chromatin accessibility, protein abundance, and gene perturbation. Here, the recent progress and applications of single-cell protein analysis technologies in the last decade are summarized. Current limitations, challenges, and possible future directions in this field are also discussed.

"Writing biochips": high-resolution droplet-to-droplet manufacturing of analytical platforms

The development of high-resolution molecular printing allows the engineering of analytical platforms enabling applications at the interface between chemistry and biology, i.e. in biosensing, electronics, single-cell biology, and point-of-care diagnostics. Their successful implementation stems from the combination of large area printing at resolutions from sub-100 nm up to macroscale, whilst controlling the composition and volume of the ink, and reconfiguring the deposition features in due course. Similar to handwriting pens, the engineering of continuous writing systems tackles the issue of the tedious ink replenishment between different printing steps. To this aim, this review article provides an unprecedented analysis of the latest continuous printing methods for bioanalytical chemistry, focusing on ink deposition systems based on specific sets of technologies that have been developed to this aim, namely nanofountain probes, microcantilever spotting, capillary-based polymer pens and continuous 3D printing. Each approach will be discussed revealing the most important applications in the fields of biosensors, lab-on-chips and diagnostics.

High-throughput and high-efficiency sample preparation for single-cell proteomics using a nested nanowell chip

Global quantification of protein abundances in single cells could provide direct information on cellular phenotypes and complement transcriptomics measurements. However, single-cell proteomics is still immature and confronts many technical challenges. Herein we describe a nested nanoPOTS (N2) chip to improve protein recovery, operation robustness, and processing throughput for isobaric-labeling-based scProteomics workflow. The N2 chip reduces reaction volume to <30 nL and increases capacity to >240 single cells on a single microchip. The tandem mass tag (TMT) pooling step is simplified by adding a microliter droplet on the nested nanowells to combine labeled single-cell samples. In the analysis of ~100 individual cells from three different cell lines, we demonstrate that the N2 chip-based scProteomics platform can robustly quantify ~1500 proteins and reveal membrane protein markers. Our analyses also reveal low protein abundance variations, suggesting the single-cell proteome profiles are highly stable for the cells cultured under identical conditions.

Automation of single-cell proteomic sample preparation

Molecular heterogeneity exists at different spatial scales in biological samples and is an important parameter in the development of pathologies and resistances to therapies. When aiming to reach molecular heterogeneity of cells at extremely low spatial scales, single-cell analysis can be the ultimate choice. Proteomics performed in bulk population of cells (macroproteomics) is prone to mask molecular heterogeneity. Mass spectrometry-based single cell proteomics (SCP-MS) is the right solution to overcome this issue. Three main problems can be identified using SCP-MS: (i) analytical loss during sample preparation, (ii) inefficient microinjection/delivery of proteins/peptides from samples to MS and (iii) low analytical throughput. Technologies for automation of SCP have recently gained attention to improve methods accuracy, sensitivity, throughput and in-depth and low-biased proteome analysis. In this minireview, we therefore overview the state-of-the-art of automation of SCP-MS sample preparation approaches.

A portable droplet generation system for ultra-wide dynamic range digital PCR based on a vibrating sharp-tip capillary

Monodisperse droplet has been widely used as a versatile tool in different disciplines including biosensing. Existing methods still struggle to balance the droplet generation performance with system simplicity. Here we introduce a novel droplet generation scheme based on the acoustic streaming generated from a vibrating sharp-tip capillary. The unique fluid pattern enables efficient droplet generation without any external pressure sources. This method achieved real-time modulation of droplet size over an ultra-wide range (6.77-661 μm), high throughput (up to 5000 droplets/s), and good monodispersity (<4%) with a power consumption below 60 mW. This method has enabled a multi-volume digital PCR with a dynamic range of ~6 orders of magnitude and multiplexing capability. It has also enabled a simple protocol to produce cell-laden alginate microcapsules in variable sizes with excellent biocompatibility. Overall, the present method combines high performance with small footprint and portability, which will be especially valuable for droplet applications requiring variable droplet size and performed in resource-limited settings.

