Constructions, Purifications and Applications of DNA-Antibody Conjugates: A Review.

A DNA-antibody conjugate is a synthetic molecule that combines the unique functions of both an antibody and DNA. With the increased accessibility of commercialized kits, the procedure for constructing conjugates is simplified and the requirement for chemistry background is reduced. As a result, the difficulty of preparing a DNA-antibody conjugate has been significantly lowered.

N-glycosylation of the SARS-CoV-2 spike protein at Asn331 and Asn343 is involved in spike-ACE2 binding, virus entry, and regulation of IL-6.

The coronavirus disease 2019 (COVID-19) pandemic is an ongoing global public health crisis. The causative agent, the SARS-CoV-2 virus, enters host cells via molecular interactions between the viral spike protein and the host cell ACE2 surface protein. The SARS-CoV-2 spike protein is extensively decorated with up to 66 N-linked glycans.

Identification and validation of circulating biomarkers for detection of liver cancer with antibody array.

The aim of this study was to find new protein biomarkers that could be used to detect hepatocellular carcinoma (HCC) in the serum. We identified 11 proteins in the tissue that could be used to classify samples from HCC and control subjects. The 11 identified tissue biomarkers were combined with 10 commonly used serum HCC biomarkers for further verification in a large number of serum samples from HCC patients and healthy controls.

Induction of a cytokine storm involves suppression of the Osteopontin-dependent TH1 response.

Cytokine release syndromes represent a severe turn in certain disease states, which may be caused by several infections, including those with the virus SARS-CoV-2. This inefficient, even harmful, immune response has been associated with a broad release of chemokines. Although a cellular (type I) immune reaction is efficacious against viral infections, we noted a type I deficit in the cytokine patterns produced by cytokine storms of all reported etiologies.

Development and evaluation of time-resolved fluorescent immunochromatographic assay for quantitative detection of SARS-CoV-2 spike antigen.

Background: The spread of COVID-19 worldwide caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has necessitated efficient, sensitive diagnostic methods to identify infected people. We report on the development of a rapid 15-minute time-resolved fluorescent (TRF) lateral flow immunochromatographic assay for the quantitative detection of the SARS-CoV-2 spike protein receptor-binding domain (S1-RBD).

Objectives: Our objective was to develop an efficient method of detecting SARS-CoV-2 within 15 min of sample collection.

Developing an Effective Peptide-Based Vaccine for COVID-19: Preliminary Studies in Mice Models.

Coronavirus disease 2019 (COVID-19) has caused massive health and economic disasters worldwide. Although several vaccines have effectively slowed the spread of the virus, their long-term protection and effectiveness against viral variants are still uncertain. To address these potential shortcomings, this study proposes a peptide-based vaccine to prevent COVID-19.

Serum molecular biomarkers in neuromyelitis optica and multiple sclerosis.

Background: Neuromyelitis optica spectrum disorder (NMOSD) is a rare and severe inflammatory demyelinating disorder of the central nervous system (CNS), which mainly affects the optic nerves and spinal cord. The aims of this study were to determine whether the expression levels of serological cytokines could distinguish 1) NMOSD from healthy controls (HCs); and 2) NMOSD patients with and without the aquaporin-4 (AQP4) antibody biomarker from each other; and 3) NMOSD patients without the antibody to AQP4 from MS patients.

Methods: The expression levels of 200 proteins in serum from 41 NMOSD (32 with antibodies to AQP4, 9 without antibodies to AQP4), 12 MS patients, and 34 HCs were measured using glass-based antibody arrays.

A Case-Control Study of Follicular Fluid Cytokine Profiles in Women with Diminished Ovarian Reserve.

Ovarian reserve is an important determinant of a woman's reproductive potential, and women with diminished ovarian reserve (DOR) often seek in vitro fertilization (IVF). The underlying etiology of DOR is unknown, but follicular fluid cytokine concentrations likely play a role in follicular development and maturation. The present study seeks to investigate the expression of cytokines in follicular fluid (FF) of women with DOR undergoing IVF and explore correlated functional pathways.

