Dual-Probe Approach for Mass Spectrometric Quantification of MUC1-Specific Terminal Gal/GalNAc In Situ

MUC1 as a diagnostic biomarker and siRNA-based therapeutic target in breast cancer: A clinical chemistry perspective

Breast cancer remains the leading cause of cancer mortality in women, and early detection coupled with real-time monitoring of tumor burden are clinical imperatives; yet existing imaging-based screening (e.g., mammography, ultrasound) suffers from sensitivities as low as 60-80% and even lower in dense breasts plus substantial false-positive rates, underscoring the critical need for molecular assays with higher accuracy. Current clinical assays for circulating MUC1 (CA15-3) achieve high specificity but exhibit limited sensitivity in early-stage disease, underscoring a critical unmet need for more sensitive, multiplexed biomarkers to enable timely intervention. Mass spectrometry-based glycoproteomic workflows offer multiplexed quantification of tumour-associated MUC1 glycoforms, substantially improving analytical specificity and dynamic range. Complementary liquid-biopsy platforms that detect anti-MUC1 autoantibodies further extend lead time for recurrence detection. Concurrently, small interfering RNA (siRNA) therapies targeting MUC1 delivered via ionizable lipid nanoparticles demonstrate efficient tumor accumulation, robust mRNA knockdown, and favourable safety in phaseI solid tumor trials. In this review, we critically assess the analytical performance and standardization challenges of current MUC1 assays, evaluate emerging mass spectrometry and immunoarray techniques, and examine chemical and nanocarrier strategies that surmount biological barriers to siRNA delivery. We propose a co-development framework for harmonized companion diagnostics and MUC1-directed RNAi therapeutics under unified regulatory pathways, paving the way for precision, biomarker-driven interventions in breast cancer care.

In Situ and In Vivo Evaluation of Multiplex Protein-Specific Glycosylation of Tumors with a Dual-SERS Encoding Strategy

A dual-SERS encoding strategy was designed for in situ and in vivo evaluation of multiplex protein-specific glycosylation of tumors. The dual-SERS encoding strategy consisted of two pairs of dual gold nanoprobes with different diameters of 10 and 30 nm, which were encoded with four different and distinguishable Raman signal molecules. The 10 and 30 nm gold nanoprobes (Au10 and Au30 probes, respectively) were further modified with lectins and aptamers to recognize the target glycans and proteins, respectively. After sequential binding to the target glycans and proteins, the adjacent Au10 and Au30 probes could emit strong surface-enhanced Raman scattering (SERS) signals to indicate the multiplex protein-specific glycosylation information on cells and in vivo, which can reveal in situ the distribution differences of different tumor markers in the central and marginal regions of tumors. This strategy has been successfully applied for in situ imaging and evaluation of the MUC1 and EpCAM-specific Sia and Gal/GalNAc information on cell surfaces and tumor xenografted mice, providing a convenient and powerful tool to study protein-specific glycosylation-related physiological and pathological mechanisms.

Profuse color-evolution based aptasensor for mucin 1 detection utilizing urease-mediated color mixing of the mixed pH indicator

Mucin 1 is a significant tumor marker, and developing portable and cost-effective methods for its detection is crucial, especially in resource-limited areas. Herein, we developed an innovative approach for mucin 1 detection using a visible multicolor aptasensor. Urease-encapsulated DNA microspheres were used to mediate multicolor change facilitated by the color mixing of the mixed pH indicator, a mixed methyl red and bromocresol green solution. Distinct color changes were exhibited in response to varying mucin 1 concentrations. Notably, the color mixing of the mixed pH indicator was used to display various hues of colors, broadening the range of color variation. And color tonality is much easier to differentiate than color intensity, improving the resolution with naked-eyes. Besides, the variation of color from red to green (a pair of complementary colors) enhanced the color contrast, heightening sensitivity for visual detection. Importantly, the proposed method was successfully applied to detect mucin 1 in real samples, demonstrating a clear differentiation of colors between the samples of healthy individuals and breast cancer patients. The use of a mixed pH indicator as a multichromatic substrate offers the merits of low cost, fast response to pH variation, and plentiful color-evolution. And the incorporation of calcium carbonate microspheres to encapsulate urease ensures stable urease activity and avoids the need for extra urease decoration. The color-mixing dependent strategy opens a new way for multicolor detection of MUC1, characterized by vivid color changes.

