Integrated analyses of proteins and their glycans in a magnetic bead-based multiplex assay format

Aptamers targeting protein-specific glycosylation in tumor biomarkers: general selection, characterization and structural modeling

Detecting specific protein glycoforms is attracting particular attention due to its potential to improve the performance of current cancer biomarkers. Although natural receptors such as lectins and antibodies have served as powerful tools for the detection of protein-bound glycans, the development of effective receptors able to integrate in the recognition both the glycan and peptide moieties is still challenging. Here we report a method for selecting aptamers toward the glycosylation site of a protein. It allows identification of an aptamer that binds with nM affinity to prostate-specific antigen, discriminating it from proteins with a similar glycosylation pattern. We also computationally predict the structure of the selected aptamer and characterize its complex with the glycoprotein by docking and molecular dynamics calculations, further supporting the binary recognition event. This study opens a new route for the identification of aptamers for the binary recognition of glycoproteins, useful for diagnostic and therapeutic applications.

Binary recognition of the glycoprotein prostate specific antigen by aptamers: a tool for detecting aberrant glycosylation associated with cancer.

Blood biomarkers as surrogate endpoints of treatment responses to aerobic exercise and cognitive training (ACT) in amnestic mild cognitive impairment: the blood biomarkers study protocol of a randomized controlled trial (the ACT Trial)

BACKGROUND

Alzheimer's disease (AD) is an epidemic with tremendous public health impacts because there are currently no disease-modifying therapeutics. Randomized controlled trials (RCTs) for prevention of AD dementia often use clinical endpoints that take years to manifest (e.g., cognition) or surrogate endpoints that are costly or invasive (e.g., magnetic resonance imaging [MRI]). Blood biomarkers represent a clinically applicable alternative surrogate endpoint for RCTs that would be both cost-effective and minimally invasive, but little is known about their value as surrogate endpoints for treatment responses in the prevention of AD dementia.

METHODS

The objective of this study is to investigate blood neuropathological, neurodegenerative, and neurotrophic biomarkers as surrogate endpoints for treatment responses to three interventions in older adults with amnestic mild cognitive impairment (aMCI, a prodromal stage of AD): aerobic exercise, cognitive training, and combined aerobic exercise and cognitive training (ACT). We chose these three sets of biomarkers for their unique mechanistic associations with AD pathology, neurodegeneration and neurogenesis. This study is built on the ACT Trial (1R01AG055469), a single-blinded, multi-site, 2 × 2 factorial phase II RCT that examines the synergistic effects of a 6-month ACT intervention on cognition and MRI biomarkers (AD-signature cortical thickness and hippocampal volume) (n = 128). In this ACT Trial blood biomarkers study, we will enroll 120 ACT Trial participants with aMCI and measure blood biomarkers at baseline and at 3, 6, 12, and 18 months. The goals are to (1) determine the effect of interventions on blood biomarkers over 6 months, (2) evaluate blood biomarkers as surrogate endpoints for predicting cognitive responses to interventions over 18 months, and (3, exploratory) examine blood biomarkers as surrogate endpoints for predicting brain MRI biomarker responses to interventions over 18 months.

DISCUSSION

This study aims to identify new blood biomarkers that can track cognitive decline or AD-related brain atrophy among patients with aMCI subjected to a regimen of aerobic exercise and cognitive training. Findings from this study will drive the further use of blood biomarkers in developing effective prevention and treatment strategies for AD dementia.

TRIAL REGISTRATION

ClinicalTrials.gov, NCT03313895. Registered on 18 October 2017.

Glycosylation Profiling of Tumor Marker in Plasma Using Bead-Based Immunoassay

As one of the most important posttranslational modifications, glycosylation plays critical roles in protein folding, trafficking, cell differentiation, immune recognition, etc. The alteration of glycosylation is closely associated with the pathological processes during and after caner development, and thus holds great value in cancer detection. In this chapter, we describe a protocol on the glycosylation profiling of tumor marker in plasma using bead-based immunoassay with CA125 as a model, including bead coupling, coupling control, glycosylation assay, as well as the plasma screening for breast cancer patients. This protocol can be used to profile the glycosylation of protein markers in clinical plasma or serum samples for different human cancers.

