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Focal and segmental glomerulosclerosis (FSGS) is a severe form of idiopathic nephrotic syndrome (INS), a glomerulopathy of presumably immune origin that is attributed to extrarenal pathogenic circulating factors. The recurrence of FSGS (rFSGS) after transplant occurs in 30% to 50% of cases. The direct analysis of patient plasma proteome has scarcely been addressed to date, mainly due to the methodological difficulties associated with plasma complexity and dynamic range. In this study, first, we compared different methods of plasma preparation, second, we compared the plasma proteomes of rFSGS and controls using two preparation methods, and third, we analyzed the early proximal signaling events in podocytes subjected to patient plasma, through a combination of phosphoproteomics and lipid-raft proteomics (raftomics). By combining immunodepletion and high pH fractionation, we performed a differential proteomic analysis of soluble plasma proteins and of extracellular vesicles (EV) obtained from healthy controls, non-INS patient controls, and rFSGS patients (n = 4). In both the soluble- and the EV-protein sets from the rFSGS patients, we found a statistically significant increase in a cluster of proteins involved in neutrophil degranulation. A group of lipid-binding proteins, generally associated with lipoproteins, was found to be decreased in the soluble set from the rFSGS patients. In addition, three amino acid transporters involved in mTORC1 activation were found to be significantly increased in the EV from the rFSGS. Next, we incubated human podocytes for 30 min with 10% plasma from both groups of patients. The phosphoproteomics and raftomics of the podocytes revealed profound differences in the proteins involved in the mTOR pathway, in autophagy, and in cytoskeleton organization. We analyzed the correlation between the abundance of plasma and plasma-regulated podocyte proteins. The observed changes highlight some of the mechanisms involved in FSGS recurrence and could be used as specific early markers of circulating-factor activity in podocytes. [ABSTRACT FROM AUTHOR]

Abstract Background Health care workers (HCWs) are at risk for occupationally acquired Mycobacterium tuberculosis infection and tuberculosis (TB) disease due to repeated exposure to workplace tubercle bacilli. To determine whether continual mycobacterial stimulation correlates with increased expression of inhibitory T cell receptors, here we compared PD-1 receptor expression on surfaces of circulating T cells between naïve (uninfected) HCWs and HCWs with latent TB infection (LTBI). Result Data collected from 133 medical workers who met study selection criteria were included in the final analysis. QuantiFERON-TB Gold In-​Tube (QFT-GIT) testing yielded positive results for 32 HCWs, for an overall LTBI rate of 24.1%. Multivariate analysis identified HCW length of service > 15 years as an independent risk factor for a positive QFT-GIT result. In addition, comparisons of blood T cell subgroup profiles between QFT- and QFT+ groups indicated QFT+ subjects possessed greater proportions of mature (TM), transitional memory (TTM) and effector memory (TEM) CD4+ T cell subgroups and lower proportions of naïve T cells (TN). Moreover, the QFT+ group percentage of CD8+ T cells with detectable surface PD-1 was significantly higher than the corresponding percentage for the QFT- group. Meanwhile, no statistical intergroup difference was observed in percentages of CD4+ T cells with detectible surface PD-1. Conclusions Our data demonstrated that upregulated PD-1 expression on circulating CD8+, but not CD4+ T cells, was associated with latent TB infection of HCWs. As compared to other hospitals, occupational TB infection risk in our hospital was substantially mitigated by implementation of multitiered infection control measures.

Background: Health care workers (HCWs) are at risk for occupationally acquired Mycobacterium tuberculosis infection and tuberculosis (TB) disease due to repeated exposure to workplace tubercle bacilli. To determine whether continual mycobacterial stimulation correlates with increased expression of inhibitory T cell receptors, here we compared PD-1 receptor expression on surfaces of circulating T cells between naïve (uninfected) HCWs and HCWs with latent TB infection (LTBI). Result: Data collected from 133 medical workers who met study selection criteria were included in the final analysis. QuantiFERON-TB Gold In-​Tube (QFT-GIT) testing yielded positive results for 32 HCWs, for an overall LTBI rate of 24.1%. Multivariate analysis identified HCW length of service > 15 years as an independent risk factor for a positive QFT-GIT result. In addition, comparisons of blood T cell subgroup profiles between QFT- and QFT+ groups indicated QFT+ subjects possessed greater proportions of mature (TM), transitional memory (TTM) and effector memory (TEM) CD4+ T cell subgroups and lower proportions of naïve T cells (TN). Moreover, the QFT+ group percentage of CD8+ T cells with detectable surface PD-1 was significantly higher than the corresponding percentage for the QFT- group. Meanwhile, no statistical intergroup difference was observed in percentages of CD4+ T cells with detectible surface PD-1. Conclusions: Our data demonstrated that upregulated PD-1 expression on circulating CD8+, but not CD4+ T cells, was associated with latent TB infection of HCWs. As compared to other hospitals, occupational TB infection risk in our hospital was substantially mitigated by implementation of multitiered infection control measures. [ABSTRACT FROM AUTHOR]

