Medical Relevance, State-of-the-Art and Perspectives of "Sweet Metacode" in Liquid Biopsy Approaches.

This review briefly introduces readers to an area where glycomics meets modern oncodiagnostics with a focus on the analysis of sialic acid (Neu5Ac)-terminated structures. We present the biochemical perspective of aberrant sialylation during tumourigenesis and its significance, as well as an analytical perspective on the detection of these structures using different approaches for diagnostic and therapeutic purposes. We also provide a comparison to other established liquid biopsy approaches, and we mathematically define an early-stage cancer based on the overall prognosis and effect of these approaches on the patient's quality of life. Finally, some barriers including regulations and quality of clinical validations data are discussed, and a perspective and major challenges in this area are summarised.

Negative Charge-Carrying Glycans Attached to Exosomes as Novel Liquid Biopsy Marker.

Prostate cancer (PCa) is the second most common cancer. In this paper, the isolation and properties of exosomes as potential novel liquid biopsy markers for early PCa liquid biopsy diagnosis are investigated using two prostate human cell lines, i.e., benign (control) cell line RWPE1 and carcinoma cell line 22Rv1. Exosomes produced by both cell lines are characterised by various methods including nanoparticle-tracking analysis, dynamic light scattering, scanning electron microscopy and atomic force microscopy. In addition, surface plasmon resonance (SPR) is used to study three different receptors on the exosomal surface (CD63, CD81 and prostate-specific membrane antigen-PMSA), implementing monoclonal antibodies and identifying the type of glycans present on the surface of exosomes using lectins (glycan-recognising proteins). Electrochemical analysis is used to understand the interfacial properties of exosomes. The results indicate that cancerous exosomes are smaller, are produced at higher concentrations, and exhibit more nega tive zeta potential than the control exosomes. The SPR experiments confirm that negatively charged α-2,3- and α-2,6-sialic acid-containing glycans are found in greater abundance on carcinoma exosomes, whereas bisecting and branched glycans are more abundant in the control exosomes. The SPR results also show that a sandwich antibody/exosomes/lectins configuration could be constructed for effective glycoprofiling of exosomes as a novel liquid biopsy marker.

MXene-based electrochemical devices applied for healthcare applications.

The initial part of the review provides an extensive overview about MXenes as novel and exciting 2D nanomaterials describing their basic physico-chemical features, methods of their synthesis, and possible interfacial modifications and techniques, which could be applied to the characterization of MXenes. Unique physico-chemical parameters of MXenes make them attractive for many practical applications, which are shortly discussed. Use of MXenes for healthcare applications is a hot scientific discipline which is discussed in detail. The article focuses on determination of low molecular weight analytes (metabolites), high molecular weight analytes (DNA/RNA and proteins), or even cells, exosomes, and viruses detected using electrochemical sensors and biosensors. Separate chapters are provided to show the potential of MXene-based devices for determination of cancer biomarkers and as wearable sensors and biosensors for monitoring of a wide range of human activities.

A Holistic 4D Approach to Optimize Intrinsic and Extrinsic Factors Contributing to Variability in Microarray Biosensing in Glycomics.

Protein-carbohydrate interactions happen to be a crucial facet of biology, discharging a myriad of functions. Microarrays have become a premier choice to discern the selectivity, sensitivity and breadth of these interactions in a high-throughput manner. The precise recognition of target glycan ligands among the plethora of others is central for any glycan-targeting probe being tested by microarray analyses. Ever since the introduction of the microarray as an elemental tool for high-throughput glycoprofiling, numerous distinct array platforms possessing different customizations and assemblies have been developed. Accompanying these customizations are various factors ushering variances across array platforms. In this primer, we investigate the influence of various extrinsic factors, namely printing parameters, incubation procedures, analyses and array storage conditions on the protein-carbohydrate interactions and evaluate these factors for the optimal performance of microarray glycomics analysis. We hereby propose a 4D approach (Design-Dispense-Detect-Deduce) to minimize the effect of these extrinsic factors on glycomics microarray analyses and thereby streamline cross-platform analyses and comparisons. This work will aid in optimizing microarray analyses for glycomics, minimize cross-platform disparities and bolster the further development of this technology.