Analysis of carbohydrates and glycoconjugates by matrix-assisted laser desorption/ionization mass spectrometry: An update for 2013-2014

This review is the eighth update of the original article published in 1999 on the application of Matrix-assisted laser desorption/ionization mass spectrometry (MALDI) mass spectrometry to the analysis of carbohydrates and glycoconjugates and brings coverage of the literature to the end of 2014. Topics covered in the first part of the review include general aspects such as theory of the MALDI process, matrices, derivatization, MALDI imaging, fragmentation, and arrays. The second part of the review is devoted to applications to various structural types such as oligo- and poly- saccharides, glycoproteins, glycolipids, glycosides, and biopharmaceuticals. Much of this material is presented in tabular form. The third part of the review covers medical and industrial applications of the technique, studies of enzyme reactions, and applications to chemical synthesis. © 2018 Wiley Periodicals, Inc. Mass Spec Rev 37:353-491, 2018.

Application of cancer-associated glycoforms and glycan-binding probes to an in vitro diagnostic multivariate index assay for precise diagnoses of cancer

Personalized medicine has emerged as a widely accepted trend in medicine for the efficacious and safe treatment of various diseases. It covers every medical treatment tailored according to various properties of individuals. Cancer-associated glycosylation mirrors cancer states more precisely, and this "sweet side of cancer" is thus intended to spur the development of an advanced in vitro diagnostic system. The changes of glyco-codes are often subtle and thus not easy to trace, thereby making it difficult to discriminate changes from various compounding factors. Special glycan-binding probes, often lectins, can be paired with aglycosylated antibodies to enable quantitative and qualitative measurements of glycoforms. With the in vitro diagnosis multivariate index assay (IVDMIA) considered to be capable of yielding patient-specific results, the combinatorial use of multiple glycoproteins may be a good modality to ensure disease-specific, personalized diagnoses.

A microfluidic multiplex proteomic immunoassay device for translational research

Objective

Microfluidic technology has the potential to miniaturize and automate complex laboratory procedures. The objective of this study was to assess a microfluidic immunoassay device, Simple Plex, which simultaneously measured IL-1β, TNF-α, IL-6, and IL-10 in serum samples. This assessment is important to understanding the potentials of this microfluidic device as a valuable tool in translational research efforts.

Methods

We studied the operational characteristics of Simple Plex, and compared to other immunoassay systems including bead-based (i.e., Bio-Plex^® from Bio-Rad) and planar micro-spot based (i.e., Multi-Array from Meso Scale Discovery) multiplex assays. We determined imprecisions for each of the Simple Plex assays and evaluated the ability of Simple Plex to detect IL-1β, TNF-α, IL-6, and IL-10 in serum samples.

Results

Simple Plex assays required 25 µL serum, and 1.5 h to run 16 samples per cartridge per instrument. Assay imprecisions, evaluated by measurement of 6 replicates in duplicate from a serum pool using three different cartridges, were less than 10 % for all 4 cytokine protein biomarkers, comparable to the imprecisions of traditional ELISAs. The Simple Plex assays were able to detect 32, 95, 97, and 100 % [i.e., percentages of the results within the respective analytical measurement ranges (AMRs)] of IL-1β, TNF-α, IL-6, and IL-10, respectively, in 66 serum samples.

Conclusions

Simple Plex is a microfluidic multiplex immunoassay device that offers miniaturized, and automated analysis of protein biomarkers. Microfluidic devices such as Simple Plex represent a promising platform to be used in translational research to measure protein biomarkers in real clinical samples.

The detection and discovery of glycan motifs in biological samples using lectins and antibodies: new methods and opportunities

Recent research has uncovered unexpected ways that glycans contribute to biology, as well as new strategies for combatting disease using approaches involving glycans. To make full use of glycans for clinical applications, we need more detailed information on the location, nature, and dynamics of glycan expression in vivo. Such studies require the use of specimens acquired directly from patients. Effective studies of clinical specimens require low-volume assays, high precision measurements, and the ability to process many samples. Assays using affinity reagents-lectins and glycan-binding antibodies-can meet these requirements, but further developments are needed to make the methods routine and effective. Recent advances in the use of glycan-binding proteins involve improved determination of specificity using glycan arrays; the availability of databases for mining and analyzing glycan array data; lectin engineering methods; and the ability to quantitatively interpret lectin measurements. Here, we describe many of the challenges and opportunities involved in the application of these new approaches to the study of biological samples. The new tools hold promise for developing methods to improve the outcomes of patients afflicted with diseases characterized by aberrant glycan expression.

