Tracing Tumor-Derived Exosomal PD-L1 by Dual-Aptamer Activated Proximity-Induced Droplet Digital PCR

Sensitive Electrochemical Sensor for Glycoprotein Detection Using a Self-Serviced-Track 3D DNA Walker and Catalytic Hairpin Assembly Enzyme-Free Signal Amplification

Approaches for the detection of targets in the cellular microenvironment have been extensively developed. However, developing a method with sensitive and accurate analysis for noninvasive cancer diagnosis has remained challenging until now. Here, we reported a sensitive and universal electrochemical platform that integrates a self-serviced-track 3D DNA walker and catalytic hairpin assembly (CHA) triggering G-Quadruplex/Hemin DNAzyme assembly signal amplification. In the presence of a target, the aptamer recognition initiated the 3D DNA walker on the cell surface autonomous running and releasing DNA (C) from the triple helix. The released DNA C as the target-triggered CHA moiety, and then G-quadruplex/hemin, was formed on the surface of electrode. Eventually, a large amount of G-quadruplex/hemin was formed on the sensor surface to generate an amplified electrochemical signal. Using N-acetylgalactosamine as a model, benefiting from the high selectivity and sensitivity of the self-serviced-track 3D DNA walker and the CHA, this designed method showed a detection limit of 39 cell/mL and 2.16 nM N-acetylgalactosamine. Furthermore, this detection strategy was enzyme free and exhibited highly sensitive, accurate, and universal detection of a variety of targets by using the corresponding DNA aptamer in clinical sample analysis, showing potential for early and prognostic diagnostic application.

Logic Nanodevice-Mediated Receptor Assembly for Nongenetic Regulation of Cell Behavior in Tumor-like Microenvironment

The reprogramming of cell signaling and behavior through the artificial control of cell surface receptor oligomerization shows great promise in biomedical research and cell-based therapy. However, it remains challenging to achieve combinatorial recognition in a complicated environment and logical regulation of receptors for desirable cellular behavior. Herein, we develop a logic-gated DNA nanodevice with responsiveness to multiple environmental inputs for logically controlled assembly of heterogeneous receptors to modulate signaling. The "AND" gate nanodevice uses an i-motif and an ATP-binding aptamer as environmental cue-responsive units, which can successfully implement a logic operation to manipulate receptors on the cell surface. In the presence of both protons and ATP, the DNA nanodevice is activated to selectively assemble MET and CD71, which modulate the HGF/MET signaling, resulting in cytoskeletal reorganization to inhibit cancer cell motility in a tumor-like microenvironment. Our strategy would be highly promising for precision therapeutics, including controlled drug release and cancer treatment.

An in situ exosomal miRNA sensing biochip based on multi-branched localized catalytic hairpin assembly and photonic crystals

Exosomal microRNAs (miRNAs) are emerging as attractive non-invasive and reliable biomarkers for disease diagnosis. In situ exosomal miRNA detection can avoid laborious and time-consuming exosome lysis, RNA extraction and effectively improve the accuracy. However, in situ exosomal miRNA detection is hampered by the low abundance of the targets and low permeability of the probes. Herein, an in situ exosomal miRNA sensing biochip based on multi-branched localized catalytic hairpin assembly (MLCHA) and photonic crystals (PCs) was proposed. The MLCHA probes could penetrate into the exosomes nondestructively due to its rigidity and generate amplified fluorescence signal upon recognizing the target miRNA. And then, the fluorescence signal was further enhanced by PCs to improve the sensitivity. The developed biosensor can not only detect exosomal miRNA in a concentration-dependent manner but also distinguish samples from cancer state and healthy state, which is potential for non-invasive clinical diagnostics.

Clinical application and detection techniques of liquid biopsy in gastric cancer

Gastric cancer (GC) is one of the most common tumors worldwide and the leading cause of tumor-related mortality. Endoscopy and serological tumor marker testing are currently the main methods of GC screening, and treatment relies on surgical resection or chemotherapy. However, traditional examination and treatment methods are more harmful to patients and less sensitive and accurate. A minimally invasive method to respond to GC early screening, prognosis monitoring, treatment efficacy, and drug resistance situations is urgently needed. As a result, liquid biopsy techniques have received much attention in the clinical application of GC. The non-invasive liquid biopsy technique requires fewer samples, is reproducible, and can guide individualized patient treatment by monitoring patients' molecular-level changes in real-time. In this review, we introduced the clinical applications of circulating tumor cells, circulating free DNA, circulating tumor DNA, non-coding RNAs, exosomes, and proteins, which are the primary markers in liquid biopsy technology in GC. We also discuss the current limitations and future trends of liquid biopsy technology as applied to early clinical biopsy technology.

Advances in optical counting and imaging of micro/nano single-entity reactors for biomolecular analysis

Ultrasensitive detection of biomarkers is of paramount importance in various fields. Superior to the conventional ensemble measurement-based assays, single-entity assays, especially single-entity detection-based digital assays, not only can reach ultrahigh sensitivity, but also possess the potential to examine the heterogeneities among the individual target molecules within a population. In this review, we summarized the current biomolecular analysis methods that based on optical counting and imaging of the micro/nano-sized single entities that act as the individual reactors (e.g., micro-/nanoparticles, microemulsions, and microwells). We categorize the corresponding techniques as analog and digital single-entity assays and provide detailed information such as the design principles, the analytical performance, and their implementation in biomarker analysis in this work. We have also set critical comments on each technique from these aspects. At last, we reflect on the advantages and limitations of the optical single-entity counting and imaging methods for biomolecular assay and highlight future opportunities in this field.

Identifying the Phenotypes of Tumor-Derived Extracellular Vesicles Using Size-Coded Affinity Microbeads

Tumor-derived extracellular vesicle (tEV) biomarkers can reflect cancer cell phenotypes and have great potential for cancer diagnosis and treatment. However, tEVs display high heterogeneity, and rapid and sensitive identification of EV biomarkers remains challenging due to their low expression. Spectral overlap also significantly limits the multiplex analysis of EV biomarkers by fluorescent probes. Herein, we developed a method for highly sensitive tEV phenotyping that uses size-coded microbeads that carry hairpin probes that can bind to aptamers targeting distinct tEV biomarkers. We also designed a microfluidic chip containing spacer arrays that segregate these microbeads in distinct chip regions according to their size to generate location-specific signals indicating the level of different EV biomarkers. The EV biomarker signal on these microbeads was amplified by in situ rolling cyclic amplification (RCA). This strategy permits the simultaneous detection of multiple tEV phenotypes by fluorescence spectroscopy without the limitations of spectral overlap. This study demonstrates that this tEV phenotyping method can rapidly and simultaneously detect six different tEV phenotypes with high sensitivity. Due to the programmability of the sensing platform, this method can be rapidly adapted to detect different tEV phenotype substitutions of the detected biomarkers. Notably, clinical cohort studies show that this strategy may provide new ideas for the precise diagnosis and personalized treatment of cancer patients.