A flexible and cost-effective manual droplet operation platform for miniaturized cell assays and single cell analysis

Herein, we developed a flexible and cost-effective manual droplet operation system (MDOS) for performing miniaturized cell assays as well as single cell analysis. The MDOS consists of a manual x-y-z translation stage for liquid transferring and switching, a high-precision syringe pump for liquid driving and metering, a tapered capillary probe for droplet manipulation, a droplet array chip for droplet loading and reaction, sample/reagent reservoirs for storage, and a microscope for droplet observation, with a total expense of only $4,000. By using the flexible combination of three elementary operations of the x-y-z stage's moving and the pump's aspirating and depositing, the MDOS can manually achieve multiple droplet handling operations in the nanoliter to picoliter range, including droplet generation, assembling, fusion, diluting, and splitting. On this basis, multiple cell-related operations could be performed, such as nanoliter-scale in-droplet cell culture, cell coculture, drug stimulation, cell washing, and cell staining, as well as formation of picoliter single-cell droplets. The feasibility and flexibility of the MDOS was demonstrated in multi-mode miniaturized cell assays, including cell-based drug test, first-pass effect assay, and single-cell enzyme assay. The MDOS with the features of low cost, easy to build and flexible to use, could provide a promising alternative for performing miniaturized assays in routine laboratories, in addition to conventional microfluidic chip-based systems and automated robot systems.

Nanoliter-scale liquid metering and droplet generation based on a capillary array for high throughput screening

Herein, we developed a simple approach for quantitative metering of nanoliter-scale liquids in parallel based on a capillary array and applied it in high throughput screening protein crystallization conditions. The quantitative metering of liquids was achieved by using capillary force to spontaneously introduce the liquids into short capillaries with fixed length and inner diameter, and the nanoliter-scale droplets were generated by using a pneumatic pump to deliver liquids out from the capillary channels. We adopted measures of sharpening the capillary tips and performing a hydrophobic treatment on the tip surface to significantly reduce the capillary residues during the liquid aspirating and dispensing process, and thus improved the precision to 0.2%-3.5% relative standard deviations (RSD, n = 3) in metering droplets in the range of 280 pL-90 nL. We evaluated the performance of the system in metering liquids of different surface tensions and viscosity. On the basis of this approach, we built a capillary array system with 12 capillaries, by which parallel generation of 12 nL droplets of 12 samples could be achieved in 40 s with a relative standard deviation (RSD) of 1.2%. We applied the system in the screening of lysozyme crystallization conditions of 48 precipitants with 7.5 nL precipitant and 7.5 nL protein solutions in each crystallization droplet reactor, to demonstrate its potentials in large-scale high-throughput screening and analysis with different samples.

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.

Microfluidic Single-Cell Omics Analysis

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

Microfluidics for Biosynthesizing: from Droplets and Vesicles to Artificial Cells

Fabrication of artificial biomimetic materials has attracted abundant attention. As one of the subcategories of biomimetic materials, artificial cells are highly significant for multiple disciplines and their synthesis has been intensively pursued. In order to manufacture robust "alive" artificial cells with high throughput, easy operation, and precise control, flexible microfluidic techniques are widely utilized. Herein, recent advances in microfluidic-based methods for the synthesis of droplets, vesicles, and artificial cells are summarized. First, the advances of droplet fabrication and manipulation on the T-junction, flow-focusing, and coflowing microfluidic devices are discussed. Then, the formation of unicompartmental and multicompartmental vesicles based on microfluidics are summarized. Furthermore, the engineering of droplet-based and vesicle-based artificial cells by microfluidics is also reviewed. Moreover, the artificial cells applied for imitating cell behavior and acting as bioreactors for synthetic biology are highlighted. Finally, the current challenges and future trends in microfluidic-based artificial cells are discussed. This review should be helpful for researchers in the fields of microfluidics, biomaterial fabrication, and synthetic biology.

