A microfluidic surface-enhanced Raman scattering (SERS) sensor for microRNA in extracellular vesicles with nucleic acid-tyramine cascade amplification

Nucleic acid-mediated SERS Biosensors: Signal enhancement strategies and applications

Surface Enhanced Raman Spectroscopy (SERS) is a powerful spectroscopic analysis technique applied in various fields due to its high selectivity, ultra-high sensitivity, and non-destructiveness. As natural biological macromolecules, nucleic acids perform a significant role in SERS biosensing. In this review, we first summarize how nucleic acids mediate the signal enhancement of SERS biosensors from three aspects: substrate self-assembly, analyte biorecognition, and molecular amplification. Among them, SERS substrates can be self-assembled by both DNA modification and coordination or electrostatic interactions. In the field of biorecognition, analyte biorecognition based on three nucleic acid recognition elements can enhance SERS signals by regulating the distance of analytes or Raman reporter molecules to the SERS substrate. In addition, nucleic acid-based enzyme and enzyme-free amplification can enhance SERS signals by enlarging the quantity of analytes or its nucleic acid intermediates. Subsequently, multidimensional applications of nucleic acid-mediated SERS signal enhancement in biomedicine, food safety, and environmental monitoring are listed. Finally, the current challenges and future exploration of nucleic acid-mediated SERS signal enhancement are discussed.

Enhancing Analysis of Extracellular Vesicles by Microfluidics

Extracellular vesicles (EVs) play crucial roles in intercellular communication and hold great promise as biomarkers for noninvasive disease diagnosis. Intensive research efforts have been devoted to discovering the EV subpopulations responsible for specific functions or with enhanced effectiveness as disease markers, through extensive EV purification and content analysis. However, their high heterogeneity in size and cargo composition poses significant challenges for reaching such goals. Isolation methods like ultracentrifugation and size-exclusion chromatography, as well as content analysis approaches like polymerase chain reaction and enzyme-linked immunosorbent assay, have made significant contributions to improving our understanding of EV biology. Nonetheless, these methods face limitations in isolation efficiency, EV purity, and detection sensitivity and specificity due to issues like large sample consumption, unsatisfactory purity, and insufficient resolution in EV subtyping. Microfluidic technology presents promising solutions to these challenges, leveraging their intrinsic capabilities in precise flow and external energy field manipulation, sample compartmentalization, and signal enhancement at the micro- and nanoscale. Hence, this review summarizes the recent developments in microfluidics-enabled EV analysis, paying special attention to the unique microfluidic features exploited. Strategies such as viscoelastic and inertial flow, fluid mixing, and external-field-assisted approaches in improving EV purification, as well as compartmentalization and micro/nanostructures for enhancing EV detection, are examined. Furthermore, the current limitations and potential future directions are discussed to inspire advancements in this rapidly developing field.

Surface-Enhanced Raman Scattering (SERS) for exosome detection

BACKGROUND

Exosomes, nanoscale extracellular vesicles secreted by various cells, are abundantly present in biological fluids. They have been identified as carriers of specific molecules, suggesting their potential role in early disease detection. However, their clinical application is hindered by several challenges, including the need for large sample volumes for enrichment, limitations of traditional detection methods, and the complexity involved in phenotype analysis and separation.

OBJECTIVE

This review aims to explore the application of Surface-Enhanced Raman Scattering (SERS) technology in exosome detection. SERS, known for its unique photonic properties and high sensitivity, offers a promising solution for detecting exosomes without the need for large sample volumes or extensive phenotypic analysis. This review focuses on the real-time and non-invasive assessment capabilities of SERS in exosome detection, providing insights into its potential for early disease diagnosis.

CONCLUSION

The review concludes by emphasizing the potential of SERS-based exosome detection in advancing early disease diagnosis. By overcoming existing challenges, SERS technology offers a promising approach for the development of sensitive and specific diagnostic assays, contributing to better patient outcomes and personalized medicine.

Raman spectroscopy in extracellular vesicles analysis: Techniques, applications and advancements

Raman spectroscopy provides a robust approach for detailed analysis of the chemical and molecular profiles of extracellular vesicles (EVs). Recent advancements in Raman techniques have significantly enhanced the sensitivity and accuracy of EV characterization, enabling precise detection and profiling of molecular components within EV samples. This review introduces and compares various Raman-based techniques for EV characterization. These include Raman spectroscopy (RS), which provides fundamental molecular information; Raman trapping analysis (RTA), which combines optical trapping with Raman scattering for the manipulation and analysis of individual EVs; surface-enhanced Raman spectroscopy (SERS), which enhances the Raman signal through the use of metallic nanostructures, significantly improving sensitivity; and microfluidic SERS, which integrates SERS with microfluidic platforms to allow high-throughput, label-free analysis of EVs in biological fluids. In addition to comparing various Raman techniques, this review provides a comprehensive analysis that includes comparisons of machine learning methods, EV isolation techniques, and characterization strategies. By integrating these approaches, the review presents a holistic perspective on Raman-based EV analysis, covering profiling, purity, heterogeneity and size analysis as well as imaging. The combined assessment of Raman technologies with advanced computational and experimental methodologies supports the development of more robust diagnostic and therapeutic applications involving EVs.