Rapid In Situ Hydrogel LAMP for On-Site Large-Scale Parallel Single-Cell HPV Detection

Rapid human papillomavirus (HPV) screening is urgently needed for preventing and early diagnosis of cervical cancer in rural areas. To date, no HPV nucleic acid test (NAT) can be implemented within a single patient visit starting from clinical samples. Here, we develop a hydrogel loop-mediated isothermal amplification (LAMP) method in a fashion of large-scale parallel (about 1000 cells) in situ HPV DNA detection in clinical cervical exfoliated cells at the single-cell level. It can be used with a hotplate and smartphone to obtain HPV NAT results in less than 30 min, which is especially suitable for the on-site scenario. We apply this rapid HPV NAT on 40 clinical cervical exfoliated cell samples and compare the results to a clinical gold standard quantitative polymerase chain reaction (qPCR) method [area under curve (AUC), 1.00]. Meanwhile, our assay can provide HPV infection information for large-scale parallel single clinical cervical exfoliated cells, which cannot be received from traditional NAT methods. Our findings suggest the potential of in situ hydrogel LAMP as a powerful tool for clinical HPV screening and fundamental research.

Ultrasensitive Automatic Detection of Small Molecules by Membrane Imaging of Single Molecule Assays

Determination of trace amounts of targets or even a single molecule target has always been a challenge in the detection field. Digital measurement methods established for single molecule counting of proteins, such as single molecule arrays (Simoa) or dropcast single molecule assays (dSimoa), are not suitable for detecting small molecule, because of the limited category of small molecule antibodies and the weak signal that can be captured. To address this issue, we have developed a strategy for single molecule detection of small molecules, called small molecule detection with single molecule assays (smSimoa). In this strategy, an aptamer is used as a recognition element, and an addressable DNA Nanoflower (DNF) attached on the magnetic beads surface, which exhibit fluorescence imaging, is employed as the output signal. Accompanied by digital imaging and automated counting analysis, E2 at the attomolar level can be measured. The smSimoa breaks the barrier of small molecule detection concentration and provides a basis for high throughput detection of multiple substances with fluorescence encoded magnetic beads.

Single-Step and Highly Sensitive Imaging of Exosomal PD-L1 through Aptamer-Activated Cascade Primer Exchange Reaction-Generated Branched DNA Nanostructures

Exosomal PD-L1 plays a critical role in tumor progress and immunotherapy. However, accurately analyzing exosomal PD-L1 is greatly limited by the small-sized and free-floating nature of exosomes and the few proteins each exosome carries. We described herein a single-step and highly sensitive method, termed aptamer-triggered cascade primer exchange reaction (PER)-generated branched DNA nanostructures, for the quantification and imaging of exosomal PD-L1. The presence of exosomal PD-L1 converted the conformation of the recognition probe, accompanied by the exposure of primer 1. Then, primer 1 actuated the cascade PER, which generated branched DNA nanostructures containing numerous G-quadruplex for binding to thioflavin T (ThT) dye, leading to an amplified fluorescence signal. Profiting from directly growing branched DNA nanostructures on the surface of exosomes, the size of exosomes was enlarged and the movement of exosomes was limited, achieving the imaging of exosomal PD-L1 by conventional optical microscopy in a wash- and label-free fashion. Analyzing exosomal PD-L1 from serum samples of 15 cancer patients and 15 healthy volunteers demonstrated that this simple strategy could distinguish NSCLC patients from healthy donors with high clinical accuracy. Therefore, the developed assay has great potential as a transformative diagnostic toolkit for cancer detection and immunotherapy monitoring.

Fluid nanoporous microinterface enables multiscale-enhanced affinity interaction for tumor-derived extracellular vesicle detection

Tumor-derived extracellular vesicles (T-EVs) represent valuable markers for tumor diagnosis and treatment guidance. However, nanoscale sizes and the low abundance of marker proteins of T-EVs restrict interfacial affinity reaction, leading to low isolation efficiency and detection sensitivity. Here, we engineer a fluid nanoporous microinterface (FluidporeFace) in a microfluidic chip by decorating supported lipid bilayers (SLBs) on nanoporous herringbone microstructures with a multiscale-enhanced affinity reaction for efficient isolation of T-EVs. At the microscale level, the herringbone micropattern promotes the mass transfer of T-EVs to the surface. At the nanoscale level, nanoporousity can overcome boundary effects for close contact between T-EVs and the interface. At the molecular level, fluid SLBs afford clustering of recognition molecules at the binding site, enabling multivalent binding with an ∼83-fold increase of affinity compared with the nonfluid interface. With the synergetic enhanced mass transfer, interface contact, and binding affinity, FluidporeFace affords ultrasensitive detection of T-EVs with a limit of detection of 10 T-EVs μL −1 , whose PD-L1 expression levels successfully distinguish cancer patients from healthy donors. We expect this multiscale enhanced interfacial reaction strategy will inspire the biosensor design and expand liquid biopsy applications, especially for low-abundant targets in clinical samples.