Integrating aptasensor with an explosive mass-tag signal amplification strategy for ultrasensitive and multiplexed analysis using a miniature mass spectrometer

Mass probes attached with aptamers and mass tags offer excellent specificity and sensitivity for multiplexed detection, wherein the dissociation of mass tags from the mass probes is as important as their labeling. Herein, aggregation-induced emission luminogen (AIEgen)-tagged mass probes (AIEMPs) were established to analyze estrogens, which integrated aptasensor with an explosive mass-tag signal amplification strategy via a simple ultrasound-assisted emulsification of nanoliposomes. The AIEMPs were assembled by the hybridization of aptamer-modified Fe3O4 nanoparticles (Fe NPs@Apt) and nanoliposomes loaded with massive AIEgen mass tags and partially complementary DNA strands (AIE NLs@cDNA). The aptamer was preferentially and specifically bound to estrogen, resulting in the detachment of AIE NLs from AIEMPs. Subsequently, the AIEMPs were deposited with electrospray solvents for explosive release of mass tags. Using nanoelectrospray ionization mass spectrometry (nanoESI-MS), the AIEMP-based aptasensor achieved ultrasensitive analysis of estrogens with limits of detection of 0.168-0.543 pg/mL and accuracies in the range of 87.9-114.0%. Compared to direct nanoESI-MS detection, the AIEMP-based aptasensor provides a signal amplification of four orders of magnitude. Furthermore, the utilization of different AIEMPs enables multiplexed detection of three estrogens with a miniature mass spectrometer, showing promising potential for on-site detection. This work expands the diversity of mass-tagging strategy and provides a versatile mass probe-based aptasensor platform for routine MS detection of trace analytes.

Harnessing aptamers for the biosensing of cell surface glycans - A review

Cell surface glycans (CSGs) are essential for cell recognition, adhesion, and invasion, and they also serve as disease biomarkers. Traditional CSG recognition using lectins has limitations such as limited specificity, low stability, high cytotoxicity, and multivalent binding. Aptamers, known for their specific binding capacity to target molecules, are increasingly being employed in the biosensing of CSGs. Aptamers offer the advantage of high flexibility, small size, straightforward modification, and monovalent recognition, enabling their integration into the profiling of CSGs on living cells. In this review, we summarize representative examples of aptamer-based CSG biosensing and identify two strategies for harnessing aptamers in CSG detection: direct recognition based on aptamer-CSG binding and indirect recognition through protein localization. These strategies enable the generation of diverse signals including fluorescence, electrochemical, photoacoustic, and electrochemiluminescence signals for CSG detection. The advantages, challenges, and future perspectives of using aptamers for CSG biosensing are also discussed.

Dual-Recognition Triggered Proximity Ligation Combined with a Rolling Circle Amplification Strategy for Analysis of Exosomal Protein-Specific Glycosylation

Exosomal surface glycan reveals the biological function and molecular information on the protein, especially in indicating the pathogenesis of certain diseases through monitoring of specific protein glycosylation accurately. However, in situ and nondestructive measurement techniques for certain Exosomal glycoproteins are still lacking. In this work, combined with on-chip purification, we designed a proximity ligation assay-induced rolling circle amplification (RCA) strategy for highly sensitive identification of Exosomal protein-specific glycosylation based on a couple of proximity probes to target Exosomal protein and the protein-specific glycosylation site. Benefiting from efficient separation, scalable dual-recognition, and proximity-triggered RCA amplification, the proposed strategy could convert different protein-specific glycan levels to prominent changes in absorbance signals, resulting in accurate quantification of specific glycosylated Exosomal protein. When detecting the glycosylated PD-L1 on MDA-MB-231 exosomes and glycosylated PTK7 on HepG2 exosomes, the detection limits were calculated to be as low as 1.04 × 104 and 2.759 × 103 particles/mL, respectively. In addition, we further expand the dual-recognition site to investigate the potential correlation of Exosomal glycosylation with polarization of THP-1 cells toward the tumor-suppressive M1 phenotype. Overall, this strategy provides a universal tool for multiple analyses of diverse protein-specific glycosylated exosomes, exhibiting enormous potential to explore exosome function and search for new early diagnosis markers.

