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Early and precise cancer diagnosis is a substantial way to improve patient survival. However, the heterogeneity of cancer and the challenges associated with sampling tissues from concealed anatomical sites hinder reliable diagnosis using conventional clinical approaches. In this case, by leveraging noninvasive sampling and real-time molecular analysis, liquid biopsy offers new opportunities for individualized cancer diagnostics. Although circulating tumor cells (CTCs) and extracellular vesicles (EVs) carry key molecular information, the effective isolation and detection of these rare circulating biomarkers remain technically demanding. Aptamers, which are initially produced by an in vitro-optimized process termed systematic evolution of ligands by exponential enrichment (SELEX), refer to a special category of single-stranded functional oligonucleotides for the specific recognition of targets by folding into unique tertiary structures. Benefiting from their flexible design, chemical/thermal stability, and convenience in modification compared with conventional antibodies, aptamers are widely applied in liquid biopsy for accurate cancer diagnosis in molecular medicine. In this review, we present the emerging methods for detecting biomarkers of liquid biopsy based on aptamers, which are screened by various methods of protein-targeting SELEX technologies. By reviewing the researh progress of aptamers in cancer-associated liquid biopsy, we present our vision on the promising application of aptamers in accurate cancer diagnosis.

Food allergies are increasing at an alarming rate, and it has become necessary to identify patient-specific allergens for personalized allergy immunotherapy treatments. Herein, a precision fish allergy test was established for patient-specific allergen identification and IgE epitope mapping in silver carp by employing an integrated microfluidic chip-MALDI-TOF MS system. Tosyl-activated magnetic beads (MGBs) were functionalized with mouse monoclonal anti-human immunoglobulin E (IgE) antibodies and patient serum to form IgE-MGBs. For patient-specific allergen identification, silver carp (Hypophthalmichthys molitrix) muscle protein extracts were mixed with IgE-MGBs and injected into a microfluidic channel to capture allergenic proteins. Captured allergens were eluted, trypsin-digested, and characterized by MALDI-TOF MS and peptide mass fingerprinting. To map IgE epitopes, tryptic peptides from silver carp proteins were similarly captured by IgE-MGBs and characterized by MALDI-TOF MS and peptide mass fingerprinting. Ten potential allergens were identified from silver carp, nine of which are novel to this fish based on the use of fish allergic serum samples. The allergenicity of identified proteins was predicted using AlgPred and ALLERDET tools, while IgE epitopes were predicted by Bepipred Linear Epitope Prediction 2.0 and experimentally validated via the microfluidic chip-MALDI-TOF MS system. ELISA confirmed the protocol, showing a parvalbumin content of 458.2 µg g⁻¹ in fish muscle. Comparison of fish allergy diagnosis methods further demonstrates the potential of the microfluidic chip-MALDI-TOF MS system to personalize fish allergy detection and aid in identifying patient-specific allergens and IgE epitopes for immunotherapy development.

Sensitive detection of carbendazim (CBZ), a widely monitored bactericidal pesticide globally, is critical to reduce risks to human health. In this study, Eu ions were embedded into a rigid metal–organic framework (MOF), to prepare Eu-MOF as a fluorescence signal source, which was subsequently post-modified with polyethyleneimine (PEI) for efficient coupling with anti-CBZ monoclonal antibodies (mAbs). On this basis, a PEI@Eu-MOF-mAbs fluorescent probe-based lateral flow immunosensor (LFIS) was developed for CBZ analysis, enabling dual-mode detection: rapid visual qualitative observation by the naked eye and intelligent fluorescence quantitative analysis by using a smartphone. PEI modification not only effectively improved the zeta potential, fluorescence intensity, quantum yield, and biological coupling ability of the Eu-MOF to mAbs, but also significantly enhanced the stability and anti-interference performance of PEI@Eu-MOF. The introduction of PEI@Eu-MOF-mAbs probes characterized by strong fluorescence emission, long fluorescence lifetime, and low background interference, markedly improved the detection sensitivity of the LFIS platform for trace CBZ. Under optimal conditions, the detection limit for smartphone-assisted fluorescence analysis was as low as 1.3 pg mL⁻¹ with a wide linear detection range of 0.25–125 ng mL⁻¹ for CBZ. The recoveries in spiked Panax notoginseng samples were 93.40–106.0% with RSD <1.69%, indicating outstanding reliability of the newly developed LFIS platform for accurate detection of CBZ. In comparison with seven other common pesticides, CBZ produced significantly weakened and stable fluorescence, indicating good specificity and stability of the developed platform over 4 weeks. Compared with current analytical methods, the smartphone-assisted PEI@Eu-MOF-mAbs dual-modal LFIS platform exhibited advantages of simple construction, easy operation, rapid response, obvious visualization to the naked eye, and intelligent quantitative analysis, highlighting its broad application potential for rapid screening and accurate point-of-care detection of CBZ in a large number of foods and agricultural products.

