Microfluidic Biochips for Single-Cell Isolation and Single-Cell Analysis of Multiomics and Exosomes

Exosome: an overview on enhanced biogenesis by small molecules

Exosomes are extracellular vesicles that received attention for their potential use in the treatment of various injuries. They communicate intercellularly by transferring genetic and bioactive molecules from parent cells. Although exosomes hold immense promise for treating neurodegenerative and oncological diseases, their actual clinical use is very limited because of their biogenesis and secretion. Recent studies have shown that small molecules can significantly enhance exosome biogenesis, thereby remarkably improving yield, functionality, and therapeutic effects. These molecules modulate critical pathways toward optimum exosome production in a mode that is either ESCRT dependent or ESCRT independent. Improved exosome biogenesis may provide new avenues for targeted cancer therapy, neuroprotection in neurodegenerative diseases, and regenerative medicine in wound healing. This review explores the role of small molecules in enhancing exosome biogenesis and secretion, highlights their underlying mechanisms, and discusses emerging clinical applications. By addressing current challenges and focusing on translational opportunities, this study provides a foundation for advancing cell-free therapies in regenerative medicine and beyond.

Elevating single-particle encapsulation in droplet microfluidics by utilizing surface acoustic wave and flow control

Target particle encapsulation is crucial in droplet microfluidics for high-throughput applications like single-cell sequencing and drug screening. However, it faces limitations, with encapsulation rates of only 10% to 30% due to suspension density and the inherent functionality of the chip being restricted by the Poisson distribution. This leads to reagent waste and reduced effectiveness in applications requiring ultra-high multiplexing or extensive particle analysis, due to the massive empty droplets. Here we propose a droplet microfluidic system integrating surface acoustic wave (SAW) and sheath flow control. Suspensions of varying concentrations within the channel are initially pre-focused by sheath fluid, and then acoustically focused into a linear arrangement by SAW. Spacing between particles can be regulated by modulating the sheath fluid, ensuring sequential encapsulation of cells or beads in individual droplets. Thermal shock generated by the SAW, particle and droplet frequency, and particle encapsulation ratio are all elaborately evaluated. The results demonstrate that our system reaches an exciting single-bead packing efficiency of up to 78%, and achieves a packing rate of more than 60% for both high and low concentrations of solutions for polystyrene microspheres, magnetic beads and H22 cells, 6 times higher than the theoretical upper limit of the conventional method and 1.8 times higher than the Poisson distribution. More importantly, our system is designed to be free of structural and parametric constraints, which is quite important in future practical application. Thus, our on-chip particle focusing control method and droplet microfluidic system provide great potential in biological applications needing a high single-particle encapsulation ratio in limited partitions, such as ultra-high multiplex digital biomolecular detection, single-cell analysis, drug screening, and single exosome detection.

An integrated microfluidic chip for synchronous drug loading, separation and detection of plasma exosomes

Exosomes have gained increasing attention as robust, biocompatible carriers for targeted therapy. However, current techniques for exosome drug loading suffer from low drug loading efficiency and substantial exosome loss during repeated purification and quantification processes. Here, we present an integrated microfluidic chip (IMC) that streamlines drug loading, separation, and electrochemical detection of exosomes from plasma in a single device. In this design, the three-dimensional (3D) macroporous scaffold and the magnetoresponsive electrode are successfully assembled into the modeling microchip, playing the functions of "3D chaotic flow mixer", "magnetic separator" and "electrochemical detector". When plasma, doxorubicin (DOX), boron clusters and immunomagnetic nanoprobes (IMPs) are simultaneously injected into the IMC, the exosomes are loaded with DOX-boron cluster (EDB) complexes and synchronously recognized by IMPs in the "3D chaotic flow mixer". Our strategy exhibits high DOX loading efficiency owing to the superchaotropic effect of boron clusters and enhanced immunolabeling efficiency by the thorough mixing of the 3D scaffold. Meanwhile, the novel magnetoresponsive electrode enables magnetic separation and real-time, enzyme-linked immunoelectrochemical quantification of exosomes, thereby simplifying the workflow from drug loading to quantification. The resulting EDB in combination with magnetic hyperthermia achieves up to 90% cell-killing efficiency against DOX-resistant breast cancer cells. Overall, our system could simultaneously realize the enhanced DOX loading into exosomes, efficient magnetic immunoseparation of exosomes, and sensitive electrochemical quantification of exosomes, offering a promising approach for autologous exosome-based drug delivery for cancer treatment.