Recent Advances in Microfluidics for Nucleic Acid Analysis of Small Extracellular Vesicles in Cancer

Small extracellular vesicles (sEVs) are membranous vesicles released from cellular structures through plasma membrane budding. These vesicles contain cellular components such as proteins, lipids, mRNAs, microRNAs, long-noncoding RNA, circular RNA, and double-stranded DNA, originating from the cells they are shed from. Ranging in size from ≈25 to 300 nm and play critical roles in facilitating cell-to-cell communication by transporting signaling molecules. The discovery of sEVs in bodily fluids and their involvement in intercellular communication has revolutionized the fields of diagnosis, prognosis, and treatment, particularly in diseases like cancer. Conventional methods for isolating and analyzing sEVs, particularly their nucleic acid content face challenges including high costs, low purity, time-consuming processes, limited standardization, and inconsistent yield. The development of microfluidic devices, enables improved precision in sorting, isolating, and molecular-level separation using small sample volumes, and offers significant potential for the enhanced detection and monitoring of sEVs associated with cancer. These advanced techniques hold great promise for creating next-generation diagnostic and prognostic tools given their possibility of being cost-effective, simple to operate, etc. This comprehensive review explores the current state of research on microfluidic devices for the detection of sEV-derived nucleic acids as biomarkers and their translation into practical point-of-care and clinical applications.

Recent Advances in Aptamer-Based Microfluidic Biosensors for the Isolation, Signal Amplification and Detection of Exosomes

Exosomes carry diverse tumor-associated molecular information that can reflect real-time tumor progression, making them a promising tool for liquid biopsy. However, traditional methods for exosome isolation and detection often rely on large, expensive equipment and are time-consuming, limiting their practical applicability in clinical settings. Microfluidic technology offers a versatile platform for exosome analysis, with advantages such as seamless integration, portability and reduced sample volumes. Aptamers, which are single-stranded oligonucleotides with high affinity and specificity for target molecules, have been frequently employed in the development of aptamer-based microfluidics for the isolation, signal amplification, and quantitative detection of exosomes. This review summarizes recent advances in aptamer-based microfluidic strategies for exosome analysis, including (1) strategies for on-chip exosome capture mediated by aptamers combined with nanomaterials or nanointerfaces; (2) aptamer-based on-chip signal amplification techniques, such as enzyme-free hybridization chain reaction (HCR), rolling circle amplification (RCA), and DNA machine-assisted amplification; and (3) various aptamer-assisted detection methods, such as fluorescence, electrochemistry, surface-enhanced Raman scattering (SERS), and magnetism. The limitations and advantages of these methods are also summarized. Finally, future challenges and directions for the clinical analysis of exosomes based on aptamer-based microfluidics are discussed.

Surface-Enhanced Raman Scattering (SERS)-based biosensors for advanced extracellular vesicle detection: A review

BACKGROUND

Extracellular Vesicles (EVs), as nano-scale vesicles rich in biological information, hold an indispensable status in the biomedical field. However, due to the intrinsic small size and low abundance of EVs, their effective detection presents significant challenges. Although various EV detection techniques exist, their sensitivity and ease of operation still need enhancement.

RESULTS

Surface-Enhanced Raman Scattering (SERS) is known for its high sensitivity and specificity. It stands out in tackling the challenges that traditional EV detection methods face. In this review, we focus on the application of SERS-based biosensors in EV detection. It provides a detailed introduction to the recognition and capture of EVs, strategies for mediating signal amplification, and detection of EV biomarkers. Finally, the challenges and prospects of SERS-based biosensors are discussed.

SIGNIFICANCE

SERS-based biosensor enhances the Raman signal, allowing for the detection of biomarkers at low concentrations. This capability reveals its substantial potential in identifying EVs and analyzing molecular data. It paves the path for advanced EV detection.

Surface-enhanced Raman scattering-based strategies for tumor markers detection: A review

The presence of malignant tumors poses a significant threat to people's life and well-being. As biochemical parameters indicate the occurrence and development of tumors, tumor markers play a pivotal role in early cancer detection, treatment, prognosis, efficient monitoring, and other aspects. Surface-enhanced Raman scattering (SERS) is considered a potent tool for the detection of tumor markers owing to its exceptional advantages encompassing high sensitivity, superior selectivity, rapid analysis speed, and photobleaching resistance nature. This review aims to provide a comprehensive understanding of SERS applications in the detection of tumor markers. Firstly, we introduce the SERS enhancement mechanism, classification of active substrates, and SERS detection techniques. Secondly, the latest research progress of in vitro SERS detection of different types of tumor markers in body fluids and the application of SERS imaging in biomedical imaging are highlighted in sections of the review. Finally, according to the current status of SERS detection of tumor markers, the challenges and problems of SERS in biomedical detection are discussed, and insights into future developments in SERS are offered.