Biomimetic 3D Recognition with 2D Flexible Nanoarchitectures for Ultrasensitive and Visual Extracellular Vesicle Detection

Despite increasing recognition of extracellular vesicles being important circulating biomarkers in disease diagnosis and prognosis, current strategies for extracellular vesicle detection remain limited due to the compromised sample purification and extensive labeling procedures in complex body fluids. Here, we developed a 2D magnetic platform that greatly improves capture efficiency and readily realizes visible signal conversion for extracellular vesicle detection. The technology, termed high-affinity recognition and visual extracellular vesicle testing (HARVEST), leverages 2D flexible Fe₃O₄-MoS₂ nanostructures to recognize extracellular vesicles through multidentate affinity binding and feasible magnetic separation, thus enhancing the extracellular vesicle capture performance with both yield and separation time, affording high sensitivity with the detection limit of 20 extracellular vesicle particles/μL. Through integration with lipid labeling chemistry and the fluorescence visualization system, the platform enables rapid and visible detection. The number of extracellular vesicles can be feasibly determined by smart mobile phones, readily adapted for point-of-care diagnosis. When clinically evaluated, the strategy accurately differentiates melanoma samples from the normal cohort with an AUC of 0.98, demonstrating the efficient extracellular vesicle detection strategy with 2D flexible platforms for cancer diagnosis.

Quantification-Promoted Discovery of Glycosylated Exosomal PD-L1 as a Potential Tumor Biomarker

Exosomal programmed cell death ligand 1 (exoPD-L1) has emerged as a promising biomarker for cancer diagnosis and immunotherapy outcome prediction. However, the existing quantitation methods are incapable of addressing the heterogeneity of exoPD-L1 glycosylation, which has been demonstrated to be the institutional basis for PD-L1/PD-1 interaction and the crucial participant in inhibiting the activity of CD8⁺ T cells. Herein, an aptamer- and lectin-induced proximity ligation assay combined with quantitative real-time polymerase chain reaction for precise quantitation of glycosylated exoPD-L1 is developed. Leveraging the metabolism-free lectin labeling of glycosylation, the glycosylation-independent aptamer tagging of PD-L1, and excellent selectivity of dual-recognition, this method enables glycosylated exoPD-L1 quantitation with high sensitivity and selectivity in a wash-free manner. As a result, this method is able to distinguish the levels of glycosylated exoPD-L1 between healthy donors and cancer patients with sensitivity and specificity of 100%. Compared with the total circulating exoPD-L1 level, glycosylated exoPD-L1 is for the first time identified to be a more reliable biomarker for tumor diagnosis. Overall, this strategy holds a great potential for revealing the significance of exoPD-L1 glycosylation and converting glycosylated exoPD-L1 into a reliable clinical indicator.

Tumor-derived small extracellular vesicles: potential roles and mechanism in glioma

Small extracellular vesicles (SEVs) are extracellular vesicles containing DNA, RNA, and proteins and are involved in intercellular communication and function, playing an essential role in the growth and metastasis of tumors. SEVs are present in various body fluids and can be isolated and extracted from blood, urine, and cerebrospinal fluid. Under both physiological and pathological conditions, SEVs can be released by some cells, such as immune, stem, and tumor cells, in a cytosolic manner. SEVs secreted by tumor cells are called tumor-derived exosomes (TEXs) because of their origin in the corresponding parent cells. Glioma is the most common intracranial tumor, accounting for approximately half of the primary intracranial tumors, and is characterized by insidious onset, high morbidity, and high mortality rate. Complete removal of tumor tissues by surgery is difficult. Chemotherapy can improve the survival quality of patients to a certain extent; however, gliomas are prone to chemoresistance, which seriously affects the prognosis of patients. In recent years, TEXs have played a vital role in the occurrence, development, associated immune response, chemotherapy resistance, radiation therapy resistance, and metastasis of glioma. This article reviews the role of TEXs in glioma progression, drug resistance, and clinical diagnosis.

Future of Digital Assays to Resolve Clinical Heterogeneity of Single Extracellular Vesicles

Extracellular vesicles (EVs) are complex lipid membrane vehicles with variable expressions of molecular cargo, composed of diverse subpopulations that participate in the intercellular signaling of biological responses in disease. EV-based liquid biopsies demonstrate invaluable clinical potential for overhauling current practices of disease management. Yet, EV heterogeneity is a major needle-in-a-haystack challenge to translate their use into clinical practice. In this review, existing digital assays will be discussed to analyze EVs at a single vesicle resolution, and future opportunities to optimize the throughput, multiplexing, and sensitivity of current digital EV assays will be highlighted. Furthermore, this review will outline the challenges and opportunities that impact the clinical translation of single EV technologies for disease diagnostics and treatment monitoring.

Highly Sensitive Detection of the Immune Checkpoint PD-L1-Positive Circulating Tumor Cells Based on Steric Hindrance

Programmed-death ligand 1 (PD-L1), as one of major immune checkpoints, is highly expressed on cancer cells and participates in the immune escape process of tumor cells. The level of PD-L1 in patients is closely related to the efficacy of anti-PD-L1 immunotherapy, and patients with a high level have better response to immunotherapy. Therefore, PD-L1 can be an indicator of patient classification and medication guidance. In this work, we have developed a novel strategy for detecting PD-L1-positive circulating tumor cells based on steric hindrance generated after cell capture, using the primer exchange reaction (PER) amplification method. The principle is to modify a single strand containing the PD-L1 aptamer and the PER primer on the electrode surface. When PD-L1-positive circulating tumor cells exist, the aptamer will capture them. The steric hindrance generated by the captured cells due to their large volume hinders the subsequent approach of PER materials, thus hindering the occurrence of PER signal amplification. The number of HRP bound to the electrode surface is reduced, and the current signal output is inversely proportional to the number of captured cells. This method realizes convenient and sensitive detection of PD-L1-positive tumor cells and provides a new means for clinical judgment of whether patients should adopt immunotherapy.

One-Step Thermophoretic AND Gate Operation on Extracellular Vesicles Improves Diagnosis of Prostate Cancer

Circulating extracellular vesicles (EVs) have emerged as a valuable source of cancer biomarkers. However, the high degree of EV heterogeneity and the complexity of clinical samples pose a challenge in the sensitive identification of tumor-derived EVs. Here we introduce a one-step thermophoretic AND gate operation (Tango) assay that integrates polyethylene glycol (PEG)-enhanced thermophoretic accumulation of EVs and simultaneous AND gate operation on EV membranes by dual-aptamers recognition. By using the Tango assay to detect tumor-derived EVs with co-presence of EpCAM and PSMA directly from serum in a homogeneous, separation-free format, we can discriminate prostate cancer (PCa) patients from benign prostatic hyperplasia (BPH) patients in the diagnostic gray zone with an accuracy of 91 % in 15 min. Our approach streamlines EV enrichment and AND gate operation on EVs in a single assay, providing a rapid, straightforward, and powerful method for precise and non-invasive diagnosis of cancer.