Isolation Techniques of Micro/Nano-Scaled Species for Biomedical Applications

Isolation of micro/nano-scaled bioparticles, such as circulating tumor cells (CTCs), exosomes, bacteria, white blood cells (WBCs), platelets, and viruses, from the sample is essential for cancer diagnosis and treatment, preventing bacterial infections, and monitoring human health. Numerous separation techniques, including magnetophoresis, dielectrophoresis, acoustophoresis, optophoresis, and fluorescence-activated sorting (FAS) have been developed to isolate the target bioparticles from complex samples accurately. However, these active methods usually rely on sophisticated instruments which are expensive and bulky. Passive platforms with high throughput, low cost, and small volume have gradually become alternative methods. Alongside this context, this review paper is no longer confined to one specific category of isolation techniques, advanced systems that have been developed in recent years are comprehensively introduced. Characteristics and limitations of each technology are discussed according to the critical performance parameters including purity, recovery rate, throughput, resolution, size, and convenience. Specific biomedical applications of separation techniques are summarized to provide practical implications for disease diagnosis, treatment, and mechanism research. This review also addresses the current challenges, potential solutions, and prospects in this field, laying the foundation for further optimization, innovation, and cross-integration of isolation techniques in the future.

A review of the role of CSCs and CSC-EXOs in increasing drug resistance in breast cancer and future applications

Breast cancer (BCa) remains a major global health challenge due to its complex etiology, varied clinical manifestations, and therapy resistance, which contributes to nearly 90 % of cancer-related deaths. A key factor in treatment failure is the presence of BCa stem cells (BCSCs), which drive drug resistance and tumor recurrence. Understanding BCSC formation, regulation, and role in therapeutic resistance is crucial for developing targeted therapies. Additionally, exosomes (EXOs) secreted by BCSCs play a critical role in cancer progression and drug resistance. These vesicles facilitate communication between cancer and stromal cells by transferring RNA and proteins, influencing treatment response. For instance, EXOs from stromal cells can enhance BCa cell survival under chemotherapy and radiation. This study explores BCSC mechanisms, their contribution to drug resistance, and emerging therapeutic strategies. We also examine how BCa-derived and BCSC-derived EXOs promote drug tolerance and tumor growth. Finally, we discuss future treatment approaches, current research limitations, and potential solutions to advance BCa therapy. Novel interventions may overcome resistance and improve patient outcomes by targeting BCSCs and EXO-mediated pathways. However, further research is needed to translate these findings into practical clinical applications.

Emerging Trends in Microfluidic Biomaterials: From Functional Design to Applications

The rapid development of microfluidics has driven innovations in material engineering, particularly through its ability to precisely manipulate fluids and cells at microscopic scales. Microfluidic biomaterials, a cutting-edge interdisciplinary field integrating microfluidic technology with biomaterials science, are revolutionizing biomedical research. This review focuses on the functional design and fabrication of organ-on-a-chip (OoAC) platforms via 3D bioprinting, explores the applications of biomaterials in drug delivery, cell culture, and tissue engineering, and evaluates the potential of microfluidic systems in advancing personalized healthcare. We systematically analyze the evolution of microfluidic materials-from silicon and glass to polymers and paper-and highlight the advantages of 3D bioprinting over traditional fabrication methods. Currently, despite significant advances in microfluidics in medicine, challenges in scalability, stability, and clinical translation remain. The future of microfluidic biomaterials will depend on combining 3D bioprinting with dynamic functional design, developing hybrid strategies that combine traditional molds with bio-printed structures, and using artificial intelligence to monitor drug delivery or tissue response in real time. We believe that interdisciplinary collaborations between materials science, micromachining, and clinical medicine will accelerate the translation of organ-on-a-chip platforms into personalized therapies and high-throughput drug screening tools.