Integrated SERS-Microfluidic Sensor Based on Nano-Micro Hierarchical Cactus-like Array Substrates for the Early Diagnosis of Prostate Cancer

The detection and analysis of cancer cell exosomes with high sensitivity and precision are pivotal for the early diagnosis and treatment strategies of prostate cancer. To this end, a microfluidic chip, equipped with a cactus-like array substrate (CAS) based on surface-enhanced Raman spectroscopy (SERS) was designed and fabricated for the detection of exosome concentrations in Lymph Node Carcinoma of the Prostate (LNCaP). Double layers of polystyrene (PS) microspheres were self-assembled onto a polyethylene terephthalate (PET) film to form an ordered cactus-like nanoarray for detection and analysis. By combining EpCAM aptamer-labeled SERS nanoprobes and a CD63 aptamer-labeled CAS, a 'sandwich' structure was formed and applied to the microfluidic chips, further enhancing the Raman scattering signal of Raman reporter molecules. The results indicate that the integrated microfluidic sensor exhibits a good linear response within the detection concentration range of 105 particles μL-1 to 1 particle μL-1. The detection limit of exosomes in cancer cells can reach 1 particle μL-1. Therefore, we believed that the CAS integrated microfluidic sensor offers a superior solution for the early diagnosis and therapeutic intervention of prostate cancer.

Versatile Bovine Serum Albumin as Ingenious Electron Operator-Enhanced Photoelectrochemical Biosensing for Ultrasensitive Detection of miRNA

Bovine serum albumin (BSA) has been widely used in biosensors as a blocking agent. Herein, conformist BSA was first exploited as an ingenious operator to enhance the photocurrent response of (2Z,2'Z)-2,2'-(1,4-phenylene)bis(3-(4-(bis(4-methoxyphenyl)amino)phenyl)acrylonitrile) (TPDCN)-based photoelectrochemical (PEC) platform via manipulating the electron transfer process of the detection system. Concretely, the presence of target molecules triggered catalytic hairpin assembly reaction and subsequently powered terminal deoxynucleotidyl transferase-mediated signal amplification to produce the AgNP@BSA-DNA dendrimer nanostructure. After being treated with HNO3, a large amount of BSA could be released from the dendrimer nanostructure. When they were transferred to the TPDCN-based PEC platform, the photocurrent response of the biosensor was largely enhanced because BSA can manipulate the electrons of TPDCN via a well-matched energy level to form a new electron transfer track. Meanwhile, tryptophan (Trp) in BSA could be oxidized to quinone Trp-O under photoirradiation, which can facilitate the oxidation of ascorbate and generate more H+ to promote the migration of photogenerated electrons. As a result, the proposed PEC biosensor exhibits excellent analytical performance for detection of miRNA-21 (as a model target) over a wide linear range of 0.01 to 10,000 pM with detection limit as low as 4.7 fM. Overall, this strategy provides a new perspective on constructing efficient PEC biosensors, which expands the potential applications in bioanalysis and clinical diagnosis.

Tailoring strategies of SERS tags-based sensors for cellular molecules detection and imaging

As an emerging nanoprobe, surface enhanced Raman scattering (SERS) tags hold significant promise in sensing and bioimaging applications due to their attractive merits of anti-photobleaching ability, high sensitivity and specificity, multiplex, and low background capabilities. Recently, several reviews have proposed the application of SERS tags in different fields, however, the specific sensing strategies of SERS tags-based sensors for cellular molecules have not yet been systematically summarized. To provide beneficial and comprehensive insights into the advanced SERS tags technique at the cellular level, this review systematically elaborated on the latest advances in SERS tags-based sensors for cellular molecules detection and imaging. The general SERS tags-based sensing strategies for biomolecules and ions were first introduced according to molecular classes. Then, aiming at such molecules located in the extracellular, cellular membrane and intracellular regions, the tailored strategies by designing and manipulating SERS tags were summarized and explored through several key examples. Finally, the challenges and perspectives of developing high performance of advanced SERS tags were briefly discussed to provide effective guidance for further development and extended applications.

SERS biosensors for liquid biopsy towards cancer diagnosis by detection of various circulating biomarkers: current progress and perspectives

Liquid biopsy has emerged as a promising non-invasive strategy for cancer diagnosis, enabling the detection of various circulating biomarkers, including circulating tumor cells (CTCs), circulating tumor nucleic acids (ctNAs), circulating tumor-derived small extracellular vesicles (sEVs), and circulating proteins. Surface-enhanced Raman scattering (SERS) biosensors have revolutionized liquid biopsy by offering sensitive and specific detection methodologies for these biomarkers. This review comprehensively examines the application of SERS-based biosensors for identification and analysis of various circulating biomarkers including CTCs, ctNAs, sEVs and proteins in liquid biopsy for cancer diagnosis. The discussion encompasses a diverse range of SERS biosensor platforms, including label-free SERS assay, magnetic bead-based SERS assay, microfluidic device-based SERS system, and paper-based SERS assay, each demonstrating unique capabilities in enhancing the sensitivity and specificity for detection of liquid biopsy cancer biomarkers. This review critically assesses the strengths, limitations, and future directions of SERS biosensors in liquid biopsy for cancer diagnosis.

A cubic DNA nanocage probe for in situ analysis of miRNA-10b in tumor-derived extracellular vesicles

A cubic DNA nanocage probe is able to enter EVs derived from MDA-MB-231 cells and react with miRNA-10b. The probe-loaded EVs were employed to monitor the process of entry of miRNA-10b into MCF-10A cells, allowing visualization of EV-mediated intercellular communication of miRNA-10b between the cancer cells.

