Luminex and other multiplex high throughput technologies for the identification of, and host response to, environmental triggers of type 1 diabetes

Nanoplasmonic microarray-based solid-phase amplification for highly sensitive and multiplexed molecular diagnostics: application for detecting SARS-CoV-2

A novel approach is introduced using nanoplasmonic microarray-based solid-phase recombinase polymerase amplification (RPA) that offers high sensitivity and multiplexing capabilities for gene detection. Nanoplasmonic microarrays were developed through one-step immobilization of streptavidin/biotin primers and fine-tuning the amplicon size to achieve high plasmon-enhanced fluorescence (PEF) on the nanoplasmonic substrate, thereby improving sensitivity. The specificity and sensitivity of solid-phase RPA on nanoplasmonic microarrays was evaluated in detecting E, N, and RdRP genes of SARS-CoV-2. High specificity was achieved by minimizing primer-dimer formation and employing a stringent washing process and high sensitivity obtained with a limit of detection of four copies per reaction within 30 min. In clinical testing with nasopharyngeal swab samples (n = 30), the nanoplasmonic microarrays demonstrated a 100% consistency with the PCR results for detecting SARS-CoV-2, including differentiation of Omicron mutations BA.1 and BA.2. This approach overcomes the sensitivity issue of solid-phase amplification, as well as offers rapidity, high multiplexing capabilities, and simplified equipment by using isothermal reaction, making it a valuable tool for on-site molecular diagnostics.

Immunoassays and Mass Spectrometry for Determination of Protein Concentrations in Genetically Modified Crops

Quantifying protein levels in genetically modified (GM) crops is crucial in every phase of development, deregulation, and seed production. Immunoassays, particularly enzyme-linked immunosorbent assay, have been the primary protein quantitation techniques for decades within the industry due to their efficiency, adaptability, and credibility. Newer immunoassay technologies like Meso Scale Discovery and Luminex offer enhanced sensitivity and multiplexing capabilities. While mass spectrometry (MS) has been widely used for small molecules and protein detection in the pharmaceutical and agricultural industries (e.g., biomarkers, endogenous allergens), its use in quantifying protein levels in GM crops has been limited. However, as trait portfolios for GM crop have expanded, MS has been increasingly adopted due to its comparable sensitivity, increased specificity, and multiplexing capabilities. This review contrasts the benefits and limitations of immunoassays and MS technologies for protein measurement in GM crops, considering factors such as cost, convenience, and specific analytical needs. Ultimately, both techniques are suitable for assessing protein concentrations in GM crops, with MS offering complementary capabilities to immunoassays. This comparison aims to provide insights into selecting between these techniques based on the user's end point needs.

Expression Pattern of Cytokines in Patients with Chronic Hepatitis B Receiving PEGinterferon Therapy

Purpose

Chronic hepatitis B virus (CHB) infection is a worldwide health problem. Polyethylene glycol (PEG)ylated interferon (PEG-IFN) is an available therapy for CHB that has antiviral and immunomodulatory effects. However, PEG-IFN therapy is limited by the fact that only a subset of patients show a sustained response, its severe side effects, and high cost. The aim of this study was to explore novel biomarkers for the early prediction of PEG-IFN treatment response and to uncover its underlying mechanism.

Patients and Methods

We enrolled 10 paired patients with Hepatitis B e antigen (HBeAg)-positive CHB who received PEG-IFN-α2a monotherapy. Patient serum samples were collected at 0, 4, 12, 24, and 48 weeks and serum samples were collected from eight healthy people as healthy controls. For confirmation, we enrolled 27 patients with HBeAg-positive CHB receiving PEG-IFN therapy and serum samples at 0 and 12 weeks were obtained. Serum samples were analyzed using Luminex technology.

Results

Among 27 assessed cytokines, 10 cytokines were identified to have high expression levels. Among them, six cytokines had significant differences in their levels between the patients with HBeAg-positive CHB and the healthy controls (P < 0.05). Potentially, treatment response could be predicted using the early time points of 4, 12, and 24 weeks. Moreover, after 12 weeks of PEG-IFN treatment, increased levels of pro-inflammatory cytokines and decreased levels of anti-inflammatory cytokines were observed. The fold change of IP-10 between 12 weeks and 0 weeks correlated with the decrease in ALT levels from 0 to 12 weeks (r = 0.2675, P = 0.0024).

Conclusion

In patients with CHB, we observed a certain pattern in the levels of cytokines during treatment with PEG-IFN, and the cytokine IP-10 might be a potential biomarker for treatment response.