Toward Clarity in Single Extracellular Vesicle Research: Defining the Field and Correcting Missteps

Single extracellular vesicle (EV) research holds the potential to revolutionize our understanding of cellular communication and enable breakthroughs in diagnostics and therapeutics. However, the lack of a clear, consensus-driven definition of single EV research has led to methodological inconsistencies, overgeneralized interpretations, and, in some cases, misleading claims. In this perspective, we propose a framework for defining single EV research, critique current challenges and misconceptions in this field, and discuss its implications for biomedical applications. We argue that precise experimental design, rigorous validation, and interdisciplinary collaboration approaches are needed to establish single EV research as a cornerstone of precision medicine.

[Progress and prospect of separation and analysis of single-cell and single-particle exosomes]

Exosomes are nanoscale vesicles secreted by cells and are encapsulated in lipid bilayers. They play crucial roles in cell communication and are involved in a variety of physiological and pathological processes, including immune regulation, angiogenesis, and tumor initiation and metastasis. Exosomes carry a variety of biomolecules from maternal cells and are therefore important vehicles for discovering disease markers. Traditional detection methods only provide average cell-population information for a given sample and cannot establish clear relationships between the biological functions of exosomes and subtype owing to the significant heterogeneity associated with exosomes from different cell subsets. Therefore, characterizing exosomes at the single-cell and single-particle levels requires exosome specificities to be further explored and the characteristics of various exosome subtypes to be distinguished. Commonly used single-particle exosome characterization technologies include flow cytometry, super-resolution microscopy, atomic force microscopy, surface-enhanced Raman spectroscopy, proximity barcoding assay and MS. In this paper, we summarize recent advances in the separation and characterization of single-cell exosomes based on microfluidics and provide future applications prospects for emerging technologies (such as Olink proteomics, click chemistry, and molecular imprinting) for studying single-cell and single-particle exosomes.

Application of plant-derived extracellular vesicles as novel carriers in drug delivery systems: a review

INTRODUCTION

Plant-derived extracellular vesicles (P-EVs) are nanoscale, lipid bilayer vesicles capable of transporting diverse bioactive substances, enabling intercellular and interspecies communication and material transfer. With inherent pharmacological effects, targeting abilities, high safety, biocompatibility, and low production costs, P-EVs are promising candidates for drug delivery systems, offering significant application potential.

AREAS COVERED

A comprehensive review of studies on P-EVs was conducted through extensive database searches, including PubMed and Web of Science, spanning the years 1959 to 2025. Drawing on animal and cellular model research, this review systematically analyzes the pharmacological activities of P-EVs and their advantages as drug delivery carriers. It also explores P-EVs' drug loading methods, extraction techniques, and application prospects, including their benefits, clinical potential, and feasibility for commercial expansion.

EXPERT OPINION

Establishing unified preparation standards and conducting a more comprehensive analysis of molecular composition, structural characteristics, and mechanisms of P-EVs are essential for their widespread application. Greater attention should be given to the potential synergistic or antagonistic effects between P-EVs as carriers and the drugs they deliver, as this understanding will enhance their practical applications. In conclusion, P-EVs-based drug delivery systems represent a promising strategy to improve treatment efficacy, reduce side effects, and ensure drug stability.

Deep Learning-Enhanced Hand-Driven Microfluidic Chip for Multiplexed Nucleic Acid Detection Based on RPA/CRISPR

The early detection of high-risk human papillomavirus (HR-HPV) is crucial for the assessment and improvement of prognosis in cervical cancer. However, existing PCR-based screening methods suffer from inadequate accessibility, which dampens the enthusiasm for screening among grassroots populations, especially in resource-limited areas, and contributes to the persistently high mortality rate of cervical cancer. Here, a portable system is proposed for multiplexed nucleic acid detection, termed R-CHIP, that integrates Recombinase polymerase amplification (RPA), CRISPR detection, Hand-driven microfluidics, and an artificial Intelligence Platform. The system can go from sample pre-processing to results readout in less than an hour with simple manual operation. Optimized for sensitivity of 10-17 M for HPV-16 and 10-18 M for HPV-18, R-CHIP has an accuracy of over 95% in 300 tests on clinical samples. In addition, a smartphone microimaging system combined with the ResNet-18 deep learning model is used to improve the readout efficiency and convenience of the detection system, with initial prediction accuracies of 96.0% and 98.0% for HPV-16 and HPV-18, respectively. R-CHIP, as a user-friendly and intelligent detection platform, has great potential for community-level HR-HPV screening in resource-constrained settings, and contributes to the prevention and early diagnosis of other diseases.