Deciphering biomolecular complexities: the indispensable role of surface-enhanced Raman spectroscopy in modern bioanalytical research

Surface-enhanced Raman spectroscopy (SERS) has emerged as an indispensable analytical tool in biomolecular research, providing unmatched sensitivity critical for the elucidation of biomolecular structures. This review presents a thorough examination of SERS, outlining its fundamental principles, cataloging its varied applications within the biomolecular sphere, and contemplating its future developmental trajectories. We begin with a detailed analysis of SERS's mechanistic principles, emphasizing both the phenomena of surface enhancement and the complexities inherent in Raman scattering spectroscopy. Subsequently, we delve into the pivotal role of SERS in the structural analysis of diverse biomolecules, including proteins, nucleic acids, lipids, carbohydrates, and biochromes. The remarkable capabilities of SERS extend beyond mere detection, offering profound insights into biomolecular configurations and interactions, thereby enriching our comprehension of intricate biological processes. This review also sheds light on the application of SERS in real-time monitoring of various bio-relevant compounds, from enzymes and coenzymes to metal ion-chelate complexes and cellular organelles, thereby providing a holistic view and empowering researchers to unravel the complexities of biological systems. We also address the current challenges faced by SERS, such as enhancing sensitivity and resolution, developing stable and reproducible substrates, and conducting thorough analyses in complex biological matrices. Nonetheless, the continual advancements in nanotechnology and spectroscopy solidify the standing of SERS as a formidable force in biomolecular research. In conclusion, the versatility and robustness of SERS not only deepen our understanding of biomolecular intricacies but also pave the way for significant developments in medical research, therapeutic innovation, and diagnostic approaches.

Exosome Isolation and Detection: From Microfluidic Chips to Nanoplasmonic Biosensor

Exosomes are becoming more widely acknowledged as significant circulating indicators for the prognosis and diagnosis of cancer. Circulating exosomes are essential to the development and spread of cancer, according to a growing body of research. Using existing technology, characterizing exosomes is quite difficult. Therefore, a direct, sensitive, and targeted approach to exosome detection will aid in illness diagnosis and prognosis. The review discusses the new strategies for exosome isolation and detection technologies from microfluidic chips to nanoplasmonic biosensors, analyzing the advantages and limitations of these new technologies. This review serves researchers to better understand exosome isolation and detection methods and to help develop better exosome isolating and detecting devices for clinical applications.

SERS-based methods for the detection of genomic biomarkers of cancer

Genomic biomarkers of cancer are based on changes in nucleic acids, which include abnormal expression levels of some miRNAs, point mutations in DNA sequences, and altered levels of DNA methylation. The presence of tumor-related nucleic acids in body fluids (blood, saliva, or urine) makes it possible to achieve a non-invasive early-stage cancer diagnosis. Currently existing techniques for the discovery of nucleic acids require complex, time-consuming, costly assays and have limited multiplexing abilities. Surface-enhanced Raman spectroscopy (SERS) is a vibrational spectroscopy technique that is able to provide molecular specificity combined with trace sensitivity. SERS has gained research attention as a tool for the detection of nucleic acids because of its promising potential: label-free SERS can decrease the complexity of assays currently used with fluorescence-based detection due to the absence of the label, while labeled SERS may outperform the gold standard in terms of the multiplexing ability. The first papers about SERS-based methods for the measurement of genomic biomarkers were written in 2008, and since then, more than 150 papers have been published. The aim of this paper is to review and evaluate the proposed SERS-based methods in terms of their level of development and their potential for liquid biopsy application, as well as to contribute to their further evolution by attracting research attention to the field. This goal will be reached by grouping, on the basis of their experimental protocol, all the published manuscripts on the topic and evaluating each group in terms of its limit of detection and applicability to real body fluids. Thus, the methods are classified according to their working principles into five main groups, including capture-based, displacement-based, sandwich-based, enzyme-assisted, and specialized protocols.

Integrated FET sensing microsystem for specific detection of pancreatic cancer exosomal miRNA10b

Tumor-derived exosome (TD-Ex) serves as a crucial early diagnostic biomarker of pancreatic cancer (PC). However, accurate identification of TD-Ex from PC is still a challenging work. In this paper, a detection microsystem that integrates magnetic separation and FET biosensor is developed, which is capable of selectively separating TD-Ex of PC from the plasma and detecting exosomal miRNA10b in a sensitive and specific manner. The magnetic beads were functionalized with dual antibody (GPC-1 antibody and EpCAM antibody), enabling selective recognition and capture of PC-derived exosomes. On the other hand, a peptide nucleic acid (PNA)- functionalized reduced graphene oxide field-effect transistor (RGO FET) biosensor was subsequently utilized to detect the exosomal miRNA10b, which is highly expressed in PC- derived exosomes. This system could achieve a low detection limit down to 78 fM, and selectively identify miRNA10b from single-base mismatched miRNA. In addition, 40 clinical plasma samples were tested with this microsystem, and the results indicate that it could effectively distinguish PC patients from healthy individuals. The assay combines specific capture and enrichment of PC-derived exosomes with sensitive and selective detection of exosomal miRNA, showing its potential to be used as an effective scheme for PC early diagnosis.