Aptamer-based sample purification for mass spectrometric quantification of trastuzumab in human serum

In this study, we developed a simple liquid chromatography-tandem mass spectrometry (LC-MS/MS) assay to quantify trastuzumab in human serum using aptamers for sample purification. Trastuzumab was extracted from serum samples using the capture probe based on its aptamer CH1S-3, followed by reduction, alkylation, trypsin digestion, and quantification using LC-MS/MS. Additionally, a unique peptide, FTISADTSK, was employed as a surrogate peptide and quantified, and *FTISADTSK (¹³C₉¹⁵N-labeled phenylalanine) was used as an internal standard to minimize variability in detection among the samples. The detection range for this method was 0.5-250 μg/mL, with a high correlation coefficient (r² > 0.99). The intra- and inter-day precision (%CV, the coefficient of variation) of the quality control samples was less than 12.7%, and the accuracy (%bias) was below 8.64%. After optimization and verification, this assay was used to determine trastuzumab levels in clinical human serum samples. The results indicated that the trastuzumab concentrations had an approximate 4-fold difference among ten patients (range: 11.80-41.90 μg/mL). This study provides a novel approach for the accurate and quantitative monitoring of the mAb-trastuzumab.

A magnetic DNAzyme walker for both in-situ imaging and sensitive detection of MUC1 on living cells

Mucin 1 (MUC1) is a transmembrane glycoprotein commonly expressed in epithelial cells with stable levels and polarized distribution. Their expression levels and spatial distribution abnormally altered during oncogenesis and play tumor-promoting roles synergistically. We herein propose a magnetic DNAzyme walker (MDW) for both in-situ imaging and sensitive detection of MUC1. This MDW was constructed by modifying specially designed track strands (TSs) and walking strands (WSs) on a streptavidin magnetic bead (SA-MB). The TSs contained cleavage sites for DNAzymes and were labeled with Cy3 at free ends. The WSs contained DNAzyme sequences and were firstly blocked by hybridizing with Cy5-labeled aptamers of MUC1. The DNAzymes were unlocked upon aptamers binding to MUC1 on cells. MDWs were then transferred to a buffer suitable for DNAzyme action, where the unlocked DNAzymes cleaved multiple TSs, releasing amplified Cy3-fragments, which were separated from the uncleaved ones by magnetic separation. In-situ imaging of MUC1 were achieved by the fluorescence of Cy5 on aptamers bound to MUC1. Sensitive detection of MUC1 were achieved by the amplified fluorescence of released Cy3. In-situ imaging and walker operation for detection were triggered by the same targets at the same time, ensuring the signals are real-time correlative. Moreover, MDWs' operation was separated from cells, reducing interference between imaging and detection. The proposed MDW offers a potential approach for comprehensive analysis of MUC1 in early diagnosis and progression assessment of tumor.

Microstructured Optical Fiber-Enhanced Light-Matter Interaction Enables Highly Sensitive Exosome-Based Liquid Biopsy of Breast Cancer

Exosome-based liquid biopsies highlight potential utility in diagnosis and determining the prognosis of patients with cancer and other diseases. However, the existing techniques are severely limited for practical applications due to the complications of high cost, low sensitivity, tedious procedures, and large sample consumption. Herein, we report a microstructured optical fiber sensor for fast, sensitive, and accurate quantification of exosomes in blood samples of breast cancer patients. Numerical simulations are applied to demonstrate that hollow-core microstructured antiresonant fibers (HARFs) can stringently confine light in the fiber core, ensuring strong light-matter interaction and thus maximumly amplifying the signal. Taking this advantage, a AuNPs-dsDNA assembly containing gold nanoparticles, a recognizing DNA aptamer, and a fluorescent reporter DNA sequence is fabricated followed by immobilization on the fiber wall to form a AuNPs-dsDNA-HARF sensor. Cancer-derived exosomes can be recognized and captured in the fiber channel and generate dose-dependent fluorescent signals for quantification. The microfiber sensor demonstrates enhanced sensitivity and specificity, enabling the detection of single digits of exosome particles at the nanoliter sample level. In addition, by tracking exosome phenotypic changes, the proposed fiber sensor can facilitate precise drug treatment monitoring. This work provides a robust platform for exosome-based biopsy for cancer diagnosis and prediction of therapeutic outcomes.