An effective strategy based on electrostatic interaction for the simultaneous sequential purification and isolation of exosomes

A material-based strategy was developed to achieve the simultaneous purification and isolation of exosomes from serum and urine. Based on the combination of electrostatic interaction and hydrophobic interaction, polyacrylic acid (PAA)-coated anionic nanoparticles (Fe3O4@PAA) were used to remove positively charged contaminant proteins and neutral proteins, and polyethyleneimine (PEI)-functionalized cationic nanoparticles (Fe3O4@PEI) were applied to remove negatively charged contaminant proteins as well as capture and mild release of negatively charged exosome. By employing this strategy (denoted as PAA-PEI), a high recovery (> 95%) of serum exosomes was achieved with a high removal efficiency of protein contaminants (87%). The strategy was further applied to purify and isolate urinary exosomes, followed by downstream proteomics analysis. Compared with the standard isolation method of ultracentrifugation (UC), the PAA-PEI strategy shows high contaminant protein removal efficiency (98.6%) and obtains a higher concentration of exosomes. Using the PAA-PEI strategy, more urinary exosomal proteins (124) than UC (92) were identified. These results indicate that the PAA-PEI strategy is not only excellent in exosome capture but also effectively mitigates the interference of protein contamination. Given that the PAA-PEI strategy demonstrates a high protein contaminant removal efficiency and requires less cost and time (1 h) than UC (3 h), it would be a promising candidate method for efficiently purifying and isolating exosomes from complex biological samples for early discovery and diagnosis diseases. Furthermore, this study provides a new direction for emphasizing the issue of protein interference in the development of biological sample isolation methods.

Lab-on-a-chip device for microfluidic trapping and TIRF imaging of single cells

Total internal reflection fluorescence (TIRF) microscopy is a powerful imaging technique that visualizes the outer surface of specimens in close proximity to a substrate, yielding crucial insights in cell membrane compositions. TIRF plays a key role in single-cell studies but typically requires chemical fixation to ensure direct contact between the cell membrane and substrate, which can compromise cell viability and promote clustering. In this study, we present a microfluidic device with structures designed to trap single yeast cells and fix them in direct contact with the substrate surface to enable TIRF measurements on the cell membrane. The traps are fabricated using two-photon polymerization, allowing high-resolution printing of intricate structures that encapsulate cells in all three dimensions while maintaining exposure to the flow within the device. Our adaptable trap design allows us to reduce residual movement of trapped cells to a minimum while maintaining high trapping efficiencies. We identify the optimal structure configuration to trap single yeast cells and demonstrate that trapping efficiency can be tuned by modifying cell concentration and injection methods. Additionally, by replicating the cell trap design with soft hydrogel materials, we demonstrate the potential of our approach for further single-cell studies. The authors have no relevant financial or non-financial interests to disclose and no competing interests to declare.

Application of Digital Polymerase Chain Reaction (dPCR) in Non-Invasive Prenatal Testing (NIPT)

This article reviews the current applications of the digital polymerase chain reaction (dPCR) in non-invasive prenatal testing (NIPT) and explores its potential to complement or surpass the capabilities of Next-Generation Sequencing (NGS) in prenatal testing. The growing incidence of genetic disorders in maternal-fetal medicine has intensified the demand for precise and accessible NIPT options, which aim to minimize the need for invasive prenatal diagnostic procedures. Cell-free fetal DNA (cffDNA), the core analyte in NIPT, is influenced by numerous factors such as maternal DNA contamination, placental health, and fragment degradation. dPCR, with its inherent precision and ability to detect low-abundance targets, demonstrates robustness against these interferences. Although NGS remains the gold standard due to its comprehensive diagnostic capabilities, its high costs limit widespread use, particularly in resource-limited settings. In contrast, dPCR provides comparable accuracy with lower complexity and expense, making it a promising alternative for prenatal testing.