Single-Cell Genotyping of Single-Nucleotide Mutations Using In Situ Allele-Specific Loop-Mediated Isothermal Amplification

Single-nucleotide mutations (SNMs) in the bacterial genome may cause antibiotic resistance. The visualization of SNMs can indicate antibiotic resistance phenotypes at the single-cell level but remains challenging. Herein, we proposed an in situ allele-specific isothermal amplification proceeded inside cells, allowing us to image bacterial genes with single-nucleotide resolution. The primer for loop-mediated isothermal amplification (LAMP) was designed with artificial mismatch bases to serve as an allele-specific probe, endowing LAMP to specifically amplify genes with SNMs. Due to the high amplification efficiency of LAMP, the method termed AlleLAMP can generate high gain for imaging SNMs and precisely quantify mutated quinolone-resistant Salmonella in bacterial mixture. We utilized AlleLAMP to survey the selection of antibiotic resistance under the preservative stress and found that the mutant quinolone-resistant strain owned a survival advantage over the wild-type quinolone-sensitive strain under the stress of preservatives. AlleLAMP can serve as a single-cell tool for analyzing the relationship between bacterial genotype and phenotype.

Advanced extracellular vesicle bioinformatic nanomaterials: from enrichment, decoding to clinical diagnostics

Extracellular vesicles (EVs) are membrane nanoarchitectures generated by cells that carry a variety of biomolecules, including DNA, RNA, proteins and metabolites. These characteristics make them attractive as circulating bioinformatic nanocabinets for liquid biopsy. Recent advances on EV biology and biogenesis demonstrate that EVs serve as highly important cellular surrogates involved in a wide range of diseases, opening up new frontiers for modern diagnostics. However, inefficient methods for EV enrichment, as well as low sensitivity of EV bioinformatic decoding technologies, hinder the use of EV nanocabinet for clinical diagnosis. To overcome these challenges, new EV nanotechnology is being actively developed to promote the clinical translation of EV diagnostics. This article aims to present the emerging enrichment strategies and bioinformatic decoding platforms for EV analysis, and their applications as bioinformatic nanomaterials in clinical settings.

Absolute Quantification of Dynamic Cellular Uptake of Small Extracellular Vesicles via Lanthanide Element Labeling and ICP-MS

Small extracellular vesicles (sEVs) are increasingly reported to play important roles in numerous physiological and pathological processes. Cellular uptake of sEVs is of great significance for functional regulation in recipient cells. Although various sEV quantification, labeling, and tracking methods have been reported, it is still highly challenging to quantify the absolute amount of cellular uptake of sEVs and correlate this information with phenotypic variations in the recipient cell. Therefore, we developed a novel strategy using lanthanide element labeling and inductively coupled plasma-mass spectrometry (ICP-MS) for the absolute and sensitive quantification of sEVs. This strategy utilizes the chelation interaction between Eu3+ and the phosphate groups on the sEV membrane for specific labeling. sEVs internalized by cells can then be quantified by ICP-MS using a previously established linear relationship between the europium content and the particle numbers. High Eu labeling efficiency and stability were demonstrated by various evaluations, and no structural or functional alterations in the sEVs were discovered after Eu labeling. Application of this method revealed that 4020 ± 171 sEV particles/cell were internalized by HeLa cells at 37 °C and 61% uptake inhibition at 4 °C. Further investigation led to the quantitative differential analysis of sEV cellular uptake under the treatment of several chemical endocytosis inhibitors. A 23% strong inhibition indicated that HeLa cells uptake sEVs mainly through the macropinocytosis pathway. This facile labeling and absolute quantification strategy of sEVs with ppb-level high sensitivity is expected to become a potential tool for studying the functions of sEVs in intracellular communication and cargo transportation.

Integrated "lab-on-a-chip" microfluidic systems for isolation, enrichment, and analysis of cancer biomarkers

The liquid biopsy has garnered considerable attention as a complementary clinical tool for the early detection, molecular characterization and monitoring of cancer over the past decade. In contrast to traditional solid biopsy techniques, liquid biopsy offers a less invasive and safer alternative for routine cancer screening. Recent advances in microfluidic technologies have enabled handling of liquid biopsy-derived biomarkers with high sensitivity, throughput, and convenience. The integration of these multi-functional microfluidic technologies into a 'lab-on-a-chip' offers a powerful solution for processing and analyzing samples on a single platform, thereby reducing the complexity, bio-analyte loss and cross-contamination associated with multiple handling and transfer steps in more conventional benchtop workflows. This review critically addresses recent developments in integrated microfluidic technologies for cancer detection, highlighting isolation, enrichment, and analysis strategies for three important sub-types of cancer biomarkers: circulating tumor cells, circulating tumor DNA and exosomes. We first discuss the unique characteristics and advantages of the various lab-on-a-chip technologies developed to operate on each biomarker subtype. This is then followed by a discussion on the challenges and opportunities in the field of integrated systems for cancer detection. Ultimately, integrated microfluidic platforms form the core of a new class of point-of-care diagnostic tools by virtue of their ease-of-operation, portability and high sensitivity. Widespread availability of such tools could potentially result in more frequent and convenient screening for early signs of cancer at clinical labs or primary care offices.

