Immune complexome analysis

Advancement in leishmaniasis diagnosis and therapeutics: An update

Leishmaniasis is regarded as a neglected tropical disease by World Health Organization (WHO) and is ranked next to malaria as the deadliest protozoan disease. The primary causative agents of the disease comprise of diverse leishmanial species sharing clinical features ranging from skin abrasions to lethal infection in the visceral organs. As several Leishmania species are involved in infection, the role of accurate diagnosis becomes pivotal in adding new dimensions to anti-leishmanial therapy. Diagnostic methods must be fast, reliable, easy to perform, highly sensitive, and specific to differentiate among similar parasitic diseases. Herein, we present the conventional and recent approaches impended for the disease diagnosis and their sensitivity, specificity, and clinical application in parasite detection. Furthermore, we have also elaborated various new methods to cure leishmaniasis, which include host-directed therapies, drug repurposing, nanotechnology, and combinational therapy. This review addresses novel techniques and innovations in leishmaniasis, which can aid in unraveling new strategies to fight against the deadly infection.

Analysis of the Repertoires of Circulating Autoantibodies' Specificities as a Tool for Identification of the Tumor-Associated Antigens: Current Problems and Solutions

Circulating autoantibodies against tumor-associated autoantigens (TAA) may serve as valuable biomarkers for a wide range of diagnostic purposes. Modern immunology offers a large variety of methods for in-depth comparative analysis of the repertoires of circulating antibodies' antigenic specificities in health and disease. Nevertheless, this research field so far has met somewhat limited clinical success, while numerous data on the repertoires of circulating autoantibodies' specificities in cancer patients are poorly integrated into the contemporary picture of the immunological and molecular landscapes of human tumors. This review is an attempt to identify and systematize the key and essentially universal conceptual and methodological limitations of analyses of the repertoires of circulating antibodies' antigenic specificities in cancer (expression bias, redundancy of TAA repertoires, identification of natural IgG, the absence of the pathogenetically relevant context in the experimental systems used to detect TAA), as well as to discuss potential and already known methodological improvements that may significantly increase the detectability of the pathogenetically relevant and diagnostically significant bona fide TAA.

Immunoproteomic Analysis Reveals Novel Candidate Antigens for the Diagnosis of Paracoccidioidomycosis Due to Paracoccidioides lutzii

Paracoccidioidomycosis (PCM) is a life-threatening systemic infection caused by the fungal pathogen Paracoccidioides brasiliensis and related species. Whole-genome sequencing and stage-specific proteomic analysis of Paracoccidioides offer the opportunity to profile humoral immune responses against P. lutzii and P. brasiliensis s. str. infection using innovative screening approaches. Here, an immunoproteomic approach was used to identify PCM-associated antigens that elicit immune responses by combining 2-D electrophoresis of P. lutzii and P. brasiliensis proteomes, immunological detection using a gold-standard serum, and mass spectrometry analysis. A total of 16 and 25 highly immunoreactive proteins were identified in P. lutzii and P. brasiliensis, respectively, and 29 were shown to be the novel antigens for Paracoccidioides species, including seven uncharacterized proteins. Among the panel of proteins identified, most are involved in metabolic pathways, carbon metabolism, and biosynthesis of secondary metabolites in both immunoproteomes. Remarkably, six isoforms of the surface-associated enolase in the range of 54 kDa were identified as the major antigens in human PCM due to P. lutzii. These novel immunoproteomes of Paracoccidioides will be employed to develop a sensitive and affordable point-of-care diagnostic assay and an effective vaccine to identify infected hosts and prevent infection and development of human PCM. These findings provide a unique opportunity for the refinement of diagnostic tools of this important neglected systemic mycosis, which is usually associated with poverty.