Accurate detection and imaging of microRNAs (miRNAs) in living cells are crucial for early cancer diagnosis and prognosis. Although previous studies have focused on developing efficient miRNA detection methods, exploring analytical techniques with high sensitivity, favorable transfection efficiency, and low toxicity remains a pressing challenge due to the low abundance of miRNAs in living cells. To overcome these limitations, we developed a dual-targeting biomimetic sensor for intracellular miRNA-21 imaging. The sensor overcame the limitations of typical catalytic hairpin assembly (CHA) by employing a dual-catalytic cascade amplification strategy that integrated a DNA walker and CHA, enhancing reaction kinetics and signal amplification efficiency. At the same time, benefiting from the dual-targeting effect of the combination of tumor cell membrane coating and aptamers, the sensor achieved specific cellular internalization, thereby enabling specific, rapid, and sensitive detection of intracellular miRNA without interfering with cell activity. Experimental results indicated that our method enabled dynamic and sensitive detection of miRNA in live cells, with a detection limit as low as 0.46 nmol L⁻¹. Owing to the superior analytical performance of the biomimetic sensor, the present strategy holds great potential for clinical cancer diagnostics and real-time monitoring of therapeutic effects and is expected to have broader applications across diverse cancer types.

Lipid membrane vesicles serve as essential cellular compartments where diverse biochemical reactions are regulated through dynamic membrane remodeling, including vesicle fusion. Reconstructing these processes in vitro is crucial for advancing artificial nanobiotechnology. Among intracellular metabolic reactions, isothermal nucleic acid amplification is particularly important because it enables sensitive detection of nucleic acid biomarkers. In this study, we focused on exponential amplification reaction (EXPAR), a straightforward isothermal amplification method initiated by microRNA (miRNA), and developed a system, in which fusion of giant unilamellar vesicles (GUVs) triggers the delivery of miRNA into the reaction compartment, thereby initiating amplification. Using our previously reported microdevice with microchambers and high-aspect-ratio electrodes, we monitored both membrane fusion and the subsequent amplification reaction in situ. This platform provides a proof of concept for detecting nucleic acid biomarkers encapsulated in membrane-bound vesicles and offers promising applications in artificial cell systems and in situ analysis of extracellular vesicles such as exosomes.

Annotation remains a significant challenge in metabolomics, in large part due to the enormous structural diversity of small molecules. PubChem represents one of the largest curated chemical structure databases, with more than 122 000 000 structures, supplemented by extensive biological metadata provided by numerous external sources. While many of these structures are relevant to metabolomics, a majority are unlikely to be measured in a typical metabolomics experiment. This article describes the R package, pubchem.bio, which enables users to: (1) download the metabolomics-centric subset of PubChem onto their local computer, (2) build a metabolomic structured library of biological compounds in PubChem, (3) develop custom metabolite structure libraries for any species or collection of species using selected or all available taxonomic data in PubChem and (4) define a core biological metabolome, comprising metabolites plausibly found in any species. Species-specific metabolomes are enabled through the adoption of a lowest-common-ancestor chemotaxonomy approach, which is implemented by associating PubChem CIDs into the NCBI Taxonomy database hierarchy, enabling extrapolation of the taxonomic range beyond the species reported. This package is available via CRAN, and can be used to simplify the annotation process and embed biological metadata into the annotation process.