Emerging integrated SERS-microfluidic devices for analysis of cancer-derived small extracellular vesicles

Cancer-derived small extracellular vesicles (sEVs) are specific subgroups of lipid bilayer vesicles secreted from cancer cells to the extracellular environment. They carry distinct biomolecules (e.g., proteins, lipids and nucleic acids) from their parent cancer cells. Therefore, the analysis of cancer-derived sEVs can provide valuable information for cancer diagnosis. However, the use of cancer-derived sEVs in clinics is still limited due to their small size, low amounts in circulating fluids, and heterogeneous molecular features, making their isolation and analysis challenging. Recently, microfluidic technology has gained great attention for its ability to isolate sEVs in minimal volume. In addition, microfluidics allows the isolation and detection of sEVs to be integrated into a single device, offering new opportunities for clinical application. Among various detection techniques, surface-enhanced Raman scattering (SERS) has emerged as a promising candidate for integrating with microfluidic devices due to its ultra-sensitivity, stability, rapid readout, and multiplexing capability. In this tutorial review, we start with the design of microfluidics devices for isolation of sEVs and introduce the key factors to be considered for the design, and then discuss the integration of SERS and microfluidic devices by providing descriptive examples of the currently developed platforms. Lastly, we discuss the current limitations and provide our insights for utilising integrated SERS-microfluidics to isolate and analyse cancer-derived sEVs in clinical settings.

Computational fluid dynamics simulation of two-phase flow patterns in a serpentine microfluidic device

In the current research work, the flow behavior of a liquid-liquid extraction (LLE) process in a serpentine microchannel was analyzed. The simulation was performed using a 3D model and the results were found to be consistent with experimental data. The impact of the flow of chloroform and water on the flow model was also examined. The data indicate that once the aqua and organic phases flow rates are low and similar, a slug flow pattern is observed. However, as the overall flow rate raises, the slug flow transforms into parallel plug flow or droplet flow. An increment in the aqua flows while maintaining a constant organic phase flow rate results in a transition from slug flow to either droplet flow or plug flow. Finally, the patterns of flow rate in the serpentine micro-channel were characterized and depicted. The results of this study will provide valuable insights into the behavior of two-phase flow patterns in serpentine microfluidic devices. This information can be used to optimize the design of microfluidic devices for various applications. Furthermore, the study will demonstrate the applicability of CFD simulation in investigating the behavior of fluids in microfluidic devices, which can be a cost-effective and efficient alternative to experimental studies.

Three-dimensional ordered DNA network constructed by a biomarker pair for accurate monitoring of colorectal cancer

Precise and early screening of colorectal cancer (CRC) is one crucial yet challenging task for its treatment, and the analysis of multi-targets of CRC in a single assay with high accuracy is essential for pathological research and clinical diagnosis. Here, a CRC-related biomarker pair, microRNA-211 (miRNA-211) and H₂S, was detected by constructing a three-dimensional (3D) ordered DNA network. First, trace amount of miRNA-211 could initiate a hybridization chain reaction-based amplification process. A highly ordered 3D DNA network was formed based on the organized assembly of DNA-cube frameworks that were constructed by DNA origamis and Ag nanoparticles (NPs) encapsulated inside. In the presence of the H₂S, Ag NPs within the network can be etched to generate Ag₂S quantum dots, which could be better visualized in fluorescence in situ cell imaging. Using the 3D DNA ordered network as the sensing platform, it can acquire dual analysis of biomolecule (miRNA-211) and inorganic gas (H₂S) in vitro, overcoming the limitations of single type of biomarker detection in a single assay. This assay achieved a wide linearity range of H₂S from 0.05 to 10 μM, and exhibited a low limit of detection of 4.78 nM. This strategy allows us to acquire the spatial distributions of H₂S and miRNA expression levels in living CRC cells simultaneously, providing a highly sensitive and selective tool for early screening and monitoring of CRC.

Tandem enrichment of serum exosomes and exosomal RNA with titanium dioxide

Exosomes have great potential as biomarker carriers for disease diagnosis and prognosis. In recent years, exosomal RNA (exoRNA) has become a promising candidate for the early diagnosis and prognosis of cancers, and its pathophysiological roles in various diseases have been revealed. For example, exosome-derived mRNAs, miRNAs, circRNAs, and lncRNAs function as signalling molecules to regulate tumour growth, angiogenesis, invasion, metastasis, and the response to chemotherapy. However, the isolation of exosomes and exoRNA with high quality and purity remains challenging due to the relatively small size of exosomes and the limited amount of RNA in exosomes. In this work, we developed a novel tandem enrichment method to isolate exoRNA from serum based on the specific interaction between titanium dioxide (TiO₂) and the phosphate groups on the lipid bilayer of exosomes and of the exoRNA. TiO₂-based RNA isolation was first demonstrated and optimized in HeLa cells. A total of 130.9 ± 8.34 µg of RNA was rapidly enriched from approximately 5 × 10⁶ HeLa cells within 10 min. This was a 41.5% higher yield than that using a commercial Ultrapure RNA Kit. TiO₂-based tandem enrichment of exoRNA was then performed using human serum, obtaining 64.53±3.41 ng of exoRNA from 500 µL of human serum within 30 min. A total of 2,137,902 reads, including seven types of exoRNAs, were identified from the exosomes. This method is compatible with various downstream RNA processing techniques and does not use toxic or irritating reagents, such as phenol or chloroform, providing a simple, economical, rapid, and safe approach for exoRNA extraction from biological samples.