Comparative Analysis of Multiple Immunoassays for Cytokine Profiling in Drug Discovery

Cytokines and their receptors play critical roles in biological processes. Dysfunction or dysregulation of cytokines may cause a variety of pathophysiological conditions. Consequently, cytokine profiling and related technologies are essential for biological studies, disease diagnosis, and drug discovery. In this report, three cytokines, interleukin (IL)-1β, IL-6, and tumor necrosis factor alpha (TNF-α), from the same sets of samples were analyzed with several commonly used technologies (enzyme-linked immunosorbent assay [ELISA], Luminex, Meso Scale Discovery [MSD], time-resolved fluorescence resonance energy transfer [TR-FRET], cytometric bead array [CBA], AlphaLISA, and FirePlex). Through experimental data analysis, several assay features were compared, including sensitivity, dynamic range, and robustness. Our studies reveal that MSD has the best sensitivity in the low detection limit and the broadest dynamic range, while CBA and Luminex also demonstrate superior performance in the sensitivity and dynamic range. Additional aspects of these technologies, including assay principles, formats, throughputs, robustness, costs, and multiplexing capabilities, were also reviewed and compared. Combining all these features, our comparison highlights MSD as the most sensitive technology, while CBA is the most suitable one for cytokine high-throughput screening with multiplexing capability. Along with perspectives on new technology development in the field, this report aims to help readers understand these technologies and select the proper one for specific applications.

Confirmation and Identification of Biomarkers Implicating Environmental Triggers in the Pathogenesis of Type 1 Diabetes

Multiple environmental triggers have been proposed to explain the increased incidence of type 1 diabetes (T1D). These include viral infections, microbiome disturbances, metabolic disorders, and vitamin D deficiency. Here, we used ELISA to examine blood plasma from juvenile T1D subjects and age-matched controls for the abundance of several circulating factors relevant to these hypotheses. We screened plasma for sCD14, mannose binding lectin (MBL), lipopolysaccharide binding protein (LBP), c-reactive protein (CRP), fatty acid binding protein 2 (FABP2), human growth hormone, leptin, total adiponectin, high molecular weight (HMW) adiponectin, total IgG, total IgA, total IgM, endotoxin core antibodies (EndoCAbs), 25(OH) vitamin D, vitamin D binding protein, IL-7, IL-10, IFN-γ, TNF-α, IL-17A, IL-18, and IL-18BPa. Subjects also were tested for prevalence of antibodies targeting adenovirus, parainfluenza 1/2/3, Coxsackievirus, cytomegalovirus, Epstein-Barr virus viral capsid antigen (EBV VCA), herpes simplex virus 1, and Saccharomyces cerevisiae. Finally, all subjects were screened for presence and abundance of autoantibodies targeting islet cell cytoplasmic proteins (ICA), glutamate decarboxylase 2 (GAD65), zinc transporter 8 (ZNT8), insulinoma antigen 2 (IA-2), tissue transglutaminase, and thyroid peroxidase, while β cell function was gauged by measuring c-peptide levels. We observed few differences between control and T1D subjects. Of these, we found elevated sCD14, IL-18BPa, and FABP2, and reduced total IgM. Female T1D subjects were notably elevated in CRP levels compared to control, while males were similar. T1D subjects also had significantly lower prevalence of EBV VCA antibodies compared to control. Lastly, we observed that c-peptide levels were significantly correlated with leptin levels among controls, but this relationship was not significant among T1D subjects. Alternatively, adiponectin levels were significantly correlated with c-peptide levels among T1D subjects, while controls showed no relationship between these two factors. Among T1D subjects, the highest c-peptide levels were associated with the lowest adiponectin levels, an indication of insulin resistance. In total, from our examination we found limited data that strongly support any of the hypotheses investigated. Rather, we observed an indication of unexplained monocyte/macrophage activation in T1D subjects judging from elevated levels of sCD14 and IL-18BPa. These observations were partnered with unique associations between adipokines and c-peptide levels among T1D subjects.

The role of systems biology approaches in determining molecular signatures for the development of more effective vaccines

INTRODUCTION

Emerging infectious diseases are a major threat to public health, and while vaccines have proven to be one of the most effective preventive measures for infectious diseases, we still do not have safe and effective vaccines against many human pathogens, and emerging diseases continually pose new threats. The purpose of this review is to discuss how the creation of vaccines for these new threats has been hindered by limitations in the current approach to vaccine development. Recent advances in high-throughput technologies have enabled scientists to apply systems biology approaches to collect and integrate increasingly large datasets that capture comprehensive biological changes induced by vaccines, and then decipher the complex immune response to those vaccines.

AREAS COVERED

This review covers advances in these technologies and recent publications that describe systems biology approaches to understanding vaccine immune responses and to understanding the rational design of new vaccine candidates.

EXPERT OPINION

Systems biology approaches to vaccine development provide novel information regarding both the immune response and the underlying mechanisms and can inform vaccine development.