Serum fucosylated prostate-specific antigen (PSA) improves the differentiation of aggressive from non-aggressive prostate cancers

BACKGROUND

Clinically, it is still challenging to differentiate aggressive from non-aggressive prostate cancers (Pca) by non-invasive approaches. Our recent studies showed that overexpression of alpha (1-6) fucosyltransferase played an important role in Pca cells. In this study, we have investigated levels of glycoproteins and their fucosylated glycoforms in sera of Pca patients, as well as the potential utility of fucosylated glycoproteins in the identification of aggressive Pca.

MATERIAL AND METHODS

Serum samples from histomorphology-proven Pca cases were included. Prostate-specific antigen (PSA), tissue inhibitor of metallopeptidase 1 (TIMP1) and tissue plasminogen activator (tPA), and their fucosylated glycoforms were captured by Aleuria Aurantia Lectin (AAL), followed by the multiplex magnetic bead-based immunoassay. The level of fucosylated glycoproteins was correlated with patients' Gleason score of the tumor.

RESULT

Among three fucosylated glycoproteins, the fucosylated PSA was significantly increased and correlated with the tumor Gleason score (p<0.05). The ratio of fucosylated PSA showed a marked increase in aggressive tumors in comparison to non-aggressive tumors. ROC analysis also showed an improved predictive power of fucosylated PSA in the identification of aggressive Pca.

CONCLUSIONS

Our data demonstrated that fucosylated PSA has a better predictive power to differentiate aggressive tumors from non-aggressive tumors, than that of native PSA and two other glycoproteins. The fucosylated PSA has the potential to be used as a surrogate biomarker.

Stationary phases for the enrichment of glycoproteins and glycopeptides

The analysis of protein glycosylation is important for biomedical and biopharmaceutical research. Recent advances in LC-MS analysis have enabled the identification of glycosylation sites, the characterisation of glycan structures and the identification and quantification of glycoproteins and glycopeptides. However, this type of analysis remains challenging due to the low abundance of glycopeptides in complex protein digests, the microheterogeneity at glycosylation sites, ion suppression effects and the competition for ionisation by co-eluting peptides. Specific sample preparation is necessary for comprehensive and site-specific glycosylation analyses using MS. Therefore, researchers continue to pursue new columns to broaden their applications. The current manuscript covers recent literature published from 2008 to 2013. The stationary phases containing various chemical bonding methods or ligands immobilisation strategies on solid supports that selectively enrich N-linked or sialylated N-glycopeptides are categorised with either physical or chemical modes of binding. These categories include lectin affinity, hydrophilic interactions, boronate affinity, titanium dioxide affinity, hydrazide chemistry and other separation techniques. This review should aid in better understanding the syntheses and physicochemical properties of each type of stationary phases for enriching glycoproteins and glycopeptides.

Analysis of serum protein glycosylation by a differential lectin immunosorbant assay (dLISA)

Background

Lectin immunosorbant assays (LISAs) have been widely used for analyzing protein glycosylation. However, the analysis of serum samples by LISAs could suffer from high sample-dependent background noise. The aim of this study is to develop a differential lectin immunosorbant assay (dLISA) with reduced background interferences.

Methods

For the analysis of protein glycosylation, dLISA establishes a dose–response curve for every serum sample. The sample is split into five aliquots. Four aliquots undergo differential removal of the glycoprotein of interest by immunoprecipitation. Then, all five aliquots are subject to two measurements: protein by immunoassay and protein glycans by LISA. A dose–response curve is established by plotting glycans signals on the y-axis and protein levels on the x-axis for all the aliquots. Slope of the curve, calculated by linear progression analysis and expressed as fluorescence per concentration of protein, is used for the measurement of protein glycosylation in the serum sample.

Results/conclusions

To demonstrate the feasibility of the dLISA approach, we used recombinant, fucosylated tissue inhibitor of metallopeptidase 1 (TIMP-1) as the target glycoprotein. Magnetic beads based TIMP1 immunoassay and TIMP-1 UEA LISA were developed for the measurement of TIMP1 protein and terminal α1, 2 fucosylated glycans on TIMP1, respectively. Serum samples supplemented with differentially fucosylated recombinant TIMP-1 were used to demonstrate that the slopes measured the TIMP-1 fucosylation, and were less prone to background interference.