Extracellular vesicle-mediated immunoregulation in cancer

Extracellular vesicles (EVs) have emerged as immunomodulatory regulators during tumor progression. These small vesicles encapsulate a variety of molecules, including DNA, RNA, and proteins. When EVs come in contact with recipient cells, the EVs transmit various physiological characteristics; for example, proteins on the surface of EVs act as ligands. Immune checkpoint blockade targeting cytotoxic T-lymphocyte-associated antigen 4 (CTLA4), programmed cell death 1 (PD-1) and programmed cell death ligand 1 (PD-L1) has shown promise in a subset of cancer patients. PD-L1 on EVs acts as a key immunomodulator. Suppression of EV secretion enhances the efficacy of immunotherapy using immune checkpoint blockade antibodies. In addition to immune checkpoint blockade therapy, chimeric antigen receptor T (CAR-T) cell therapy has also been used to successfully eliminate cancer cells. Interestingly, CAR-T-cell-derived EVs express CAR on their surface. Compared with CAR-T cells, CAR-expressing EVs do not express PD1, so their antitumor effect cannot be weakened. In this review, we describe the current understanding of EVs in cancer immunity and summarize their crucial roles in immunomodulation.

Noninvasive Diagnosis of Nasopharyngeal Carcinoma Based on Phenotypic Profiling of Viral and Tumor Markers on Plasma Extracellular Vesicles

Nasopharyngeal carcinoma (NPC) is a malignant tumor commonly associated with Epstein-Barr virus (EBV) infection, and its early diagnosis as well as its differentiation from nasopharyngitis (NPG) remains challenging due to the insufficient sensitivity of routine screening methods in clinical practice. To date, circulating extracellular vesicles (EVs, 40-1000 nm) have shown appealing potential in liquid biopsy for cancer diagnosis and prognosis. Herein, nanoflow cytometry (nFCM) capable of single EV analysis was applied to examine the expression of surface proteins with very low copy numbers on individual EVs as small as 40 nm. The particle concentrations of five EV subsets exposing EBV-encoded latent membrane proteins (LMP1 and LMP2A) and tumor markers (PD-L1, EGFR, and EpCAM) in plasma were determined rapidly via single-particle enumeration. We identified a five-marker panel named EV^SUM5 (an unweighted sum of the concentration of the five individual EV subsets) that significantly surpassed the traditional VCA-IgA assay in discriminating NPC patients from both healthy donors and NPG patients with accuracies of 96.3 and 83.1%, respectively. Moreover, EV^SUM2 (an unweighted sum of virus-specific LMP1- and LMP2A-positive EVs) could achieve the diagnosis of NPG with an accuracy of 82.6%. Collectively, the work presented a rapid, reliable, and noninvasive method as well as two diagnostic markers to help more accurately differentiate NPC from NPG patients and healthy donors in clinical practice.

Aptamer-Functionalized Barcodes in Herringbone Microfluidics for Multiple Detection of Exosomes

Tumor-derived exosomes are vital for clinical dynamic and accurate tumor diagnosis, thus developing sensitive and multiple exosomes detection technology has attracted remarkable attention of scientists. Here, a novel herringbone microfluidic device with aptamer-functionalized barcodes integration for specific capture and multiple detection of tumor-derived exosomes is presented. The barcodes with core-shell constructions are obtained by partially replicating the periodically ordered hexagonal close-packaged colloidal crystal beads. As their inverse opal hydrogel shell possesses rich interconnected pores, the barcodes could provide abundant surface area for functionalization of DNA aptamers to realize specific recognition of target exosomes. Besides, the encoded structure colors of the barcodes can be maintained stably during the detection events as their hardish cores are with sufficient mechanical strength. It is demonstrated that by embedding these barcodes in herringbone groove microfluidic device with designed patterns, the specific capture efficiency and synergetic detection of multiple tumor-derived exosomes in peripheral blood can be significantly improved due to enhanced resistance of turbulent flow. These features make the aptamer-functionalized barcodes and herringbone microfluidics integrated platform promising for exosomes extraction and dynamic tumor diagnosis.

MicroRNA-21 expression in single living cells revealed by fluorescence and SERS dual-response microfluidic droplet platform

Analysis of single-cell microRNA is essential to reveal cell heterogeneity at the genetic level. It raises a high demand for single-cell analytical methods because single-cell microRNA sequences are highly similar and small in size and feature low-level expression. Herein, SERS and fluorescence imaging technology were introduced into a microfluidic droplet platform to realize direct in situ, nondestructive, and highly sensitive detection of a small number of microRNA-21 (miR-21) in a single intact living cell. A multifunctional plasmonic nanoprobe was designed by decorating a gold nanoparticle with fluorescent dye (ROX)-labeled probe DNA and capture DNA strands. The dual-signal switching of fluorescence turn-off and SERS turn-on of ROX in response to miR-21 achieves highly sensitive and reliable detection of miR-21 in a single cell. The turn-on of SERS signal with a zero background guarantees the sensitivity of the detection. The fluorescence-SERS simultaneous response strategy was able to mutually corroborate the test results, improving the reliability of determining low-level expression of miR-21. SERS combined with encapsulation of microdroplets provides a feasible way to conduct in situ, nondestructive determination of miR-21 secreted by single cells, avoiding cell lysis and tedious time-consuming steps of miR-21 isolation. As a result, the miR-21 expressed by various types of single cells was investigated by fluorescence imaging and the cellular heterogeneity in miR-21 expression was evaluated accurately and quantitatively by SERS. This research would provide important reference information for understanding the effects of miRNAs on cancer diseases at the single-cell level.