Structural characteristics of circulating immune complexes in calves with bronchopneumonia: Impact on the quiescent leukocytes

Calf bronchopneumonia is accompanied by increased level of circulating immune complexes (CIC), and we analysed size, and protein and lipid constituents of these CIC with an attempt to elucidate the connection between the CIC structural properties and their capacity to modulate leukocyte function. CIC of heathy calves (CIC_H) and calves with naturally occurring bronchopneumonia (CIC_D) were isolated by PEG precipitation and analysed by electrophoresis and chromatography. The predominant CIC proteins were IgG, albumin, and transferrin. Affinity isolated serum and CIC IgG coprecipitated several proteins, but only 75 and 80 kDa proteins bound CIC IgG, exclusively. 60 and 65 kDa proteins co-precipitated with CIC_D IgG, unlike CIC_H IgG. In both CIC_H and CIC_D, oleic acid-containing phospholipids predominated. In CIC_D, the content of oleic and vaccenic acid was higher than in CIC_H, while myristic, palmitic, stearic, linoleic and arachidonic acid showed lower content. Dynamic light scattering displayed difference in particle size distribution between CIC_H and CIC_D; 1280 nm large particles were present only in CIC_D. The effect of CIC_H and CIC_D on mononuclear cells (MNC) and granulocytes was analysed in vitro. CIC_H and CIC_D, with slight difference in intensity, stimulate MNC apoptosis, promote cell cycle arrest of unstimulated MNC, and cell cycle progression of PHA stimulated MNC. Both CIC reduced granulocyte apoptosis after 24 h while after 48 h this effect was detected for CIC_D only. These results indicate that structural differences of CIC_H and CIC_D might interfere with the CIC functional capacity, which we consider important for evaluation of CIC immunoregulatory function.

Revisiting immune complexes: Key to understanding immune-related diseases

Immune complexes (ICs) formed by foreign or self-antigens and antibodies in biological fluids affect various tissues and are thought to cause several diseases. Biological and physical properties of IC, abnormal IC amounts, IC deposition and their relationships with disease pathogenesis had been studied. However, the relationship between ICs and each disease is not well understood and little is known of what determined ICs deposition in particular organ and why different organs are affected in different diseases. Recent technological advance enables identification of ICs in particular its antigens in tissues and body fluids, which may provide a key to discover an important trigger for immunological abnormality occurrence. Further identification of their epitopes, that are the exact origin of antigenicity, is developing and may be useful for diagnosis, elucidation of pathogenesis and treatment against IC-induced diseases. Here, we first make an overview of clearance of ICs, IC-induced pathogenesis and biological properties of ICs. Then, we introduce various methods developed to recover ICs from biological fluids or to identify antigens incorporated into ICs. Furthermore, several methods that can be used in epitope mapping for IC antigens are also documented.

Association Between ApoA-I (Apolipoprotein A-I) Immune Complexes and Adverse Cardiovascular Events-Brief Report

OBJECTIVE

The immune response is linked to the progression of atherosclerotic cardiovascular disease (CVD). Free autoantibodies targeting ApoA-I (apolipoprotein A-I) have been identified as a component of the inflammatory milieu in patients and have a moderate association with CVD progression. Based on the presence of these antibodies and the high concentration of circulating ApoA-I, we hypothesized that antibodies bound to ApoA-I as an immune complex would be predictive of incident adverse CVD outcomes. Approach and Results: The presence of ApoA-I/IgG immune complexes (ICs) in plasma was confirmed by ELISA in 3 subject cohorts. Characterization of the protein components of ApoAI/IgG ICs indicate that ICs are not correlated with total ApoA-I concentration and are enriched in the anti-inflammatory subclass, IgG4, relative to total plasma IgG (>30% versus 6%). In 359 patients with coronary artery disease (CAD), there were 71 incident adverse CVD events (death, myocardial infarction, and stroke) during a median 4.1-year follow-up. In Cox proportional hazard regression analysis, low levels of ApoA-I/IgG ICs were independent predictors of adverse cardiovascular outcomes after adjustment for age, sex, diabetes mellitus, estimated glomerular filtration rate, presence of obstructive CAD, heart failure, total cholesterol, and HDL (high-density lipoprotein) cholesterol (adjusted hazard ratio of 1.90 [95% CI, 1.03-3.49; P=0.038] between the lowest and the highest tertiles).

CONCLUSIONS

Low levels of ApoA-I/IgG ICs are associated with an increased risk of adverse events in patients with CAD, raising their potential to be used as a biomarker to predict CVD progression.