Amperometric Miniaturised Portable Enzymatic Nanobiosensor for the Ultrasensitive Analysis of a Prostate Cancer Biomarker.

Screen-printing technology is a game changer in many fields including electrochemical biosensing. Two-dimensional nanomaterial MXene Ti3C2Tx was integrated as a nanoplatform to immobilise enzyme sarcosine oxidase (SOx) onto the interface of screen-printed carbon electrodes (SPCEs). A miniaturised, portable, and cost-effective nanobiosensor was constructed using chitosan as a biocompatible glue for the ultrasensitive detection of prostate cancer biomarker sarcosine. The fabricated device was characterised with energy-dispersive X-ray spectroscopy (EDX), electrochemical impedance spectroscopy (EIS) and cyclic voltammetry (CV). Sarcosine was detected indirectly via the amperometric detection of H2O2 formed during enzymatic reaction. The nanobiosensor could detect sarcosine down to 7.0 nM with a maximal peak current output at 4.10 ± 0.35 × 10-5 A using only 100 µL of a sample per measurement. The assay run in 100 µL of an electrolyte showed the first linear calibration curve in a concentration window of up to 5 µM with a slope of 2.86 µA·µM-1, and the second linear calibration curve in the range of 5-50 µM with a slope of 0.32 ± 0.01 µA·µM-1 (R2 = 0.992). The device provided a high recovery index of 92.5% when measuring an analyte spiked into artificial urine, and could be used for detection of sarcosine in urine for at least a period of 5 weeks after the preparation.

How to choose proper magnetic particles for bioaffinity interactions? The case for immobilised glyconanoconjugate.

In this study, an assay for detection of the cancer biomarker Thomsen-nouvelle (Tn) antigen on the ELISA plates format was designed and developed. The effects of size and the interfacial density of the negative charge of magnetic beads (MBs) on the specific sensitivity of the bioaffinity interaction were studied. In particular, glyconanoconjugate, i.e. glycan Tn antigen conjugated to bovine serum albumin (BSA) was covalently immobilised on MBs for the bioaffinity detection of anti-Tn antibodies as cancer biomarkers. Six different MBs were used in the study, i.e. carboxy-modified MBs of 250 nm, 500 nm, 1000 nm and 2800 nm and epoxy-modified MBs of 2800 nm and 4500 nm. In order to evaluate which MBs are the best suited for detection of the analyte anti-Tn antibodies, sensitivities of detection (slopes from calibration curves) were calculated. Next, specific sensitivities were calculated for each type of MBs as a ratio of sensitivity of detection to the mass of MBs. From zeta potential ζ for each type of MBs, the interfacial charge density on MBs was calculated, expressed as the density of zeta potential ζd (ratio of zeta potential to surface area of MBs, i.e. ζd = Î¶/A). Then, we evaluated the effect of size and ζd on the specific sensitivity of detection of anti-Tn antibodies in order to understand the immobilisation process on nanoscale. We also identified an optimal value of ζd on MBs; this was essential to achieve highly sensitive detection of the analyte, which made it possible to attain limit of detection (LOD) of (0.31 ± 0.01) ng mL-1 or (2.10 ± 0.04) pM for analyte detection. In addition, the optimal assay configuration was highly selective and enabled reliable detection of the analyte in human serum with a recovery index in the range of 102-104%.

MXene as a novel cartridge for N-glycan enrichment.