Landscape of circulating metabolic fingerprinting for keloid

Background

Keloids are a fibroproliferative disease characterized by unsatisfactory therapeutic effects and a high recurrence rate.

Objective

This study aimed to investigate keloid-related circulating metabolic signatures.

Methods

Untargeted metabolomic analysis was performed to compare the metabolic features of 15 keloid patients with those of paired healthy volunteers in the discovery cohort. The circulating metabolic signatures were selected using the least absolute shrinkage. Furthermore, the selection operators were quantified using multiple reaction monitoring-based target metabolite detection methods in the training and test cohorts.

Results

More than ten thousand metabolic features were consistently observed in all the plasma samples from the discovery cohort, and 30 significantly different metabolites were identified. Four differentially expressed metabolites including palmitoylcarnitine, sphingosine, phosphocholine, and phenylalanylisoleucine, were discovered to be related to keloid risk in the training and test cohorts. In addition, using linear and logistic regression models, the respective risk scores for keloids based on a 4-metabolite fingerprint classifier were established to distinguish keloids from healthy volunteers.

Conclusions

In summary, our findings show that the characteristics of circulating metabolic fingerprinting manifest phenotypic variation in keloid onset.

Construction of a Recyclable DNAzyme Motor for MUC1-Specific Glycoform In Situ Quantification

Changes in the glycosylation content, especially in specific proteins, are of great importance for interpreting the mechanisms and development of certain diseases. However, current detection techniques are limited by the weak ionization efficiency of glycosyls and poor anti-interference of fluorescence signals. Herein, we present a general in situ quantification strategy for protein-specific glycoforms by constructing a recyclable DNAzyme motor for mass spectrometric detection using MUC1-specific sialic acid (Sia) as a model. This approach relies on a DNAzyme-based recycling strategy and two well-designed probes: a protein and a glycan probe. The protein probe consists of an aptamer and a DNAzyme. The glycan probe contains three functional domains: a DNAzyme complementary sequence, a substrate peptide segment, and a dibenzocyclooctyne tag. First, these two probes bind to their corresponding targets and trigger hybridization between adjacent probes on the same protein. With the help of the metal cofactor, the DNAzyme of the protein probe hydrolyzes the double-stranded glycan probe. The protein probe then reverts to a single-stranded state and remains intact for the next round of hybridization and cleavage. In this way, the recyclable DNAzyme motor can hydrolyze all glycan probes bound to the target protein. Finally, the reporter peptide released from the hydrolyzed glycan probes can be quantified by mass spectrometry, thereby converting the signal of the protein-specific glycoform to that of mass spectrometry. This strategy has been successfully used for in situ quantification of MUC1-specific Sia in different breast cancer cell lines. It provides a promising platform for protein-specific glycoform quantification.

Construction of a Mass-Tagged Oligo Probe Set for Revealing Protein Ratiometric Relationship Associated with EGFR-HER2 Heterodimerization in Living Cells