Immunoproteomics Methods and Techniques

The varied landscape of the adaptive immune response is determined by the peptides presented by immune cells, derived from viral or microbial pathogens or cancerous cells. The study of immune biomarkers or antigens is not new, and classical methods such as agglutination, enzyme-linked immunosorbent assay, or Western blotting have been used for many years to study the immune response to vaccination or disease. However, in many of these traditional techniques, protein or peptide identification has often been the bottleneck. Recent progress in genomics and mass spectrometry have led to many of the rapid advances in proteomics approaches. Immunoproteomics describes a rapidly growing collection of approaches that have the common goal of identifying and measuring antigenic peptides or proteins. This includes gel-based, array-based, mass spectrometry-based, DNA-based, or in silico approaches. Immunoproteomics is yielding an understanding of disease and disease progression, vaccine candidates, and biomarkers. This review gives an overview of immunoproteomics and closely related technologies that are used to define the full set of protein antigens targeted by the immune system during disease.

Peculiarities of the formation and subsequent removal of the circulating immune complexes from the bloodstream during the process of digestion

Background: Large protein aggregates, known as circulating immune complexes (CICs), are formed in biological fluids as a result of the development of the body's immune response to various provoking factors. The kinetic characteristics of the formation and removal of immune complexes (ICs), their physical parameters, the isotypic composition of immunoglobulins (Igs) and the antigenic component of the CICs may reflect certain aspects of certain pathological and metabolic processes taking place in humans and animals. The aim of this study is to assess the kinetic characteristics of the formation and removal of the CICs that form in blood after eating. We also analyze the changes in the isotypic composition of Igs of ICs that accompany this biological process in rodents and humans. Methods: We identified the CICs, which differed in size and class of Igs, using dynamic light scattering. To remove ICs from the plasma, we used immune-affinity sedimentation. Monoclonal antibodies for the Igs of different isotypes were added to the plasma samples to determine the isotypic composition of the ICs. Results: A large number of ICs were formed in the blood of rats and humans after eating (food CICs). In rats, food ICs are almost immediately filtered in the liver, without circulating in the bloodstream through the body. In humans, the level of food ICs in the blood increases for 3.5 h after ingestion, then within 7-8 h their gradual removal takes place. It was found that in the process of digestion in humans, the isotypic composition of Igs in the CICs changes and becomes more diverse. Conclusions: The molecular-cellular mechanisms of the formation and utilization of food CICs in humans and rodents do not match completely.

Immunoproteomics technologies in the discovery of autoantigens in autoimmune diseases

Proteomics technologies are often used for the identification of protein targets of the immune system. Here, we discuss the immunoproteomics technologies used for the discovery of autoantigens in autoimmune diseases where immune system dysregulation plays a central role in disease onset and progression. These autoantigens and associated autoantibodies can be used as potential biomarkers for disease diagnostics, prognostics and predicting/monitoring drug responsiveness (theranostics). Here, we compare a variety of methods such as mass spectrometry (MS)-based [serological proteome analysis (SERPA), antibody mediated identification of antigens (AMIDA), circulating immune complexome (CIC) analysis, surface enhanced laser desorption/ionization-time of flight (SELDI-TOF)], nucleic acid based serological analysis of antigens by recombinant cDNA expression cloning (SEREX), phage immunoprecipitation sequencing (PhIP-seq) and array-based immunoscreening (proteomic microarrays), luciferase immunoprecipitation systems (LIPS), nucleic acid programmable protein array (NAPPA) methods. We also review the relevance of immunoproteomic data generated in the last 10 years, with a focus on the aforementioned MS based methods.

Global profiling of protein complexes: current approaches and their perspective in biomedical research

INTRODUCTION

Despite the rapid evolution of proteomic methods, protein interactions and their participation in protein complexes - an important aspect of their function - has rarely been investigated on the proteome-wide level. Disease states, such as muscular dystrophy or viral infection, are induced by interference in protein-protein interactions within complexes. The purpose of this review is to describe the current methods for global complexome analysis and to critically discuss the challenges and opportunities for the application of these methods in biomedical research. Areas covered: We discuss advancements in experimental techniques and computational tools that facilitate profiling of the complexome. The main focus is on the separation of native protein complexes via size exclusion chromatography and gel electrophoresis, which has recently been combined with quantitative mass spectrometry, for a global protein-complex profiling. The development of this approach has been supported by advanced bioinformatics strategies and fast and sensitive mass spectrometers that have allowed the analysis of whole cell lysates. The application of this technique to biomedical research is assessed, and future directions are anticipated. Expert commentary: The methodology is quite new, and has already shown great potential when combined with complementary methods for detection of protein complexes.