Treatment with alemtuzumab is followed by an early increase in Treg frequencies. Whether naïve and memory subsets are differentially affected and how depletion influences dysfunctional MS-Treg is unclear. In this study, we analyzed the effect of alemtuzumab on regulatory T-cells (Treg) in patients with multiple sclerosis (MS). For this purpose 182 blood samples from 25 MS patients were taken shortly before treatment and serially for up to 24 months after two alemtuzumab cycles. We studied Treg by flow cytometry (quantitation, phenotypical characterization), real-time polymerase chain reaction (T-cell receptor (TCR) excision circles [TREC] content), CDR3-spectratyping (clonal distribution), and proliferation assays (suppressive function). CD52-mediated cytolysis of Treg and conventional T-cells was determined by a complement-dependent cytolysis assay. Our studies revealed that 1 week post-alemtuzumab, Treg were depicted at constant frequencies among CD4+ T-cells. In contrast, Treg frequencies were massively increased at month 1. Post-depletional Treg exhibited a CD45RO+ memory phenotype, a skewed TCR repertoire, and contained minimum TREC numbers. Naïve Treg, thymic markers, and TCR-variability commenced to rise after 6 months but did not attain baseline levels. In vitro, Treg exhibited higher susceptibility to lysis than Tcon. Treg suppressive function constantly increased within 1 year when co-cultured with syngeneic T-cells, but remained stable against allogeneic T-cells from normal donors. Our findings suggest that (1) Treg are not spared from alemtuzumab-mediated depletion and thymopoiesis does not considerably contribute to long-term recovery, (2) either homeostatic proliferation and/or conversion from residual Tcon contributes to Treg expansion during the early post-treatment phase (3) the enhanced inhibitory effect of Treg following alemtuzumab is due to altered composition and reactivity of post-depletional Tcon.

Phytophthora cinnamomi Rands, a soil-borne oomycete plant pathogen, is a major threat to natural vegetation in many countries, especially Australia. The disease that it causes also has economic impacts on several agricultural and forestry systems worldwide. To investigate the virulence mechanisms of P. cinnamomi the roles of elicitins and elicitin-like proteins were examined using a susceptible model species, Lupinus angustifolius. Elicitins are 10 kDa proteins secreted by many Phytophthora species. Here, elicitins were isolated from P. cinnamomi liquid culture and separated according to their isoelectric point. A β-cinnamomin elicitin was then purified and used to develop an immunoaffinity purified antibody as a tool to examine virulence. The specificity of the β-cinnamomin antiserum was confirmed through Western-blot analysis. β-cinnamomin was found to be produced at different P. cinnamomi life stages and in inoculated plant roots by using immuno detection via confocal laser scanning microscopy. Pre-treatment of P. cinnamomi zoospores with β-cinnamomin antiserum and then inoculation of susceptible L. angustifolius roots revealed a partial loss of virulence of the pathogen. In addition, the expression of the β-cinnamomin gene at an early infection stage in susceptible L. angustifolius suggested an intrinsic role of the elicitin. Furthermore, the identification of covalently bound cell wall proteins in P. cinnamomi mycelia in this study has opened up the opportunity to investigate their role in virulence. • A protein extract from a P. cinnamomi liquid culture showed a single band at 10 kDa suggesting the presence of elicitin(s). • A purified anti-β-cinnamomin antibody recognised a single band on a western blot confirming the specificity of the antiserum. • β-cinnamomin immuno-labelling was found at different P. cinnamomi life stages and in inoculated roots. • Immunodepletion tests showed a loss of pathogen virulence towards Lupinus angustifolius confirming β-cinnamomin's role. • Elucidation of cell wall-associated proteins revealed an opportunity to examine the role of individual proteins in virulence. [ABSTRACT FROM AUTHOR]