Single-Cell Array Enhanced Cell Damage Recognition Using Artificial Intelligence for Anticancer Drug Discovery

This work developed a cell damage recognition method based on single-cell arrays using an artificial intelligence tool. The method uses micropatterns (single-cell micropatches and microwells) to isolate each cell in an ordered array to minimize cell overlapping and to maintain cell contours. After exposure to a therapeutic drug (e.g., doxorubicin), a large number of single cells are monitored, and the cell damage levels are determined with both morphology and intensity changes in reactive oxygen species recorded under fluorescence microscopy. The convolutional neural network model is trained by the time-series cancer cell images before and after low and high concentrations of drug exposure. The trained model can identify cancer cell status (live/dead) and classify damage levels (major/moderate/minor) with high accuracy. The single-cell pattern allows cells physically segmented at the single-cell level, which not only eliminates the need for computational cell segmentation but also reduces background noise and neighboring interference, which highly enhances the accuracy of analysis via image recognition. The single-cell array accelerates the computational analysis for toxicity with a trained AI model, which can be used to predict cell damage response for screening potential anticancer drugs.

Multi-Vortex Regulation in a Simple Semicircular Microchannel with Ordered Micro-Obstacles for High-Throughput Buffer Exchange

Microfluidics is an emerging technology for buffer exchange in bioprocessing applications. However, achieving buffer exchange with simplicity of operation and high throughput in a straightforward channel design remains a challenge. This study presents a novel semicircular microchannel design that allows for the deterministic regulation of helical and Dean vortices through geometric confinement. By incorporating micro-obstacles into semicircular microchannels with large dimensions (900 μm wide and 100 μm high), we observe a substantial enhancement in secondary flows, leading to a unique fluid distribution across a wide range of flow rates. This design enables a high particle separation efficiency (>96.27%) coupled with a low fluorescein purity (<4.46%) at a high throughput of 3 × 106 particles/min. The proposed methodology, characterized by ease of production (simple semicircular microchannels with large dimensions), user-friendly operation (uniform flow rates in both sheath and sample inlets), and efficient buffer exchange capabilities (typically 3 mL min-1), demonstrates significant potential for advancing microfluidic systems in biological and biomedical research.

Single-Cell Isolation Chip Integrated with Multicolor Barcode Array for High-Throughput Single-Cell Exosome Profiling in Tissue Samples

Exosomes, functional biomarkers involved in cancer progression, have gained widespread attention for promoting tumor formation, growth, and metastasis. Current bulk exosome detections in bodily fluids enable cancer functional analysis, but average secretion levels from cell populations, losing parent cell information and ignoring exosome heterogeneity from diverse cell subgroups, necessitating an effective platform for analyzing single-cell exosome functional heterogeneity. Here, a high-throughput platform is presented, capable of efficient single-cell isolation and multi-color exosome phenotype analysis, as well as quantifying trace exosomes secreted by single cells. Photothermal-driven single-cell chips achieve significant single-cell isolation efficiency (≈97%) within 5 min, facilitating the ultra-high throughput single-cell exosome analysis. By conducting mass spectrometry and protein interaction of breast cancer exosome phenotypic proteins, key exosome phenotypes are identified. Tens of thousands of single cells from breast cancer cell lines, and clinical tissues are analyzed, revealing various subgroup differences. The study finds more CD44 and EGFR co-expressing exosome subgroups in breast cancer cell lines, while immune-evasion PD-L1 high-phenotype exosome subgroups are primarily presented in complex tumor microenvironments, especially in HER2-positive tissues. This platform offers powerful single-cell isolation, exosome quantification, and phenotypic analysis capabilities, making it a powerful tool for advancing single-cell exosome analysis in cancer research.

A Machine Vision Perspective on Droplet-Based Microfluidics

Microfluidic droplets, with their unique properties and broad applications, are essential in in chemical, biological, and materials synthesis research. Despite the flourishing studies on artificial intelligence-accelerated microfluidics, most research efforts have focused on the upstream design phase of microfluidic systems. Generating user-desired microfluidic droplets still remains laborious, inefficient, and time-consuming. To address the long-standing challenges associated with the accurate and efficient identification, sorting, and analysis of the morphology and generation rate of single and double emulsion droplets, a novel machine vision approach utilizing the deformable detection transformer (DETR) algorithm is proposed. This method enables rapid and precise detection (detection relative error < 4% and precision > 94%) across various scales and scenarios, including real-world and simulated environments. Microfluidic droplets identification and analysis (MDIA), a web-based tool powered by Deformable DETR, which supports transfer learning to enhance accuracy in specific user scenarios is developed. MDIA characterizes droplets by diameter, number, frequency, and other parameters. As more training data are added by other users, MDIA's capability and universality expand, contributing to a comprehensive database for droplet microfluidics. The work highlights the potential of artificial intelligence in advancing microfluidic droplet regulation, fabrication, label-free sorting, and analysis, accelerating biochemical sciences and materials synthesis engineering.