From Conventional to Microfluidic: Progress in Extracellular Vesicle Separation and Individual Characterization

Extracellular vesicles (EVs) are nanoscale membrane vesicles, which contain a wide variety of cargo such as proteins, miRNAs, and lipids. A growing body of evidence suggests that EVs are promising biomarkers for disease diagnosis and therapeutic strategies. Although the excellent clinical value, their use in personalized healthcare practice is not yet feasible due to their highly heterogeneous nature. Taking the difficulty of isolation and the small size of EVs into account, the characterization of EVs at a single-particle level is both imperative and challenging. In a bid to address this critical point, more research has been directed into a microfluidic platform because of its inherent advantages in sensitivity, specificity, and throughput. This review discusses the biogenesis and heterogeneity of EVs and takes a broad view of state-of-the-art advances in microfluidics-based EV research, including not only EV separation, but also the single EV characterization of biophysical detection and biochemical analysis. To highlight the advantages of microfluidic techniques, conventional technologies are included for comparison. The current status of artificial intelligence (AI) for single EV characterization is then presented. Furthermore, the challenges and prospects of microfluidics and its combination with AI applications in single EV characterization are also discussed. In the foreseeable future, recent breakthroughs in microfluidic platforms are expected to pave the way for single EV analysis and improve applications for precision medicine.

Enzyme-Assisted Nucleic Acid Amplification in Molecular Diagnosis: A Review

Infectious diseases and tumors have become the biggest medical challenges in the 21st century. They are driven by multiple factors such as population growth, aging, climate change, genetic predispositions and more. Nucleic acid amplification technologies (NAATs) are used for rapid and accurate diagnostic testing, providing critical information in order to facilitate better follow-up treatment and prognosis. NAATs are widely used due their high sensitivity, specificity, rapid amplification and detection. It should be noted that different NAATs can be selected according to different environments and research fields; for example, isothermal amplification with a simple operation can be preferred in developing countries or resource-poor areas. In the field of translational medicine, CRISPR has shown great prospects. The core component of NAAT lies in the activity of different enzymes. As the most critical material of nucleic acid amplification, the key role of the enzyme is self-evident, playing the upmost important role in molecular diagnosis. In this review, several common enzymes used in NAATs are compared and described in detail. Furthermore, we summarize both the advances and common issues of NAATs in clinical application.

Microfluidic Strategies for Extracellular Vesicle Isolation: Towards Clinical Applications

Extracellular vesicles (EVs) are double-layered lipid membrane vesicles released by cells. Currently, EVs are attracting a lot of attention in the biological and medical fields due to their role as natural carriers of proteins, lipids, and nucleic acids. Thus, they can transport useful genomic information from their parental cell through body fluids, promoting cell-to-cell communication even between different organs. Due to their functionality as cargo carriers and their protein expression, they can play an important role as possible diagnostic and prognostic biomarkers in various types of diseases, e.g., cancers, neurodegenerative, and autoimmune diseases. Today, given the invaluable importance of EVs, there are some pivotal challenges to overcome in terms of their isolation. Conventional methods have some limitations: they are influenced by the starting sample, might present low throughput and low purity, and sometimes a lack of reproducibility, being operator dependent. During the past few years, several microfluidic approaches have been proposed to address these issues. In this review, we summarize the most important microfluidic-based devices for EV isolation, highlighting their advantages and disadvantages compared to existing technology, as well as the current state of the art from the perspective of the use of these devices in clinical applications.

Recent progress in surface-enhanced Raman spectroscopy-based biosensors for the detection of extracellular vesicles

Extracellular vesicles (EVs) are a type of mediator that enables intercellular communication. Moreover, EVs carry critical molecular information from parental cells, making them ideal biomarkers for clinical screening and diagnosis. Currently, several sensing technologies have been established to sensitively detect EVs. Among them, surface-enhanced Raman spectroscopy (SERS) has become a powerful analytical tool with high sensitivity and low detection limits. In this review, we first cover the biological characteristics of EVs and the principle of SERS amplification. Then, we describe the recent progress in SERS technology applied to detect EVs, including direct label-free methods and indirect labeling strategies, in which substrate fabrication and nanoprobe assembly were emphasized. Furthermore, SERS technology could also be used to characterize or monitor the behavior of programmable EVs. Finally, we discuss the prospects and issues to be addressed for the development of SERS technology for EV analysis.