Damage-Free and Time-Saving Platform Integrated by a Flow Membrane Separation Device and a Dual-Target Biofuel Cell-Based Biosensor for Continuous Sorting and Detection of Exosomes and Host Cells in Human Serum

The growth relationship between exosomes (EXOs) and the host cells is highly desired for tumor evaluations, which puts forward high demand on the accurate and convenient acquisition of their individual quantitative information. However, the tedious and destructive separation process and the requirement of dual-channel detection make it become an extremely challenging task. Herein, we integrated an enzymatic biofuel cell (EBFC)-powered biosensor with a flow cell-supported membrane separation device (FMSC) to develop a continuous separation and detection platform for EXOs and host cancer cells in human serum. The FMSC equipped with an aluminum oxide membrane served as a size-dependent sorting unit to nondestructively extract EXOs from human serum within 5 min, representing a 99.3% reduction in isolating time compared to ultracentrifugation. The EBFC-powered biosensors modified with different aptamers on anodes and cathodes were used as a dual-channel sensing unit. By regulating the controlling valves of different fluid passages, the extracted EXOs and residual host cells could be successively inputted into EBFC-powered biosensors, which generated a segmental degradation in output performance due to the EXO-and host cell-caused increase in the steric hindrance of anodes and cathodes, respectively. Based on these degradations, we obtained the quantitative information of EXOs and host cells with a record-breaking sensitivity (EXOs: 5.59 × 10³ particles/mL and host cells: 25 cells/mL). Moreover, the growth relationship between EXOs and host cells was also built, which would be beneficial for the disclosure of the growth state or even more detailed biology information of tumor.

Spatial confinement toward creating artificial living systems

Lifeforms are regulated by many physicochemical factors, and these factors could be controlled to play a role in the construction of artificial living systems. Among these factors, spatial confinement is an important one, which mediates biological behaviors at multiscale levels and participates in the biomanufacturing processes accordingly. This review describes how spatial confinement, as a fundamental biological phenomenon, provides cues for the construction of artificial living systems. Current knowledge about the role of spatial confinement in mediating individual cell behavior, collective cellular behavior, and tissue-level behavior are categorized. Endeavors on the synthesis of biomacromolecules, artificial cells, engineered tissues, and organoids in spatially confined bioreactors are then emphasized. After that, we discuss the cutting-edge applications of spatially confined artificial living systems in biomedical fields. Finally, we conclude by assessing the remaining challenges and future trends in the context of fundamental science, technical improvement, and practical applications.

A Self-Serviced-Track 3D DNA Walker for Ultrasensitive Detection of Tumor Exosomes by Glycoprotein Profiling

Sensitive and accurate analysis of low-concentration of tumor-derived exosomes (Exos) in biofluids is essential for noninvasive cancer diagnosis but is still challenging due to the lack of high-sensitive methods with low-cost and easy-operation. Herein, exploiting target Exos as a three-dimensional (3D) track for the first time, we developed a self-serviced-track DNA walker (STDW) for wash-free detection of tumor Exos using exosomal glycoprotein, which was enabled by split aptamer-recognition-initiated autonomous running powered by a catalytic hairpin assembly (CHA). Benefiting from high selectivity and sensitivity of the STDW assay, direct detection of tumor Exos in cell culture medium and serum could also be realized. Furthermore, this method exhibited high accuracy in clinical sample analysis, offering the potential for early cancer diagnosis and postoperative response prediction.

Rapid Capturing and Chemiluminescent Sensing of Programmed Death Ligand-1 Expressing Extracellular Vesicles

Cancer specific extracellular vesicles (EVs) are of significant clinical relevance, for instance programmed death ligand-1 (PD-L1) expressing EVs (PD-L1@EVs) have been shown to be ideal biomarker for non-invasive diagnosis of cancer and can predate the response of cancer patients to anti-PD-1/PD-L-1 immunotherapy. The development of sensitive and straightforward methods for detecting PD-L1@EVs can be a vital tool for non-invasive diagnosis of cancer. Most of the contemporary methods for EVs detection have limitations such as involvement of long and EV’s loss prone isolation methods prior to detection or they have employed expensive antibodies and instruments to accomplish detection. Therefore, we designed an ultracentrifugation-free and antibody-free sensing assay for PD-L1@EV by integrating Titanium oxide (TiO2) coated magnetic beads (Fe3O4@TiO2) rapid capturing of EVs from undiluted serum with aptamers specificity and chemiluminescence (CL) sensitivity. To accomplish this we used Fe3O4@TiO2 beads to rapidly capture EVs from the undiluted patient serum and added biotin labelled PD-L1 aptamer to specifically recognize PD-L1@EVs. Later, added streptavidin-modified Alkaline phosphates (ALP) taking advantage of biotin-streptavidin strong binding. Addition of CDP-star, a chemiluminescent substrate of ALP, initiates the chemiluminiscense that was recorded using spectrophotometer. The sensing assay showed high sensitivity with limit of detection (LOD) as low as 2.584×105 EVs/mL and a wider linear correlation of CL intensity (a.u.) with the concentration of PD-L1@EVs from 105 to 108 EVs/mL. To examine the clinical utility of sensing assay we used undiluted serum samples from lung cancer patients and healthy individuals and successfully discern between healthy individuals and lung cancer patients. We are optimistic that the sensing assay can ameliorate our ability to be able to diagnose lung cancer non-invasively and can be helpful to predate the patient’s response to anti-PD-1/PD-L1 immunotherapy.

Triple-color fluorescence co-localization of PD-L1-overexpressing cancer exosomes

Programed cell death ligand 1 (PD-L1) is a protein biomarker overexpressed on exosomes derived from tumor cells. It plays an important role in tumor diagnosis, screening, evaluation of therapeutic efficacy, and prognosis. In this study, a facile method is presented to detect PD-L1-overexpressing cancer exosomes with high specificity and sensitivity. First, gold nanospheres (GNSs) were attached to the bottom of an eight-well chambered slide by electrostatic adsorption, forming the detection substrate. Then, Cy5-labeled CD63 aptamers (i.e., the capture probes) were modified on the GNSs by Au-S bond. After adding samples containing target exosomes which were stained by membrane dyes DiI in advance, FAM-labeled PD-L1 aptamers (i.e., the immunoprobes) were added to recognize PD-L1 on the target exosomes. By triple-color fluorescence co-localization (TFC) of the Cy5, DiI, and FAM channels, highly sensitive and reliable detection of the PD-L1-overexpressing exosomes was achieved in the concentration range 7.78 × 10¹ to 7.78 × 10⁴ particles/mL with a detection limit down to 6 particles/mL. The advantages of the proposed detection method include the following; first, the detection substrate is easy to prepare and convenient to clean. Second, the TFC strategy can completely exclude nonspecific reaction sites and thus significantly improves the accuracy. Such a facile and reliable detection method holds a great potential in exosome-based cancer theranostics. In this paper, we proposed a triple-color fluorescence co-localization (TFC) strategy to significantly improve the reliability of exosome detection and the detection substrate is easy to prepare and convenient to clean. In addition, the LOD is down to 6 particles/mL, which is quite low compared with other detection methods.

