Bioprobes-regulated precision biosensing of exosomes: From the nanovesicle surface to the inside

Buoyant Metal-Organic Framework Corona-Driven Fast Isolation and Ultrasensitive Profiling of Circulating Extracellular Vesicles

Accurately assaying tumor-derived circulating extracellular vesicles (EVs) is fundamental in noninvasive cancer diagnosis and therapeutic monitoring but limited by challenges in efficient EV isolation and profiling. Here, we report a bioinspired buoyancy-driven metal-organic framework (MOF) corona that leverages on-bubble coordination and dual-encoded surface-enhanced Raman scattering (SERS) nanotags to streamline rapid isolation and ultrasensitive profiling of plasma EVs in a single assay for cancer diagnostics. This integrated bubble-MOF-SERS EV assay (IBMsv) allows barnacle-like high-density adhesion of MOFs on a self-floating bubble surface to enable fast isolation (2 min, near 90% capture efficiency) of tumor EVs via enhanced EV-MOF binding. Also, IBMsv harnesses four-plexed SERS nanotags to profile the captured EV surface protein markers at a single-particle level. Such a sensitive assay allows multiplexed profiling of EVs across five cancer types, revealing heterogeneous EV surface expression patterns. Furthermore, the IBMsv assay enables cancer diagnosis in a pilot clinical cohort (n = 55) with accuracies >95%, improves discrimination between cancer and noncancer patients via an algorithm, and monitors the surgical treatment response from hepatocellular carcinoma patients. This assay provides a fast, sensitive, streamlined, multiplexed, and portable blood test tool to enable cancer diagnosis and response monitoring in clinical settings.

Force-Encoding DNA Nanomachines for Simultaneous and Direct Detection of Multiple Pathogenic Bacteria in Blood

Pathogen detection is growing in importance in the early stages of bacterial infection and treatment due to the significant morbidity and mortality associated with bloodstream infections. Although various diagnostic approaches for pathogen detection have been proposed, most of them are time-consuming, with insufficient sensitivity and limited specificity and multiplexing capability for clinical use. Here, we report a force-encoding DNA nanomachine for simultaneous and high-throughput detection of multiple pathogens in blood through force-induced remnant magnetization spectroscopy (FIRMS). The force-encoding DNA nanomachines coupled with DNA walkers enable analytical sensitivity down to a single bacterium via a cascade signal amplification strategy. More importantly, it allows for rapid and specific profiling of various pathogens directly in blood samples, without being affected by factors such as light color and solution properties. We expect that this magnetic sensing platform holds great promise for various applications in biomedical research and clinical diagnostics.

Exosome-tuned MOF signal amplifier boosting tumor exosome phenotyping with high-affinity nanostars

The natural phospholipid structure imparts exosomes with not only cargo protection, but rich sites for coordination with metal-organic frameworks (MOFs) to assemble functional nanocomplexes, such as signal amplifiers. Here, we exploit exosomes to tune MOF signal amplifiers (Exo-MOF) for ultrasensitive phenotyping of tumor-derived exosomes (tExo) based on self-driven coordination assembly and high-affinity nanostars. Exo-MOF leverages the specific coordination interaction between exosome and MOF that cages abundant redox molecules to assemble a super-redox signal amplifier. Moreover, the dispersed immuno-magnetic nanostars, which are assembled with antibodies on the surface of Au nanostars-coated magnetic nanoparticles, allow for rapid capturing of target tExo, addressing the limited mass transfer on electrode surface. Both Exo-MOF and high-affinity nanostars orchestrate the ultrahigh sensitivity (1 particle per 100 μL, higher than that no Exo-MOF by at least 10-fold), specificity and speed of the sensor in tExo detection. Such a sensitive strategy allows profiling tExo across seven cancer types, and revealing the distinct exosomal surface expression patterns. Further, the Exo-MOF sensor accurately distinguishes cancer patients from healthy individuals in a clinical cohort, and provides new opportunities for functional materials assembly and precision diagnostics.