Quantitative Detection of Anti-SARS-CoV-2 Antibodies Using Indirect ELISA.

Objective: Real-time reverse transcription-polymerase chain reaction is the gold standard for the diagnosis of COVID-19, but it is necessary to utilize other tests to determine the burden of the disease and the spread of the outbreak such as IgG-, IgM-, and IgA-based antibody detection using enzyme-linked immunosorbent assay (ELISA).

Materials And Methods: We developed an indirect ELISA assay to quantitatively measure the amount of COVID-19 IgG, IgM, and IgA antibodies present in patient serum, dried blood, and plasma.

Results: The population cutoff values for positivity were determined by receiver operating characteristic curves to be 1.

Dried blood sample analysis by antibody array across the total testing process.

Dried blood samples (DBSs) have many advantages; yet, impediments have limited the clinical utilization of DBSs. We developed a novel volumetric sampling device that collects a precise volume of blood, which overcomes the heterogeneity and hematocrit issues commonly encountered in a traditional DBS card collection as well as allowing for more efficient extraction and processing procedures and thus, more efficient quantitation, by using the entire sample. We also provided a thorough procedure validation using this volumetric DBS collection device with an established quantitative proteomics analysis method, and then analyzed 1000 proteins using this approach in DBSs concomitantly with serum for future consideration of utility in clinical applications.

Three subtypes of lung cancer fibroblasts define distinct therapeutic paradigms.

Cancer-associated fibroblasts (CAFs) are highly heterogeneous. With the lack of a comprehensive understanding of CAFs' functional distinctions, it remains unclear how cancer treatments could be personalized based on CAFs in a patient's tumor. We have established a living biobank of CAFs derived from biopsies of patients' non-small lung cancer (NSCLC) that encompasses a broad molecular spectrum of CAFs in clinical NSCLC.

Comprehensive Profiling of Inflammatory Factors Revealed That Growth Differentiation Factor-15 Is an Indicator of Disease Severity in COVID-19 Patients.

To systematically explore potential biomarkers which can predict disease severity in COVID-19 patients and prevent the occurrence or development of severe COVID-19, the levels of 440 factors were analyzed in patients categorized according to COVID-19 disease severity; including asymptomatic, mild, moderate, severe, convalescent and healthy control groups. Factor candidates were validated by ELISA and functional relevance was uncovered by bioinformatics analysis. To identify potential biomarkers of occurrence or development of COVID-19, patient sera from three different severity groups (moderate, severe, and critical) at three time points (admission, remission, and discharge) and the expression levels of candidate biomarkers were measured.

Data Analysis for Antibody Arrays.

When obtaining high-throughput data from antibody arrays, researchers have to face a couple of questions: How and by what means can they get reasonable results significant to their research from these data? Similar to a gene microarray, the classical statistical pipeline of an antibody array includes data preprocessing transformation, differential expression analysis, classification, and biological annotation analysis. In this chapter, we will provide a pipeline of statistical approaches suitable for antibody arrays to facilitate better understanding of the results gained from each of these steps.

Using Antibody Arrays for Biomarker Discovery.

Biomarkers for diseases are important for the development of clinical diagnostic tests and can provide early intervention for cancer or cardiovascular patients. Over the past decade, antibody array technology has achieved significant technological improvement in the quantitative measurement of more than a thousand proteins simultaneously and has been utilized to screen and identify unique proteins as disease biomarkers. However, few biomarkers have been translated into clinical application.

Analyzing Signaling Pathways Using Antibody Arrays.

Cell signaling is comprised of complex networks that regulate homeostasis and human diseases. The analyses of such pathways would improve our understanding of disease pathology and direct drug development. However, it remains a great challenge to study pathways using traditional methods.

Dried Blood-Based Protein Profiling Using Antibody Arrays.

Dried blood samples have been increasingly considered for clinical applications in recent years. The main disadvantages that limit DBS utility in clinical applications are the small sample volume collected, area bias and homogeneity issues, and sample preparation requirements for the necessary sensitivity and reproducibility required for clinical assessment. The recent advances in antibody array technology overcome the common disadvantages of immunoassay approaches by increasing the multiplex capabilities and decreasing the sample volume requirements as well as minimizing the expense and technical expertise required with many alternative high-density approaches like mass spectrometry.