Aptamer-Initiated Catalytic Hairpin Assembly Fluorescence Assay for Universal, Sensitive Exosome Detection

Cancer-cell-derived exosomes are regarded as noninvasive biomarkers for early cancer diagnosis because of their critical roles in intercellular communication and molecular exchange. A robust aptamer-initiated catalytic hairpin assembly (AICHA) fluorescence assay is proposed for universal, sensitive detection of cancer-derived exosomes. The AICHA was verified with the specific detection of MCF-7 cell-derived exosomes with a wide calibration range of 8.4 particles/μL to 8.4 × 10⁵ particles/μL and a low detection limit (LOD) of 0.5 particles/μL. The universality of the AICHA method was verified for PANC-1 cell-derived exosomes, the LOD of which was determined to be 0.1 particles/μL. The performances in serum samples were detected with a recovery rate range of 95.45-106.2%, which demonstrates its significant potential for protein biomarker analysis and cancer diagnosis.

Current methods and emerging approaches for detection of programmed death ligand 1

Various tumor cells overexpress programmed death ligand 1 (PD-L1), a main immune checkpoint protein (ICP) embedded in the tumor cells membrane, to evade immune recognition through the interaction between PD-L1 and its receptor programmed death 1 (PD-1) which is from T-cells for maintaining immune tolerance. So inhibitors targeting the PD-1 or PD-L1 can block the PD-1/PD-L1 signaling pathway to restore the recognition activity of the immune system to tumor cells, which also have been utilized as a novel approach to improve the clinical therapeutic effect for cancer patients. Since not all cancer patients can respond to these inhibitors effectively, previous diagnosis of PD-L1 is significant to target the right treatments for cancer patients. This review pays attention to the PD-L1 detection and recent progress in the measurement of PD-L1 concentration, including various detection methods based on optical sensors as well as electrochemical assays. Apart from above those, we also focus on the prospects of PD-L1 detection in precision medicine.

An entropy-driven signal-off DNA circuit for label-free, visual detection of small molecules with enhanced accuracy

An entropy-driven DNA circuit offers an efficient means of sensitive analyte detection with signal amplification. In this article, we rationally engineered an aptamer-based entropy-driven signal-off DNA circuit for colorimetric detection of small molecules. The proposed signal-off DNA circuit is activated by target small molecule binding to drive the collapse of G-quadruplex DNAzyme, accompanied by the colour change of the detection solution from dark blue to light blue. Entropy-driven recycling hybridization significantly magnified the input signal of the target small molecule. Such an assay enables naked-eye detection of adenosine triphosphate and oxytetracycline at concentrations as low as 0.5 μM and 1 μM respectively. Moreover, when compared with the signal-on DNA circuit, the entropy-driven signal-off DNA circuit for colorimetric detection has two advantages. Firstly, unlike in the signal-on DNA circuit, the unavoidable formation of waste complexes in the absence of a target in the signal-off DNA circuit has no influence on target detection performance as its background signal is only determined by the substrate complex. Secondly, the signal-on DNA circuit cannot distinguish false-positive signals generated by invasive catalysts (e.g., HRP, serum, Fe₃O₄), while the signal-off DNA circuit can distinguish those signals as undesired signals. Overall, the signal-off DNA circuit affords a novel strategy for sensitive and accurate detection of small molecules.

The generation of PD-L1 and PD-L2 in cancer cells: From nuclear chromatin reorganization to extracellular presentation

The immune checkpoint blockade (ICB) targeting on PD-1/PD-L1 has shown remarkable promise in treating cancers. However, the low response rate and frequently observed severe side effects limit its broad benefits. It is partially due to less understanding of the biological regulation of PD-L1. Here, we systematically and comprehensively summarized the regulation of PD-L1 from nuclear chromatin reorganization to extracellular presentation. In PD-L1 and PD-L2 highly expressed cancer cells, a new TAD (topologically associating domain) (chr9: 5,400,000-5,600,000) around CD274 and CD273 was discovered, which includes a reported super-enhancer to drive synchronous transcription of PD-L1 and PD-L2. The re-shaped TAD allows transcription factors such as STAT3 and IRF1 recruit to PD-L1 locus in order to guide the expression of PD-L1. After transcription, the PD-L1 is tightly regulated by miRNAs and RNA-binding proteins via the long 3'UTR. At translational level, PD-L1 protein and its membrane presentation are tightly regulated by post-translational modification such as glycosylation and ubiquitination. In addition, PD-L1 can be secreted via exosome to systematically inhibit immune response. Therefore, fully dissecting the regulation of PD-L1/PD-L2 and thoroughly detecting PD-L1/PD-L2 as well as their regulatory networks will bring more insights in ICB and ICB-based combinational therapy.

Recent Progress of Exosome Isolation and Peptide Recognition-Guided Strategies for Exosome Research

Exosomes are membrane extracellular vesicles secreted by almost all kinds of cells, which are rich in proteins, lipids, and nucleic acids. As a medium of intercellular communication, exosomes play important roles in biological processes and are closely related to the occurrence, and development of many diseases. The isolation of exosomes and downstream analyses can provide important information to the accurate diagnosis and treatment of diseases. However, exosomes are various in a size range from 30 to 200 nm and exist in complex bio-systems, which provide significant challenges for the isolation and enrichment of exosomes. Different methods have been developed to isolate exosomes, such as the “gold-standard” ultracentrifugation, size-exclusion chromatography, and polymer precipitation. In order to improve the selectivity of isolation, affinity capture strategies based on molecular recognition are becoming attractive. In this review, we introduced the main strategies for exosome isolation and enrichment, and compared their strengths and limitations. Furthermore, combined with the excellent performance of targeted peptides, we summarized the application of peptide recognition in exosome isolation and engineering modification.