In this study, we applied MXene as column cartridge for N-glycan enrichment from human samples with a focus on the analysis of sialic acid linkages using a derivatisation protocol followed by glycan analysis via Matrix Assisted Laser Desorption Ionisation-Time Of Flight Mass Spectrometry (MALDI-TOF-MS). The MXene-based cartridge enriches a higher number of glycans (i.e., sialylated and bisecting N-glycans) when compared to the commercial HILIC columns. We demonstrate the strong potential of MXene as a stationary phase in MS glycomic analysis.

Redox features of hexaammineruthenium(III) on MXene modified interface: Three options for affinity biosensing.

In this article we describe construction of a bioreceptive interface for detection of a breast cancer biomarker carbohydrate antigen CA15-3. The conductive interface was patterned by a 2D nanomaterial MXene, to which a mixed layer containing sulfobetaine and carboxybetaine was electrochemically grafted through a diazonium moiety. Such a modified interface was then applied for covalent immobilisation of anti-CA15-3 antibody as a bioreceptive probe for detection of a breast cancer biomarker. Two different strategies were applied for final construction of an immunosensor i.e. an interface finally blocked by bovine serum albumin or an immunosensor without such modification. Finally, electrochemical reading was accomplished using a soluble redox probe Ru(NH3)63+ ion for detection of CA15-3 in a clinically relevant range up to 50 U mL-1. The results indicate that immunosensor based on non-blocked interface can be applied for biosensing using two modes of action: 1. differential pulse voltammetry (a plot of a peak current vs. analyte concentration) and 2. an electrochemical impedance spectroscopy (a plot of a charge transfer resistance vs. analyte concentration). The electrode blocked by bovine serum albumin (BSA) can be used by additional 3. mode of action: through detection of changes in the potential (a plot Epvs. c). Additionally, we reveal and explain that Ru(NH3)63+ is redox probe, which can be applied as interfacial molecular nanoscale ruler to distinguish negatively charged protein molecules present in the close proximity (≤ 6 nm) of the electrode (in our case adsorbed BSA molecules) from the negatively charged protein molecules at a larger distance (>12 nm) from the electrode (i.e. CA15-3 analyte).

Facile fabrication of screen-printed MoS2 electrodes for electrochemical sensing of dopamine.

Molybdenum disulfide (MoS2) screen-printed working electrodes were developed for dopamine (DA) electrochemical sensing. MoS2 working electrodes were prepared from high viscosity screen-printable inks containing various concentrations and sizes of MoS2 particles and ethylcellulose binder. Rheological properties of MoS2 inks and their suitability for screen-printing were analyzed by viscosity curve, screen-printing simulation and oscillatory modulus. MoS2 inks were screen-printed onto conductive FTO (Fluorine-doped Tin Oxide) substrates. Optical microscopy and scanning electron microscopy with energy-dispersive X-ray spectroscopy (SEM/EDX) analysis were used to characterize the homogeneity, topography and thickness of the screen-printed MoS2 electrodes. The electrochemical performance was assessed through differential pulse voltammetry. Results showed an extensive linear detection of dopamine from 1 µM to 300 µM (R2 = 0.996, sensitivity of 5.00 × 10-8 A µM-1), with the best limit of detection being 246 nM. This work demonstrated the possibility of simple, low-cost and rapid preparation of high viscosity MoS2 ink and their use to produce screen-printed FTO/MoS2 electrodes for dopamine detection.

Amplified suspension magnetic bead-based assay for sensitive detection of anti-glycan antibodies as potential cancer biomarkers.

The development of a novel SUspension Magnetic-Bead-based Assay (SUMBA) for the detection of antibodies against aberrant glycans (AGA) as potential cancer biomarkers is presented here. The SUMBA method was extensively optimised by choosing proper commercially available AGA able to specifically, and with high affinity, recognise aberrant glycans, which were attached to the protein backbone working as a molecular scaffold (a glycoconjugate). The whole SUMBA was optimised using several analytical techniques such as Surface Plasmon Resonance and Energy Dispersive X-ray Spectroscopy. Additionally, the SUMBA method was extensively optimised for signal enhancement. With all steps optimised, we were able to detect AGA ultrasensitively with a limit of detection of 0.45 pM. Moreover, AGA could be detected in serum samples with a recovery index in the range of 98%-104%.