Advancements in the Application of scRNA-Seq in Breast Research: A Review

Single-cell sequencing technology provides apparent advantages in cell population heterogeneity, allowing individuals to better comprehend tissues and organs. Sequencing technology is currently moving beyond the standard transcriptome to the single-cell level, which is likely to bring new insights into the function of breast cells. In this study, we examine the primary cell types involved in breast development, as well as achievements in the study of scRNA-seq in the microenvironment, stressing the finding of novel cell subsets using single-cell approaches and analyzing the problems and solutions to scRNA-seq. Furthermore, we are excited about the field's promising future.

Immuno-Rolling Circle Amplification (Immuno-RCA): Biosensing Strategies, Practical Applications, and Future Perspectives

In the rapidly evolving field of life sciences and biomedicine, detecting low-abundance biomolecules, and ultraweak biosignals presents significant challenges. This has spurred a rapid development of analytical techniques aiming for increased sensitivity and specificity. These advancements, including signal amplification strategies and the integration of biorecognition events, mark a transformative era in bioanalytical precision and accuracy. A prominent method among these innovations is immuno-rolling circle amplification (immuno-RCA) technology, which effectively combines immunoassays with signal amplification via RCA. This process starts when a targeted biomolecule, such as a protein or cell, binds to an immobilized antibody or probe on a substrate. The introduction of a circular DNA template triggers RCA, leading to exponential amplification and significantly enhanced signal intensity, thus the target molecule is detectable and quantifiable even at the single-molecule level. This review provides an overview of the biosensing strategy and extensive practical applications of immuno-RCA in detecting biomarkers. Furthermore, it scrutinizes the limitations inherent to these sensors and sets forth expectations for their future trajectory. This review serves as a valuable reference for advancing immuno-RCA in various domains, such as diagnostics, biomarker discovery, and molecular imaging.

Microfluidic Chip for Cell Fusion and In Situ Separation of Fused Cells

Electrofusion is an effective method for fusing two cells into a hybrid cell, and this method is widely used in immunomedicine, gene recombination, and other related fields. Although cell pairing and electrofusion techniques have been accomplished with microfluidic devices, the purification and isolation of fused cells remains limited due to expensive instruments and complex operations. In this study, through the optimization of microstructures and electrodes combined with buffer substitution, the entire cell electrofusion process, including cell capture, pairing, electrofusion, and precise separation of the targeted fused cells, is achieved on a single chip. The proposed microfluidic cell electrofusion achieves an efficiency of 80.2 ± 7.5%, and targeted cell separation could be conveniently performed through the strategic activation of individual microelectrodes via negative dielectrophoresis, which ensures accurate release of the fused cells with an efficiency of up to 91.1 ± 5.1%. Furthermore, the survival rates of the cells after electrofusion and release are as high as 94.7 ± 0.6% and 91.7 ± 1.2%, respectively. These results demonstrate that the in situ cell electrofusion and separation process did not affect the cell activity. This chip offers integrated multifunctional manipulation of cells in situ, and can be applied to multiple fields in the future, thus laying the foundation for the field of precise single-cell analysis.

Extracellular Vesicles: Diagnostic and Therapeutic Applications in Cancer

In recent years, knowledge of cell-released extracellular vesicle (EV) functions has undergone rapid growth. EVs are membrane vesicles loaded with proteins, nucleic acids, lipids, and bioactive molecules. Once released into the extracellular space, EVs are delivered to target cells that may go through modifications in physiological or pathological conditions. EVs are nano shuttles with a crucial role in promoting short- and long-distance cell-cell communication. Comprehension of the mechanism that regulates this process is a benefit for both medicine and basic science. Currently, EVs attract immense interest in precision and nanomedicine for their potential use in diagnosis, prognosis, and therapies. This review reports the latest advances in EV studies, focusing on the nature and features of EVs and on conventional and emerging methodologies used for their separation, characterization, and visualization. By searching an extended portion of the relevant literature, this work aims to give a summary of advances in nanomedical applications of EVs. Moreover, concerns that require further studies before translation to clinical applications are discussed.