Exosomes as a new frontier of cancer liquid biopsy

Liquid biopsy, characterized by minimally invasive detection through biofluids such as blood, saliva, and urine, has emerged as a revolutionary strategy for cancer diagnosis and prognosis prediction. Exosomes are a subset of extracellular vesicles (EVs) that shuttle molecular cargoes from donor cells to recipient cells and play a crucial role in mediating intercellular communication. Increasing studies suggest that exosomes have a great promise to serve as novel biomarkers in liquid biopsy, since large quantities of exosomes are enriched in body fluids and are involved in numerous physiological and pathological processes. However, the further clinical application of exosomes has been greatly restrained by the lack of high-quality separation and component analysis methods. This review aims to provide a comprehensive overview on the conventional and novel technologies for exosome isolation, characterization and content detection. Additionally, the roles of exosomes serving as potential biomarkers in liquid biopsy for the diagnosis, treatment monitoring, and prognosis prediction of cancer are summarized. Finally, the prospects and challenges of applying exosome-based liquid biopsy to precision medicine are evaluated.

Nucleic Acid Substrate-Independent DNA Polymerization on the Exosome Membrane: A Mechanism Study and Application in Exosome Analysis

As generally acknowledged, terminal deoxynucleotidyl transferase (TdT) can only elongate DNA substrates from their 3'-OH ends. Herein, for the first time, we report that TdT-catalyzed DNA polymerization can directly proceed on the exosome membrane without the mediation of any nucleic acids. We prove that both the glycosyl and phenolic hydroxyl groups on the membrane proteins can initiate the DNA polymerization. Accordingly, we have developed powerful strategies for high-sensitive exosome profiling based on a conventional flow cytometer and an emerging CRISPR/Cas system. By using our strategy, the featured membrane protein distributions of different cancer cell-derived exosomes can be figured out, which can clearly distinguish plasma samples of breast cancer patients from those of healthy people. This work paves new ways for exosome profiling and liquid biopsy and expands the understanding of TdT, holding great significance in developing TdT-based sensing systems as well as establishing protein/nucleic acid hybrid biomaterials.

Emerging Advances of Detection Strategies for Tumor-Derived Exosomes

Exosomes derived from tumor cells contain various molecular components, such as proteins, RNA, DNA, lipids, and carbohydrates. These components play a crucial role in all stages of tumorigenesis and development. Moreover, they reflect the physiological and pathological status of parental tumor cells. Recently, tumor-derived exosomes have become popular biomarkers for non-invasive liquid biopsy and the diagnosis of numerous cancers. The interdisciplinary significance of exosomes research has also attracted growing enthusiasm. However, the intrinsic nature of tumor-derived exosomes requires advanced methods to detect and evaluate the complex biofluid. This review analyzes the relationship between exosomes and tumors. It also summarizes the exosomal biological origin, composition, and application of molecular markers in clinical cancer diagnosis. Remarkably, this paper constitutes a comprehensive summary of the innovative research on numerous detection strategies for tumor-derived exosomes with the intent of providing a theoretical basis and reference for early diagnosis and clinical treatment of cancer.

Recent Advances in Aptamer-Based Liquid Biopsy

Liquid biopsy capable of noninvasive and real-time molecular profiling is considered as a breakthrough technology, endowing an opportunity for precise diagnosis of individual patients. Extracellular vesicles (EVs) and circulating tumor cells (CTCs) consisting of substantial disease-related molecular information play an important role in liquid biopsy. Therefore, it is critically significant to exploit high-performance recognition ligands for efficient isolation and analysis of EVs and CTCs from complex body fluids. Aptamers exhibit extraordinary merits of high specificity and affinity, which are considered as superior recognition ligands for liquid biopsy. In this review, we first summarize recent advanced strategies for the evolution of high-performance aptamers and the construction of various aptamer-based recognition elements. Subsequently, we mainly discuss the isolation and analysis of EVs and CTCs based on the aptamer functioned biomaterials/biointerface. Ultimately, we envision major challenges and future direction of aptamer-based liquid biopsy for clinical utilities.

Rapid Determination of Phase Diagrams for Biomolecular Liquid-Liquid Phase Separation with Microfluidics

Biomolecular phase separation is currently emerging in both the medical and life science fields. Meanwhile, the application of liquid-liquid phase separation has been extended to many fields including drug discovery, fibrous material fabrication, 3D printing, and polymer design. Although more than 8600 proteins and other synthetic macromolecules are capable of phase separation as recently reported, there is still a lack of a high-throughput approach to quantitatively characterize its phase behaviors. To meet this requirement, here, we proposed fast and high-resolution acquisition of biomolecular phase diagrams using microfluidic chips. Using this platform, we demonstrated the phase behavior of polyU/RRASLRRASLRRASL in a quantitative manner. Up to 1750 concentration conditions can be generated in 140 min. The detection limitation of our device to capture the saturation concentration for phase separation is about 5 times lower than that of the traditional turbidity method. Thus, our results provide a basis for the rapid acquisition of phase diagrams with high-throughput and pave the way for its wide application.

A simple, rapid and low-cost qPCR assay for evaluating the severity of exosomal PD-L1-mediated T cell exhaustion in blood samples

A novel dual-aptamer activated proximity-induced qPCR assay was developed for the quantitative analysis of exosomal PD-L1 on T cell-exosome complexes in blood samples.

Rapid enrichment and sensitive detection of extracellular vesicles through measuring the phospholipids and transmembrane protein in a microfluidic chip

Extracellular vesicles (EVs) have attracted tremendous attention in recent years and quantification of EVs is a key issue in the evaluation of vesicle-based diagnostics and therapeutic development, but it's quite challenging to determine whether higher protein expression signals are due to larger vesicle amount or higher protein content within each vesicle. To solve this problem, herein, we proposed a strategy based on staining phospholipid bilayers of EVs with lipophilic dyes to evaluate their lipid amount, which was subsequently normalized as an internal standard for studying the expression of transmembrane protein (i.e., CD63) on EVs in different samples. In addition, a microfluidic platform based on electrophoresis technology was invented to effectively enrich and detect EVs. Small fluorescent labeling molecules (i.e., uncombined aptamers) were on-chip removed from EVs without pre-separation via ultracentrifugation or ultrafiltration which were indispensable in nanoparticle tracking analysis (NTA) and flow cytometry techniques and the performance of this assay is comparable to NTA. Finally, it was found obvious difference in the expression of CD63 on EVs before and after normalization based on lipid amount in plasma samples. This method is expected to provide more accurate information when comparing the expression levels of EVs biomarkers in different samples.