Ultrasensitive Ti3C2TX MXene/Chitosan Nanocomposite-Based Amperometric Biosensor for Detection of Potential Prostate Cancer Marker in Urine Samples.

Two-dimensional layered nanomaterial Ti3C2TX (a member of the MXene family) was used to immobilise enzyme sarcosine oxidase to fabricate a nanostructured biosensor. The device was applied for detection of sarcosine, a potential prostate cancer biomarker, in urine for the first time. The morphology and structures of MXene have been characterised by atomic force microscopy (AFM) and scanning electron microscopy (SEM). Electrochemical measurements, SEM and AFM analysis revealed that MXene interfaced with chitosan is an excellent support for enzyme immobilisation to fabricate a sensitive biosensor exhibiting a low detection limit of 18 nM and a linear range up to 7.8 µM. The proposed biosensing method also provides a short response time of 2 s and high recovery index of 102.6% for detection of sarcosine spiked into urine sample in a clinically relevant range.

Validating fPSA Glycoprofile as a Prostate Cancer Biomarker to Avoid Unnecessary Biopsies and Re-Biopsies.

BACKGROUND: To compare the clinical performance of a new PCa serum biomarker based on fPSA glycoprofiling to fPSA% and PHI. METHODS: Serum samples from men who underwent prostate biopsy due to increased PSA were used. A comparison between two equal groups (with histologically confirmed PCa or benign, non-cancer condition) was used for the clinical validation of a new glycan-based PCa oncomarker. SPSS and R software packages were used for the multiparametric analyses of the receiver operating curve (ROC) and for genetic algorithm metaheuristics. RESULTS: When comparing the non-cancer and PCa cohorts, the combination of four fPSA glycoforms with two clinical parameters (PGI, prostate glycan index (PGI)) showed an area under receiver operating curve (AUC) value of 0.821 (95% CI 0.754-0.890). AUC values were 0.517 for PSA, 0.683 for fPSA%, and 0.737 for PHI. A glycan analysis was also applied to discriminate low-grade tumors (GS = 6) from significant tumors (GS ≥ 7). CONCLUSIONS: Compared to PSA on its own, or fPSA% and the PHI, PGI showed improved discrimination between presence and absence of PCa and in predicting clinically significant PCa. In addition, the use of PGI would help practitioners avoid 63.5% of unnecessary biopsies, while the use of fPSA% and PHI would help avoid 17.5% and 33.3% of biopsies, respectively, while missing four significant tumors (9.5%).

Electrochemical Investigation of Interfacial Properties of Ti3C2T x MXene Modified by Aryldiazonium Betaine Derivatives.

For efficient and effective utilization of MXene such as biosensing or advanced applications, interfacial modification of MXene needs to be considered. To this end, we describe modification of Ti3C2Tx MXene by aryldiazonium-based grafting with derivatives bearing a sulfo- (SB) or carboxy- (CB) betaine pendant moiety. Since MXene contains free electrons, betaine derivatives could be grafted to MXene spontaneously. Kinetics of spontaneous grafting of SB and CB toward MXene was electrochemically examined in two different ways, and such experiments confirmed much quicker spontaneous SB grafting compared to spontaneous CB grafting. Moreover, a wide range of electrochemical methods investigating non-Faradaic and Faradaic redox behavior also in the presence of two redox probes together with contact-angle measurements and secondary ion mass spectrometry (SIMS) confirmed substantial differences in formation and interfacial presentation of betaine layers, when spontaneously grafted on MXene. Besides spontaneous grafting of CB and SB toward MXene, also electrochemical grafting by a redox trigger was performed. Results suggest that electrochemical grafting provides a denser layer of SB and CB on the MXene interface compared to spontaneous grafting of SB and CB. Moreover, an electrochemically grafted SB layer offers much lower interfacial resistance and an electrochemically active surface area compared to an electrochemically grafted CB layer. Thus, by adjusting the SB/CB ratio in the solution during electrochemical grafting, it is possible to effectively tune the redox behavior of an MXene-modified interface. Finally, electrochemically grafted CB and SB layers on MXene were evaluated against non-specific protein binding and compared to the anti-fouling behavior of an unmodified MXene interface.