Protein dimerization, as the most common form of protein-protein interaction, can manifest more significant roles in cellular signaling than individual monomers. For example, excessive formation of EGFR-HER2 dimer has been implicated in cancer development and therapeutic resistance in addition to the overexpression of EGFR and HER2 proteins. Thus, quantitative evaluation of these heterodimers in living cells and revelation of their ratiometric relationship with protein monomers in dimerization may provide insights into clinical cancer management. To achieve this goal, the prerequisite is protein heterodimer quantification. Given the current lack of quantitative methods, we constructed a mass-tagged oligo nanoprobe set for quantification of EGFR-HER2 dimer in living cells. The mass-tagged oligo nanoprobe set contained two targeting probes (nucleic acid aptamers), a connector probe, a hairpin probe, and a photocleavable mass-tagged probe. Two distinct aptamers can recognize target protein monomers and initiate the subsequent hybridization cascade involving binding to the connector probe, formation of an initiator strand, opening of a hairpin probe, and ensuing hybridization with a photocleavable mass-tagged probe. Ultimately, the mass tag was released under ultraviolet light and then subjected to mass spectrometric analysis. In this way, the information regarding the interaction between two protein monomers was successfully converted to the quantitative signal of the mass tag. Using the assay, the expression level of EGFR-HER2 dimer and its relationship with individual protein monomers were determined in four breast cancer cell lines. We are among the first to obtain the absolute level of protein heterodimer, and this quantitative information may be vital in understanding the molecular basis of cancer.

A mass-tagged MOF nanoprobe approach for ultra-sensitive protein quantification in tumor-educated platelets

A mass-tagged metal-organic framework (MOF) nanoprobe approach was developed for ultra-sensitive quantification of platelet protein CD44 by integrating activable aptamer recognition and MOF nanoprobe signal amplification with mass spectrometric detection. This approach offered high sensitivity and quantitative capability for low abundant protein analysis in tumor-educated platelets (TEPs), exhibiting great potential in cancer diagnosis and management.

Tetrahedral DNA Nanostructure with Multiple Target-Recognition Domains for Ultrasensitive Electrochemical Detection of Mucin 1

In this work, a tetrahedral DNA nanostructure (TDN) designed with multiple biomolecular recognition domains (m-TDN) was assembled to construct an ultrasensitive electrochemical biosensor for the quantitative detection of tumor-associated mucin 1 (MUC-1) protein. This new nanostructure not only effectively increased the capture efficiency of target proteins compared to the traditional TDN with a single recognition domain but also enhanced the sensitivity of the constructed electrochemical biosensors. Once the target MUC-1 was captured by the protein aptamers, the ferrocene-marked DNA strands as electrochemical signal probes at the vertices of m-TDN would be released away from the electrode surface, causing significant reduction of the electrochemical signal, thereby enhancing significantly the detection sensitivity. As a result, this well-designed biosensor achieved ultrasensitive detection of the biomolecule at a linear range from 1 fg mL^-1 to 1 ng mL^-1, with the limit of detection down to 0.31 fg mL^-1. This strategy provides a new approach to enhance the detection sensitivity for the diagnosis of diseases.

Breast cancer glycan biomarkers: their link to tumour cell metabolism and their perspectives in clinical practice

INTRODUCTION

Breast cancer (BCa) is the most common cancer type diagnosed in women and 5^th most common cause of deaths among all cancer deaths despite the fact that screening program is at place. This is why novel diagnostics approaches are needed in order to decrease number of BCa cases and disease mortality.

AREAS COVERED

In this review paper, we aim to cover some basic aspects regarding cellular metabolism and signalling in BCa behind altered glycosylation. We also discuss novel exciting discoveries regarding glycan-based analysis, which can provide useful information for better understanding of the disease. The final part deals with clinical usefulness of glycan-based biomarkers and the clinical performance of such biomarkers is compared to already approved BCa biomarkers and diagnostic tools based on imaging.

EXPERT OPINION

Recent discoveries suggest that glycan-based biomarkers offer high accuracy for possible BCa diagnostics in blood, but also for better monitoring and management of BCa patients. The review article was written using Web of Science search engine to include articles published between 2019 and 2021.