Multiplexed Profiling of Extracellular Vesicles for Biomarker Development

Extracellular vesicles (EVs) are cell-derived membranous particles that play a crucial role in molecular trafficking, intercellular transport and the egress of unwanted proteins. They have been implicated in many diseases including cancer and neurodegeneration. EVs are detected in all bodily fluids, and their protein and nucleic acid content offers a means of assessing the status of the cells from which they originated. As such, they provide opportunities in biomarker discovery for diagnosis, prognosis or the stratification of diseases as well as an objective monitoring of therapies. The simultaneous assaying of multiple EV-derived markers will be required for an impactful practical application, and multiplexing platforms have evolved with the potential to achieve this. Herein, we provide a comprehensive overview of the currently available multiplexing platforms for EV analysis, with a primary focus on miniaturized and integrated devices that offer potential step changes in analytical power, throughput and consistency.

Future of PD-1/PD-L1 axis modulation for the treatment of triple-negative breast cancer

Triple-negative breast cancer (TNBC) has the worst prognosis among the subtypes of breast cancer, with no targeted therapy available. Immunotherapy targeting programmed cell death protein-1 (PD-1) and its ligand (PD-L1) has resulted in some promising outcomes in cancer patients. The common treatments are monoclonal antibodies (mAbs). Despite novel methodologies in developing mAbs, there are several drawbacks with these medications. Immunological reactions, expensive and time-consuming production and requiring refrigeration are some of the challenging characteristics of mAbs that are addressed with using aptamers. Aptamers are nucleotide-based structures with high selectivity and specificity for target. Their small size helps aptamers penetrate the tissue better. In this review, we have discussed the nature of PD-1/PD-L1 interaction and summarised the available mAbs and aptamers specific for these two targets. This review highlights the role of aptamers as a future pathway for PD-1/PD-L1 modulation.

Microchamber-Free Digital Flow Cytometric Analysis of T4 Polynucleotide Kinase Phosphatase Based on Single-Enzyme-to-Single-Bead Space-Confined Reaction

Digital bioassays have attracted extensive attention in biomedical applications due to their ultrahigh sensitivity. However, traditional digital bioassays require numerous microchambers such as droplets or microwells, which restricts their application scope. Herein, we propose a microchamber-free flow cytometric method for the digital quantification of T4 polynucleotide kinase phosphatase (T4 PNKP) based on an unprecedented phenomenon that each T4 PNKP molecule-catalyzed reaction can be spatially self-confined on a single microbead, which ultimately enables the one-target-to-one-fluorescence-positive microbead digital signal transduction. The digital signal-readout mode can clearly detect T4 PNKP concentrations as low as 1.28 × 10^-10 U/μL, making it most sensitive method to date. Significantly, T4 PNKP can be specifically distinguished from other phosphatases and nucleases in complex samples by digitally counting the fluorescence-positive microbeads, which cannot be realized by traditional bulk measurement-based methods. Taking advantage of the novel space-confined enzymatic feature of T4 PNKP, this digital mechanism can use T4 PNKP as the enzyme label to fabricate digital sensing systems toward various biomolecules such as digital enzyme-linked immunosorbent assay (ELISA). Therefore, this work not only enlarges the toolbox for high-sensitivity biomolecule detection but also opens new gates to fabricate next-generation digital assays.

Accurate and Nonpurified Identification of Extracellular Vesicles Using Dual-Binding Recognition Mode

Circulating extracellular vesicles (EVs) are promising biomarkers for the early diagnosis and prognosis of cancer in a non-invasive manner. However, the rapid and accurate identification of EVs in complex biological samples is technically challenging, which is attributed to the requirement of extensive sample purification and unsatisfactory detection accuracy due to the disturbance of interfering proteins. Herein, a simultaneous binding of double-positive EV membrane protein-based recognition mode (DRM) is proposed. By the combination of DRM-mediated toehold activation and G-quadruplex DNAZyme-catalyzed etching of Au@Ag nanorods (Au@Ag NRs), we have developed an accurate, non-purified, low-cost, and visual strategy for EV identification. The synchronous binding of double-positive proteins on EV membranes is validated by confocal laser scanning microscopy analysis. This approach exhibits excellent specificity and sensitivity toward EVs ranging from 1.0 × 10⁵ to 1.0 × 10⁹ particles/mL with a detection limit of 6.31 × 10⁴ particles/mL. Moreover, we have successfully realized non-purified EV quantification in complex biological media. In addition, target-initiated catalyzed hairpin assembly (CHA) is integrated with G-quadruplex DNAZyme-catalyzed color variation of Au@Ag NRs; thus, low-background EV detection can be achieved by the naked eye. Furthermore, our strategy is easy to adapt to high-throughput formats by using an automatic microplate reader, which could be expected to meet the requirements for high-throughput detection of clinical samples. With its capacities of rapidness, portability, affordability, high throughput, non-purification, and visual detection, this strategy could provide a practical tool for accurate identification of EVs and early diagnosis of cancer.

Advances in microfluidic extracellular vesicle analysis for cancer diagnostics

Extracellular vesicles (EVs) secreted by cells into the bloodstream and other bodily fluids, including exosomes, have been demonstrated to be a class of significant messengers that mediate intercellular communications. Tumor-derived extracellular vesicles are enriched in a selective set of biomolecules from original cells, including proteins, nucleic acids, and lipids, and thus offer a new perspective of liquid biopsy for cancer diagnosis and therapeutic monitoring. Owing to the heterogeneity of their biogenesis, physical properties, and molecular constituents, isolation and molecular characterization of EVs remain highly challenging. Microfluidics provides a disruptive platform for EV isolation and analysis owing to its inherent advantages to promote the development of new molecular and cellular sensing systems with improved sensitivity, specificity, spatial and temporal resolution, and throughput. This review summarizes the state-of-the-art advances in the development of microfluidic principles and devices for EV isolation and biophysical or biochemical characterization, in comparison to the conventional counterparts. We will also survey the progress in adapting the new microfluidic techniques to assess the emerging EV-associated biomarkers, mostly focused on proteins and nucleic acids, for clinical diagnosis and prognosis of cancer. Lastly, we will discuss the current challenges in the field of EV research and our outlook on future development of enabling microfluidic platforms for EV-based liquid biopsy.