Bioorthogonal Microbubbles with Antifouling Nanofilm for Instant and Suspended Enrichment of Circulating Tumor Cells

Integrating clinical rare cell enrichment, culture, and single-cell phenotypic profiling is currently hampered by the lack of competent technologies, which typically suffer from weak cell-interface collision affinity, strong nonspecific adsorption, and the potential uptake. Here, we report cells-on-a-bubble, a bioinspired, self-powered bioorthogonal microbubble (click bubble) that leverages a clickable antifouling nanointerface and a DNA-assembled sucker-like polyvalent cell surface, to enable instant and suspended isolation of circulating tumor cells (CTCs) within minutes. Using this biomimetic engineering strategy, click bubbles achieve a capture efficiency of up to 98%, improved by 20% at 15 times faster over their monovalent counterparts. Further, the buoyancy-activated bubble facilitates self-separation, 3D suspension culture, and in situ phenotyping of the captured single cancer cells. By using a multiantibody design, this fast, affordable micromotor-like click bubble enables suspended enrichment of CTCs in a cohort (n = 42) across three cancer types and treatment response evaluation, signifying its great potential to enable single-cell analysis and 3D organoid culture.

Bottom-Up Signal Boosting with Fractal Nanostructuring and Primer Exchange Reaction for Ultrasensitive Detection of Cancerous Exosomes

Exosomes are emerging as promising biomarkers for cancer diagnosis, yet sensitive and accurate quantification of tumor-derived exosomes remains a challenge. Here, we report an ultrasensitive and specific exosome sensor (NPExo) that initially leverages hierarchical nanostructuring array and primer exchange reaction (PER) for quantitation of cancerous exosomes. This NPExo uses a high-curvature nanostructuring array (bottom) fabricated by single-step electrodeposition to enhance capturing of the target exosomes. The immuno-captured exosome thus provides abundant membrane sites to insert numerous cholesterol-DNA probes with a density much higher than that by immune pairing, which further allows PER-based DNA extension to assemble enzyme concatemers (up) for signal amplification. Such a bottom-up signal-boosting design imparts NPExo with ultrahigh sensitivity up to 75 particles/mL (i.e., <1 exosome per 10 μL) and a broad dynamic range spanning 6 orders of magnitude. Furthermore, our sensor allows monitoring subtle exosomal phenotypic transition and shows high accuracy in discrimination of liver cancer patients from healthy donors via blood samples, suggesting the great potential of NPExo as a promising tool in clinical diagnostics.

Self-Assembly and Disassembly of Membrane Curvature-Sensing Peptide-Based Deep-Red Fluorescent Probe for Highly Sensitive Sensing of Exosomes

With increasing knowledge of the diverse roles of exosomes in biological processes, much attention has been paid to the development of analytical methods for exosome analysis. Here, we developed a new class of amphipathic helical (AH) peptide-based fluorescent probes for highly sensitive detection of exosomes in a mix and read manner. Membrane curvature-sensing AH peptide (ApoC) was coupled with lipophilic tail (C12)-carrying thiazole red (TR) for construction of a self-assembly/disassembly based fluorescence "off-on" sensing system for target exosomes. ApoC-TR_C12 has extremely weak emission due to the formation of the aggregates, whereas it becomes emissive in response to the target exosomes through the binding-induced disassembly of ApoC-TR_C12. We demonstrated that the C12 unit attached to the TR unit had a favorable effect on both fluorescence response (signal-to-background: S/B) and binding affinity. ApoC-TR_C12 was applicable to rapid and simple detection of exosomes with high detection sensitivity (limit of detection ≈ 10³ particles/μL).