Mass spectrometry-based chemical mapping and profiling toward molecular understanding of diseases in precision medicine

Precision medicine has been strongly promoted in recent years. It is used in clinical management for classifying diseases at the molecular level and for selecting the most appropriate drugs or treatments to maximize efficacy and minimize adverse effects. In precision medicine, an in-depth molecular understanding of diseases is of great importance. Therefore, in the last few years, much attention has been given to translating data generated at the molecular level into clinically relevant information. However, current developments in this field lack orderly implementation. For example, high-quality chemical research is not well integrated into clinical practice, especially in the early phase, leading to a lack of understanding in the clinic of the chemistry underlying diseases. In recent years, mass spectrometry (MS) has enabled significant innovations and advances in chemical research. As reported, this technique has shown promise in chemical mapping and profiling for answering "what", "where", "how many" and "whose" chemicals underlie the clinical phenotypes, which are assessed by biochemical profiling, MS imaging, molecular targeting and probing, biomarker grading disease classification, etc. These features can potentially enhance the precision of disease diagnosis, monitoring and treatment and thus further transform medicine. For instance, comprehensive MS-based biochemical profiling of ovarian tumors was performed, and the results revealed a number of molecular insights into the pathways and processes that drive ovarian cancer biology and the ways that these pathways are altered in correspondence with clinical phenotypes. Another study demonstrated that quantitative biomarker mapping can be predictive of responses to immunotherapy and of survival in the supposedly homogeneous group of breast cancer patients, allowing for stratification of patients. In this context, our article attempts to provide an overview of MS-based chemical mapping and profiling, and a perspective on their clinical utility to improve the molecular understanding of diseases for advancing precision medicine.

Electrofluorochromic Imaging Analysis of Glycan Expression on Living Single Cell with Bipolar Electrode Arrays

The in situ glycan profiling of a single tumor cell plays an important role in personalized cancer treatment. Herein, an integrated microfluidic system was designed for living single-cell trapping and real-time monitoring of galactosyl expression on the surface, combining closed bipolar electrode (BPE) arrays and electrofluorochromic (EFC) imaging. Galactosyl groups on human liver cancer HepG2 cells were used as the model analysts, galactose oxidase (GAO) could selectively oxidize hydroxyl sites of galactosyl groups on the cell surface to aldehydes, and then biotin hydrazide (BH) was used to label the aldehydes by aniline-catalyzed hydrazone ligation. With the biotin-avidin system, nanoprobes were finally introduced to the galactosyl groups on the cell surface with avidin as a bridge, which was prepared by simultaneously assembling ferrocene-DNA (Fc-DNA) and biotin-DNA (Bio-DNA) on gold nanoparticles (AuNPs) due to their large surface area and excellent electrical conductivity. After a labeled single cell was captured in the anodic microchannel, the Fc groups attached on the cell surface were oxidized under suitable potential, and the nonfluorescent resazurin on the cathode was correspondingly reduced to produce highly fluorescent resorufin, collected by fluorescence confocal microscope. The combination of EFC imaging and BPE realized monitoring galactosyl group expression of 5.0 × 10⁸ molecules per cell. Furthermore, the proposed platform had the ability to distinguish a single cancer cell from a normal cell according to the expression level of galactosyl groups and to dynamically monitor the galactosyl group variation on the cell surface, providing a simple and accessible method for the single-cell analysis.

A SERS-colorimetric dual-mode aptasensor for the detection of cancer biomarker MUC1

Human mucin-1 (MUC1) has attracted considerable attention owing to its overexpression in diverse malignancies. Here, for the rapid and efficient detection of MUC1, we present a SERS-colorimetric dual-mode aptasensor, by integrating SERS probes with magnetic separation, which has several distinctive advantages. Using such a dual-mode aptasensor, the colorimetric functionality is distinguishable by the naked eye, providing a fast and straightforward screening ability for the detection of MUC1. Moreover, SERS-based detection greatly improves the detection sensitivity, reaching a limit of detection of 0.1 U/mL. In addition, the combination of SERS and colorimetric method holds the advantages of these two techniques and thereby increases the reliability and efficiency of MUC1 detection. On the one hand, the magnetic nanobeads functionalized with MUC1-specific aptamer were utilized as an efficient capturing substrate for separating MUC1 from biological complex medium. On the other hand, the gold-silver core-shell nanoparticles modified with Raman reporters and the complementary sequences of MUC1 were used as the signal indicator, which could simultaneously report the SERS signal and colorimetric change. This strategy can achieve a good detection range and realize MUC1 analysis in real patients' samples. Thus, we anticipate that this kind of aptasensor would provide promising potential applications in the diagnosis and prognosis of cancers. Graphical abstract.