Detection and Sourcing of Gluten in Grain with Multiple Floating-Gate Transistor Biosensors

We report a chemically tunable electronic sensor for quantitation of gluten based on a floating-gate transistor (FGT) architecture. The FGTs are fabricated in parallel and each one is functionalized with a different chemical moiety designed to preferentially bind a specific grain source of gluten. The resulting set of FGT sensors can detect both wheat and barley gluten below the gluten-free limit of 20 ppm (w/w) while providing a source-dependent signature for improved accuracy. This label-free transduction method does not require any secondary binding events, resulting in a ca. 45 min reduction in analysis time relative to state-of-the-art ELISA kits with a simple and easily implemented workflow.

Point-of-Care Testing and Personalized Medicine for Metabolic Disorders

This chapter describes innovations in biomarker testing that can facilitate earlier and better treatment of patients who suffer from metabolic disorders. The use of new microfluidic devices along with miniaturized biosensors and transducers enables analysis of a single drop of a blood within the time frame of a typical visit to a doctor's office. Steps are underway so that these approaches will incorporate both biochemical and clinical data, resulting in unique bioprofiles for each patient. This will allow earlier, personalized, and more effective therapeutic options. In addition, smartphone apps for self-monitoring will be used increasingly for the best possible patient outcomes.

Utilizing the Luminex Magnetic Bead-Based Suspension Array for Rapid Multiplexed Phosphoprotein Quantification

The study of protein phosphorylation is critical for the advancement of our understanding of cellular responses to external and internal stimuli. Phosphorylation, the addition of phosphate groups, most often occurs on serine, threonine, or tyrosine residues due to the action of protein kinases. This structural change causes the protein to become activated (or deactivated) and enables it in turn to initiate the phosphorylation of other proteins in a cascade, eventually causing cell-wide changes such as apoptosis, cell differentiation, and growth (among others). Cellular phosphoprotein pathway dysregulation by mutation or chromosomal instability can often give the cell a selective advantage and lead to cancer. Obviously the understanding of these systems is of huge importance to the field of oncology.This chapter aims to provide a "how to" manual for one such technology, the 96-well plate-based xMAP® platform from Luminex. The system utilizes antibody-bound free-floating magnetic spheres which can easily be removed from suspension via magnetization. There are 100 unique bead sets (moving up to 500 bead sets for the most recent system) identified by the ratio of two dyes coating the microsphere. Each bead set is conjugated to a specific antibody which allows targeted protein extraction from low-concentration lysate solution. Biotinylated secondary antibodies/streptavidin-R-phycoerythrin (SAPE) complexes provide the quantification mechanism for the phosphoprotein of interest.

High throughput toxicity screening and intracellular detection of nanomaterials

With the growing numbers of nanomaterials (NMs), there is a great demand for rapid and reliable ways of testing NM safety—preferably using in vitro approaches, to avoid the ethical dilemmas associated with animal research. Data are needed for developing intelligent testing strategies for risk assessment of NMs, based on grouping and read‐across approaches. The adoption of high throughput screening (HTS) and high content analysis (HCA) for NM toxicity testing allows the testing of numerous materials at different concentrations and on different types of cells, reduces the effect of inter‐experimental variation, and makes substantial savings in time and cost. HTS/HCA approaches facilitate the classification of key biological indicators of NM‐cell interactions. Validation of in vitroHTS tests is required, taking account of relevance to in vivo results. HTS/HCA approaches are needed to assess dose‐ and time‐dependent toxicity, allowing prediction of in vivo adverse effects. Several HTS/HCA methods are being validated and applied for NM testing in the FP7 project NANoREG, including Label‐free cellular screening of NM uptake, HCA, High throughput flow cytometry, Impedance‐based monitoring, Multiplex analysis of secreted products, and genotoxicity methods—namely High throughput comet assay, High throughput in vitro micronucleus assay, and γH2AX assay. There are several technical challenges with HTS/HCA for NM testing, as toxicity screening needs to be coupled with characterization of NMs in exposure medium prior to the test; possible interference of NMs with HTS/HCA techniques is another concern. Advantages and challenges of HTS/HCA approaches in NM safety are discussed. WIREs Nanomed Nanobiotechnol 2017, 9:e1413. doi: 10.1002/wnan.1413

For further resources related to this article, please visit the WIREs website.

Autoimmune diseases - connecting risk alleles with molecular traits of the immune system

Genome-wide strategies have driven the discovery of more than 300 susceptibility loci for autoimmune diseases. However, for almost all loci, understanding of the mechanisms leading to autoimmunity remains limited, and most variants that are likely to be causal are in non-coding regions of the genome. A critical next step will be to identify the in vivo and ex vivo immunophenotypes that are affected by risk variants. To do this, key cell types and cell states that are implicated in autoimmune diseases will need to be defined. Functional genomic annotations from these cell types and states can then be used to resolve candidate genes and causal variants. Together with longitudinal studies, this approach may yield pivotal insights into how autoimmunity is triggered.