Treatment with alemtuzumab is followed by an early increase in Treg frequencies. Whether naïve and memory subsets are differentially affected and how depletion influences dysfunctional MS-Treg is unclear. In this study, we analyzed the effect of alemtuzumab on regulatory T-cells (Treg) in patients with multiple sclerosis (MS). For this purpose 182 blood samples from 25 MS patients were taken shortly before treatment and serially for up to 24 months after two alemtuzumab cycles. We studied Treg by flow cytometry (quantitation, phenotypical characterization), real-time polymerase chain reaction (T-cell receptor (TCR) excision circles [TREC] content), CDR3-spectratyping (clonal distribution), and proliferation assays (suppressive function). CD52-mediated cytolysis of Treg and conventional T-cells was determined by a complement-dependent cytolysis assay. Our studies revealed that 1 week post-alemtuzumab, Treg were depicted at constant frequencies among CD4+ T-cells. In contrast, Treg frequencies were massively increased at month 1. Post-depletional Treg exhibited a CD45RO+ memory phenotype, a skewed TCR repertoire, and contained minimum TREC numbers. Naïve Treg, thymic markers, and TCR-variability commenced to rise after 6 months but did not attain baseline levels. In vitro , Treg exhibited higher susceptibility to lysis than Tcon. Treg suppressive function constantly increased within 1 year when co-cultured with syngeneic T-cells, but remained stable against allogeneic T-cells from normal donors. Our findings suggest that (1) Treg are not spared from alemtuzumab-mediated depletion and thymopoiesis does not considerably contribute to long-term recovery, (2) either homeostatic proliferation and/or conversion from residual Tcon contributes to Treg expansion during the early post-treatment phase (3) the enhanced inhibitory effect of Treg following alemtuzumab is due to altered composition and reactivity of post-depletional Tcon. [ABSTRACT FROM AUTHOR]

Simian-human immunodeficiency virus (SHIV) infection in rhesus macaques (RMs) resembles human immunodeficiency virus type 1 (HIV-1) infection in humans and serves as a tool to evaluate candidate AIDS vaccines. HIV-1 clade A (HIV-A) predominates in parts of Africa. We constructed an R5 clade A SHIV (SHIV-A; strain SHIV-KNH1144) carrying env from a Kenyan HIV-A. SHIV-A underwent rapid serial passage through six RMs. To allow unbridled replication without adaptive immunity, we simultaneously ablated CD8+ and B cells with cytotoxic monoclonal antibodies in the next RM, resulting in extremely high viremia and CD4+ T-cell loss. Infected blood was then transferred into two non-immune-depleted RMs, where progeny SHIV-A showed increased replicative capacity and caused AIDS. We reisolated SHIV-KNH1144p4, which was replication-competent in peripheral blood mononuclear cells (PBMC) of all RMs tested. Next-generation sequencing of early and late-passage SHIV-A strains identified mutations that arose due to "fitness" virus optimization in the former and mutations exhibiting signatures typical for adaptive host immunity in the latter. "Fitness" mutations are best described as mutations that allow for better fit of the HIV-A Env with SIV-derived virion building blocks or host proteins and mutations in non-coding regions that accelerate virus replication, all of which result in the outgrowth of virus variants in the absence of adaptive T-cell and antibody-mediated host immunity. [ABSTRACT FROM AUTHOR]

Over the past decade, chemical labeling with isobaric tandem mass tags, such as isobaric tags for relative and absolute quantification reagents (iTRAQ) and tandem mass tag (TMT) reagents, has been employed in a wide range of different clinically orientated serum and plasma proteomics studies. In this review the scope of these works is presented with attention to the areas of research, methods employed and performance limitations. These applications have covered a wide range of diseases, disorders and infections, and have implemented a variety of different preparative and mass spectrometric approaches. In contrast to earlier works, which struggled to quantify more than a few hundred proteins, increasingly these studies have provided deeper insight into the plasma proteome extending the numbers of quantified proteins to over a thousand. [ABSTRACT FROM AUTHOR]