Roll-to-Roll DNA Nanomachine for Ultrasensitive Electrochemical Determination of miRNA

MicroRNAs (miRNAs) are a family of endogenous noncoding RNAs with the functions of gene regulation, which serve as promising markers for a range of diseases such as diabetic foot ulcers, cancers, etc. In this work, we engineered a roll-to-roll DNA nanomachine for highly sensitive electrochemical detection of miRNA. A dumbbell-structured DNA probe could be transitioned to be wheel-structured conformation upon target recognition, which rolls around track strands on the surface of gold nanoparticles (AuNPs) in the presence of nicking endonuclease. The resulting single strands on AuNPs are activated for the second round of rolling at the DNA-modified electrode interface, leading to the variation of electrochemical responses. The roll-to-roll amplification behavior allows a wide detection range with a limit of detection as low as 10 aM. The practicability is also demonstrated by the application in human serum samples with satisfactory results. It is expected that the proposed electrochemical method offers a new paradigm to develop miRNA assays based on DNA nanotechnology.

A light-activated magnetic bead strategy utilized in spatio-temporal controllable exosomes isolation

Tumor-derived exosomes are considered as a key biomarker in the field of liquid biopsy. However, conventional separation techniques such as ultracentrifugation, co-precipitation and column chromatography cannot isolate samples with high throughput, while traditional immunomagnetic separation techniques, due to steric effect of magnetic beads, reducing sensitivity of exosomes optical detection. Herein, we provide a novel and simple nanoplatform for spatiotemporally controlling extraction and elution of exosomes via magnetic separation and light-activated cargo release. In this system, magnetic beads are co-modified by photoresponsive groups -nitrobenzyl group and aptamers that are compatible with CD63-a highly expressed exosomal surface-specific protein. Through exosomes extracted from cell model and nude mice xenograft tumor model morphological characterization and proteomic analysis, results showed that our novel magnetic bead system outperformed current ultracentrifugation in serum exosome extraction in terms of extraction time, yield, and proportion of populations with high CD63 expression. This strategy may be a powerful tool for exosome isolation in clinical liquid biopsies of cancer disease.

Imitation-mussel fluorescent silicon quantum dots for selective labeling and imaging of bacteria and biofilms

Selective labeling of distinct bacteria and biofilm is poised for the fundamental understanding of bacterial activities, interactions, and coupled phenomena occurring at the microscale. However, a simple and effective way to achieve selective bacterial labeling is still lacking. Herein, we report a fluorescence probe with core-shell nanostructure that has polydopamine (PDA) coating on the surface of fluorescent silicon quantum dots (SiQDs@PDA). The surface of the SiQDs@PDA can be functionalized by various molecules (2-mercaptoethylamine hydrochloride, PEG, d-alanine, glucose amide) through different strategies (Michael addition, π-π interaction, and ion–ion interaction). Importantly, the d-alanine (D-Ala)- and gluconamide (Glc)-functionalized SiQDs@PDA fluorescence probes are capable of selectively labeling gram-positive and gram-negative bacteria, as well as their biofilms. The excellent performance in universal functionalization and selective labeling and imaging of bacteria and their biofilms demonstrate that SiQDs@PDA are a promising fluorescence tool in microbe research.

Highly efficient and automated isolation technology for extracellular vesicles microRNA

MicroRNA (miRNA) in extracellular vesicles (EVs) has great potential to be a promising marker in liquid biopsy. However, the present EV isolation methods, such as ultracentrifugation, have complicated and long-time operation, which impedes research on EV miRNA. The downstream complex miRNA extraction process will also significantly increase the detection cycle and loss. We first established a simple automated technique to efficiently extract target miRNAs in EVs from plasma based on Fe₃O₄@TiO₂ beads with high affinity and capture efficiency. We combined a heat-lysis method for quick and simple EV miRNA extraction and detection. The results indicated that our method has more RNA yield than TRIzol or a commercial kit and could complete EV enrichment and miRNA extraction in 30 min. Through the detection of miRNA-21, healthy people and lung cancer patients were distinguished, which verified the possibility of the application in clinical detection. The automated isolation technology for EV miRNA has good repeatability and high throughput, with great application potential in clinical diagnosis.

Circulating Abnormal Extracellular Vesicles: Their Mechanism for Crossing Blood-Brain Barrier, Effects on Central Nervous System and Detection Methods

Central nervous system (CNS) diseases are difficult to treat and harmful. Many CNS diseases are secondary to peripheral diseases, such as tumor brain metastases (BMS), viral infections and inflammation of the brain, and their pathogenic factors travel through the circulatory system to the brain, eventually leading to lesions. Extracellular vesicles (EVs) play an important role in this process. Recent studies have shown that, extracellular EVs can effectively cross the blood- brain barrier (BBB) through endocytosis and they transmit molecular signals in cell-to-cell communication. Abnormal EVs produced in the lesion portion transport pathogenic factors, including miRNAs, proteins, and virions into the CNS. These pathogenic factors participate in cellular pathways to interfere with homeostasis or are themselves pathogens that directly damage CNS. In addition, different or specific pathological molecules in EVs are potential disease markers. We herein reviewed pathways through which the abnormal EVs cross BBB and adverse effects of abnormal exosomes. We also and summarized their existing detection techniques, so as to provide basis for prevention and early diagnosis of secondary diseases.