Electrochemical Nanobiosensors for Detection of Breast Cancer Biomarkers.

This comprehensive review paper describes recent advances made in the field of electrochemical nanobiosensors for the detection of breast cancer (BC) biomarkers such as specific genes, microRNA, proteins, circulating tumor cells, BC cell lines, and exosomes or exosome-derived biomarkers. Besides the description of key functional characteristics of electrochemical nanobiosensors, the reader can find basic statistic information about BC incidence and mortality, breast pathology, and current clinically used BC biomarkers. The final part of the review is focused on challenges that need to be addressed in order to apply electrochemical nanobiosensors in a clinical practice.

A Graphene-Based Glycan Biosensor for Electrochemical Label-Free Detection of a Tumor-Associated Antibody.

The study describes development of a glycan biosensor for detection of a tumor-associated antibody. The glycan biosensor is built on an electrochemically activated/oxidized graphene screen-printed electrode (GSPE). Oxygen functionalities were subsequently applied for covalent immobilization of human serum albumin (HSA) as a natural nanoscaffold for covalent immobilization of Thomsen-nouvelle (Tn) antigen (GalNAc-O-Ser/Thr) to be fully available for affinity interaction with its analyte-a tumor-associated antibody. The step by step building process of glycan biosensor development was comprehensively characterized using a battery of techniques (scanning electron microscopy, atomic force microscopy, contact angle measurements, secondary ion mass spectrometry, surface plasmon resonance, Raman and energy-dispersive X-ray spectroscopy). Results suggest that electrochemical oxidation of graphene SPE preferentially oxidizes only the surface of graphene flakes within the graphene SPE. Optimization studies revealed the following optimal parameters: activation potential of +1.5 V vs. Ag/AgCl/3 M KCl, activation time of 60 s and concentration of HSA of 0.1 g L-1. Finally, the glycan biosensor was built up able to selectively and sensitively detect its analyte down to low aM concentration. The binding preference of the glycan biosensor was in an agreement with independent surface plasmon resonance analysis.

Remarkable differences in the voltammetric response towards hydrogen peroxide, oxygen and Ru(NH3)63+ of electrode interfaces modified with HF or LiF-HCl etched Ti3C2Tx MXene.

An electrochemical study was performed on the behavior of Ti3C2Tx MXenes prepared by using either HF (MXene1) or LiF/HCl as etchants (MXene2). The use of two redox probes indicates the presence of a higher negative charge density on MXene2 in comparison to MXene1. The characterization of two nanomaterials shows that titanium and fluoride are present higher by one order of magnitude at the interface of MXene2, compared to MXene1. The high Ti and F content is accompanied by a 82-fold larger (249 µA·cm-2 vs. 5.64 µA·cm-2) anodic peak at the peak potential near 0.4 V (vs. Ag/AgCl). Similarly, the peak current on MXene2 is 317-fold higher for the oxygen reduction at pH 7.0 (at a voltage of -0.84 V) and 215-fold higher for the reduction of H2O2 at -0.89 V, when compared to MXene1. Graphical abstractDifference in electrochemical behavior of MXene prepared by HF (MXene1) and LiF/HCl (MXene2) as etchants.

Synthesis and characterization of Au nanoshells with a magnetic core and betaine derivatives.