Methods for Membranes and Other Absorbent Surfaces.

Membrane arrays are a unique array platform option for the detection of multiple analytes or materials simultaneously. Their naturally absorptive properties and near universal use in various laboratory methods make it an excellent source with which to probe multiple factors simultaneously. Any liquid sample type can be probed, from bacterial strains, tissue lysates, secreted proteins, to DNA aptamers.

Enhanced Protein Profiling Arrays for High-Throughput Quantitative Measurement of Cytokine Expression.

The antibody array has become a powerful technology in recent years and is widely used to detect the expression levels of various proteins such as cytokines, growth factors, chemokines, and angiogenic factors, some of which are involved in cancer progression. In this chapter, we describe a protein array technology called enhanced protein profiling array, which can simultaneously and quantitatively measure the expression levels of a few proteins in hundreds or thousands of samples, and an example of its use is presented.

Cytometry Multiplex Bead Antibody Array.

The flow cytometry-based multiplex bead array is an advanced technology using antibody-conjugated multiplex beads to detect soluble targets in a liquid phase. This technology has been widely used for detection of soluble analytes like cytokines, chemokines, allergens, viral antigens, and cancer markers. RayPlex Multiplex Beads Antibody Array series are developed by RayBiotech Life, Inc.

Global Detection of Proteins by Label-Based Antibody Array.

Because of narrow availability of antibody pairs and potential cross-reactivity between antibodies, the development of sandwich-based antibody arrays which need a pair of antibodies for each target has been restricted to higher density resulting in limited proteomic breadth of detection. Label-based array is one way to overcome this obstacle by directly labeling all targets in samples with fluorescent dyes such as Cy3 and Cy5. The labeled samples are then applied on the antibody array chip composed of capture antibodies.

Sandwich-Based Antibody Arrays for Protein Detection.

Sandwich-based antibody arrays enable the detection of multiple proteins simultaneously, thus offering a time- and cost-effective alternative to single-plex platforms. The protein of interest is "sandwiched" between an antibody that captures it to the array and a second antibody that is used for detection. Here we describe a 1-day procedure to process samples, such as serum or cell lysates, with a quantitative sandwich-based antibody array on a glass substrate using fluorescence.

Differences in serum proteins in traditional Chinese medicine constitutional population: Analysis and verification.

Traditional Chinese medicine assigns individuals into different categories called "constitutions" to help guide the clinical treatment according to subjective physiologic, psychologic analyses, large-scale clinical observations, and epidemiologic studies. To further explore more objective expressions of constitutions, antibody microarrays were used to analyze the serologic protein profiles of two different constitutions, a balanced (or healthy) constitution (BC) and the dampness constitution (DC) comprising phlegm-dampness and damp-heat constitutions. The profiles of changing constitutions across time were also analyzed.

Identification of eight-protein biosignature for diagnosis of tuberculosis.

Background: Biomarker-based tests for diagnosing TB currently rely on detecting (Mtb) antigen-specific cellular responses. While this approach can detect Mtb infection, it is not efficient in diagnosing TB, especially for patients who lack aetiological evidence of the disease.

Methods: We prospectively enrolled three cohorts for our study for a total of 630 subjects, including 160 individuals to screen protein biomarkers of TB, 368 individuals to establish and test the predictive model and 102 individuals for biomarker validation.

Developing a periodontal disease antibody array for the prediction of severe periodontal disease using machine learning classifiers.

Background: The aim of this study was to simultaneously and quantitatively assess the expression levels of 20 periodontal disease-related proteins in gingival crevicular fluid (GCF) from normal controls (NOR) and severe periodontitis (SP) patients with an antibody array.

Methods: Antibodies against 20 periodontal disease-related proteins were spotted onto a glass slide to create a periodontal disease antibody array (PDD). The array was then incubated with GCF samples collected from 25 NOR and 25 SP patients.