Concentrating Single Cells in Picoliter Droplets for Phospholipid Profiling on a Microfluidic System

Cellular membranes are composed of a variety of lipids in different amounts and proportions, and alterations of them are usually closely related to various diseases. To reveal the intercellular heterogeneity of the lipid variation, an integrated microfluidic system is designed, which consists of droplet-based inkjet printing, dielectrophoretic electrodes, and de-emulsification interface to achieve on-line single-cell encapsulation, manipulation, and mass spectrometry (MS) detection. This integrated system effectively improves the single-cell encapsulation rate, and meanwhile reduces the matrix interference and continuous oil phase interference to the MS detection. Using this system, the heterogeneities between the normal and cancer cells are compared, and the heterogeneity of the same cells before and after the drug treatment changed obviously, indicating that this system can be used as a promising tool for studying the link between the alterations of lipid homeostasis and various diseases.

Single-cell identification by microfluidic-based in situ extracting and online mass spectrometric analysis of phospholipids expression

This work describes a microfluidic system for in situ extraction of a single-cell and its phosphatidylcholine analysis through mass spectrometry. This approach uncovered cellular heterogeneity among seemingly identical cells and provided a new platform for identification and classification of cells.

Slip-driven microfluidic devices for nucleic acid analysis

Slip-driven microfluidic devices can manipulate fluid by the relative movement of microfluidic plates that are in close contact. Since the demonstration of the first SlipChip device, many slip-driven microfluidic devices with different form factors have been developed, including SlipPAD, SlipDisc, sliding stripe, and volumetric bar chart chip. Slip-driven microfluidic devices can be fabricated from glass, quartz, polydimethylsiloxane, paper, and plastic with various fabrication methods: etching, casting, wax printing, laser cutting, micromilling, injection molding, etc. The slipping operation of the devices can be performed manually, by a micrometer with a base station, or autonomously, by a clockwork mechanism. A variety of readout methods other than fluorescence microscopy have been demonstrated, including both fluorescence detection and colorimetric detection by mobile phones, direct visual detection, and real-time fluorescence imaging. This review will focus on slip-driven microfluidic devices for nucleic acid analysis, including multiplex nucleic acid detection, digital nucleic acid quantification, real-time nucleic acid amplification, and sample-in-answer-out nucleic acid analysis. Slip-driven microfluidic devices present promising approaches for both life science research and clinical molecular diagnostics.

Recent advances in single cell manipulation and biochemical analysis on microfluidics

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

Printing Life-Inspired Subcellular Scale Compartments with Autonomous Molecularly Crowded Confinement

A simple, rapid, and highly controlled platform to prepare life-inspired subcellular scale compartments by inkjet printing has been developed. These compartments consist of fL-scale aqueous droplets (few µm in diameter) incorporating biologically relevant molecular entities with programmed composition and concentration. These droplets are ink-jetted in nL mineral oil drop arrays allowing for lab-on-chip studies by fluorescence microscopy and fluorescence life time imaging. Once formed, fL-droplets are stable for several hours, thus giving the possibility of readily analyze molecular reactions and their kinetics and to verify molecular behavior and intermolecular interactions. Here, this platform is exploited to unravel the behavior of different molecular probes and biomolecular systems (DNA hairpins, enzymatic cascades, protein-ligand couples) within the compartments. The fL-scale size induces the formation of molecularly crowded confined shell structures (hundreds of nanometers in thickness) at the droplet surface, allowing discovery of specific features (e.g., heterogeneity, responsivity to molecular triggers) that are mediated by the intermolecular interactions in these peculiar environments. The presented results indicate the possibility of using this platform for designing nature-inspired confined reactors allowing for a deepened understanding of molecular confinement effects in living subcellular compartments.

Single-cell assay on microfluidic devices

Advances in microfluidic techniques have prompted researchers to study the inherent heterogeneity of single cells in cell populations.