The article describes preparation, characterization and further modification of hybrid magnetic particles (Au nanoshells with a magnetic core (MPs@silica@Au)) by zwitterionic molecules bearing diazonium functional groups. Such hybrid magnetic particles modified by zwitterionic molecules exhibit the following features: •Responsiveness towards external magnetic field applicable for various enrichment strategies due to magnetic core;•Golden outer layer exhibiting free surface plasmons could be used for grafting of zwitterionic molecules via diazonium functionality;•Zwitterionic interface on such particles provides resistivity towards non-specific protein binding; and at the same time such interface was applied for immobilization of antibodies against prostate specific antigen (PSA) applied for selective enrichment of PSA from serum samples with subsequent electrochemical assays. The approach presented here using hybrid magnetic particles can be easily applied for immobilization of antibodies using a highly robust surface patterning protocols i.e. by formation of a self-assembled monolayer with delivery of functional groups on the outer surface of magnetic particles. Hybrid magnetic particles with immobilized antibodies are applied for highly efficient and quick separation of protein of interest i.e. PSA from complex sample. Finally, hybrid magnetic particles with "fished-out" protein molecules could be incubated with lectins to form a sandwich configuration for glycoprofiling of PSA.

Prostate-specific antigen glycoprofiling as diagnostic and prognostic biomarker of prostate cancer.

The initial part of this review details the controversy behind the use of a serological level of prostate-specific antigen (PSA) for the diagnostics of prostate cancer (PCa). Novel biomarkers are in demand for PCa diagnostics, outperforming traditional PSA tests. The review provides a detailed and comprehensive summary that PSA glycoprofiling can effectively solve this problem, thereby considerably reducing the number of unnecessary biopsies. In addition, PSA glycoprofiling can serve as a prognostic PCa biomarker to identify PCa patients with an aggressive form of PCa, avoiding unnecessary further treatments which are significantly life altering (incontinence or impotence).

Advanced impedimetric biosensor configuration and assay protocol for glycoprofiling of a prostate oncomarker using Au nanoshells with a magnetic core.

In this paper several advances were implemented for glycoprofiling of prostate specific antigen (PSA), what can be applied for better prostate cancer (PCa) diagnostics in the future: 1) application of Au nanoshells with a magnetic core (MP@silica@Au); 2) use of surface plasmons of Au nanoshells with a magnetic core for spontaneous immobilization of zwitterionic molecules via diazonium salt grafting; 3) a double anti-fouling strategy with integration of zwitterionic molecules on Au surface and on MP@silica@Au particles was implemented to resist non-specific protein binding; 4) application of anti-PSA antibody modified Au nanoshells with a magnetic core for enrichment of PSA from a complex matrix of a human serum; 5) direct incubation of anti-PSA modified MP@silica@Au with affinity bound PSA to the lectin modified electrode surface. The electrochemical impedance spectroscopy (EIS) signal was enhanced 43 times integrating Au nanoshells with a magnetic core compared to the biosensor without them. This proof-of-concept study shows that the biosensor could detect PSA down to 1.2 fM and at the same time to glycoprofile such low PSA concentration using a lectin patterned biosensor device. The biosensor offers a recovery index of 108%, when serum sample was spiked with a physiological concentration of PSA (3.5 ng mL-1).

Glycomics of prostate cancer: updates.

Introduction: Prostate cancer (PCa) is a life-threatening disease affecting millions of men. The current best PCa biomarker (level of prostate-specific antigen in serum) lacks specificity for PCa diagnostics and this is why novel PCa biomarkers in addition to the conventional ones based on biomolecules such as DNA, RNA and proteins need to be identified. Areas covered: This review details the potential of glycans-based biomarkers to become diagnostic, prognostic, predictive and therapeutic PCa biomarkers with a brief description of the innovative approaches applied to glycan analysis to date. Finally, the review covers the possibility to use exosomes as a rich source of glycans for future innovative and advanced diagnostics of PCa. The review covers updates in the field since 2016. Expert commentary: The summary provided in this review paper suggests that glycan-based biomarkers can offer high-assay accuracy not only for diagnostic purposes but also for monitoring/surveillance of the PCa disease.