In situ detection of exosomal RNAs for cancer diagnosis

Exosomes are considered as biomarkers reflecting the physiological state of the human body. Studies have revealed that the expression levels of specific exosomal RNAs are closely associated with certain cancers. Thus, detection of exosomal RNA offers a new avenue for liquid biopsy of cancers. Many exosomal RNA detection methods based on various principles have been developed, and most of the methods detect the extracted RNAs after lysing exosomes. Besides complex and time-consuming extraction steps, a major drawback of this approach is the degradation of the extracted RNAs in the absence of plasma membrane and cytosol. In addition, there is considerable loss of RNAs during their extraction. In situ detection of exosomal RNAs can avoid these drawbacks, thus allowing higher diagnostic reliability. In this paper, in situ detection of exosomal RNAs was systematically reviewed from the perspectives of detection methods, transport methods of the probe systems, probe structures, signal amplification strategies, and involved functional materials. Furthermore, the limitations and possible improvements of the current in situ detection methods for exosomal RNAs towards the clinical diagnostic application are discussed. This review aims to provide a valuable reference for the development of in situ exosomal RNA detection strategies for non-invasive diagnosis of cancers. STATEMENT OF SIGNIFICANCE: Certain RNAs have been identified as valuable biomarkers for some cancers, and sensitive detection of cancer-related RNAs is expected to achieve better diagnostic efficacy. Currently, the detection of exosomal RNAs is receiving increasing attention due to their high stability and significant concentration differences between patients and healthy individuals. In situ detection of exosomal RNAs has greater diagnostic reliability due to the avoidance of RNA degradation and loss. However, this mode is still limited by some factors such as detection methods, transport methods of the probe systems, probe structures, signal amplification strategies, etc. This review focuses on the progress of in situ detection of exosomal RNAs and aims to promote the development of this field.

DNA Nanomaterial-Based Optical Probes for Exosomal miRNA Detection

Micro ribonucleic acids (miRNAs) in exosomes have been proven as reliable biomarkers to detect disease progression. In recent years, deoxyribonucleic acid (DNA)-based nanomaterials show great potential in the field of diagnosis due to the programmable sequence, various molecule recognition and predictable assembly/disassembly of DNA. In this review, we focus on the molecular design and detection mechanism of DNA nanomaterials, and the developed DNA nanomaterial-based optical probes for exosomal miRNA detection are summarized and discussed. The rationally-designed DNA sequences endows these probes with low background signal and high sensitivity in exosomal miRNA detection, and the detection mechanisms based on different DNA nanomaterials are detailly introduced. At the end, the challenges and future opportunities of DNA nanomaterial-based optical probes in exosomal miRNA detection are discussed. We envision that DNA nanomaterial-based optical probes will be promising in precise biomedicine.

Simultaneous detection of cancerous exosomal miRNA-21 and PD-L1 with a sensitive dual-cycling nanoprobe

Simultaneous detection of specific exosomal surface proteins and inner microRNAs are hampered by their heterogeneity, low abundance and spatial segregation in nanovesicles. Here, we design a dual-cycling nanoprobe (DCNP) to enable single-step simultaneous quantitation of cancerous exosomal surface programmed death-ligand 1 (PD-L1) (ExoPD-L1) and miRNA-21 (ExomiR-21) directly in exosome lysates, without resorting to either RNA extraction or time-consuming transmembrane penetration. In this design, DNA molecular machine-based dual-recognition probes co-assemble onto gold nanoparticle surface for engineering 'silent' DCNPs, which enable signal-amplified synchronous response to dual-targets as activated by ExomiR-21 and ExoPD-L1 within 20 min. Benefiting from cycling amplification of the molecular machine, DCNPs sensor achieves detection limits of tumor exosomes, ExoPD-L1 and ExomiR-21 down to 10 particles/μL, 0.17 pg/mL and 66 fM, respectively. Such a sensitive dual-response strategy allows simultaneous tracking the dynamic changes of ExoPD-L1 and ExomiR-21 expression regulated by signaling molecules or therapeutics. This approach further detects circulating ExoPD-L1 and ExomiR-21 in human plasma to differentiate breast cancer patients from healthy individuals with high accuracy, showing great potential of DCNPs for simultaneous profiling exosomal surface and inside biomarkers, and for clinical precision diagnosis.