Almost all immunological approaches [immunohistochemistry, enzyme-linked immunosorbent assay (ELISA), Western blot], that are used to quantitate specific proteins have had to address high backgrounds due to non-specific reactivity. We report here for the first time a quantitative comparison of methods for reduction of the background of commercial biotinylated antibodies using the Python-based ELISA_QC program. This is demonstrated using a recombinant humanized anti-cocaine monoclonal antibody. Several approaches, such as adjustment of the incubation time and the concentration of blocking agent, as well as the dilution of secondary antibodies, have been explored to address this issue. In this report, systematic comparisons of two different methods, contrasted with other more traditional methods to address this problem are provided. Addition of heparin (HP) at 1 μg/ml to the wash buffer prior to addition of the secondary biotinylated antibody reduced the elevated background absorbance values (from a mean of 0.313 ± 0.015 to 0.137 ± 0.002). A novel immunodepletion (ID) method also reduced the background (from a mean of 0.331 ± 0.010 to 0.146 ± 0.013). Overall, the ID method generated more similar results at each concentration of the ELISA standard curve to that using the standard lot 1 than the HP method, as analyzed by the Python-based ELISA_QC program. We conclude that the ID method, while more laborious, provides the best solution to resolve the high background seen with specific lots of biotinylated secondary antibody. [ABSTRACT FROM AUTHOR]

Compact bones (CB) are major reservoirs of mouse mesenchymal stem cells (mMSC). Here, we established a protocol to isolate MSC from CB and tested their immunosuppressive potential. Collagenase type II digestion of BM-flushed CB from C57B/6 mice was performed to liberate mMSC precursors from bone surfaces to establish nondepleted mMSC. CB cells were also immunodepleted based on the expression of CD45 (leukocytes) and TER119 (erythroid cells) to eliminate hematopoietic cells. CD45−TER119− CB cells were subsequently used to generate depleted mMSC. CB nondepleted and depleted mMSC progenitors were cultured under hypoxic conditions to establish primary mMSC cultures. CB depleted mMSC compared to nondepleted mMSC showed greater cell numbers at subculturing and had increased functional ability to differentiate into adipocytes and osteoblasts. CB depleted mMSC had high purity and expressed key mMSC markers (>85% Sca-1, CD29, CD90) with no mature hematopoietic contaminating cells (<5% CD45, CD11b) when subcultured to passage 5 (P5). Nondepleted mMSC cultures, however, were less pure and heterogenous with <72% Sca-1+, CD29+, and CD90+ cells at early passages (P1 or P2), along with high percentages of contaminating CD11b+ (35.6%) and CD45+ (39.2%) cells that persisted in culture long term. Depleted and nondepleted mMSC nevertheless exhibited similar potency to suppress total (CD3+), CD4+ and CD8+ T cell proliferation, in a dendritic cell allostimulatory one-way mixed lymphocyte reaction. CB depleted mMSC, pretreated with proinflammatory cytokines IFN-γ, TNF-α, and IL-17A, showed superior suppression of CD8+ T cell, but not CD4+ T cell proliferation, relative to untreated-mMSC. In conclusion, CB depleted mMSC established under hypoxic conditions and treated with selective cytokines represent a novel source of potent immunosuppressive MSC. As these cells have enhanced immune modulatory function, they may represent a superior product for use in clinical allotransplantation. [ABSTRACT FROM AUTHOR]

Background: Challenge tests for food-dependent exercise-induced anaphylaxis (FDEIA) carry some risk and have a high rate of false negatives. Our aim was to explore the usefulness of an in vitro immunodepletion assay and an allergen microarray test in the identification of IgE-mediated cross-reactive food allergens in patients with suspected FDEIA or food-dependent exercise-induced urticaria and panallergen sensitization. Methods: Three patients with a history of food dependent exercise induced urticaria/anaphylaxis and food panallergen sensitization in whom a food-exercise challenge was not feasible were selected: a 25-year-old man with cholinergic urticaria who experienced generalized urticaria and angioedema during a soccer match after drinking a peachbased soft drink; a 19-year-old woman with allergic rhinitis and controlled asthma who experienced anaphylactic shock while playing soccer, having eaten walnuts in the previous 90 min; and a 57-year-old man with baker's asthma who experienced four episodes of anaphylaxis during exercise after ingesting wheat-containing food. All individuals underwent a diagnostic work-up with skin prick tests, specific IgE (sIgE) and ImmunoCAP ISAC test. For the in vitro immunodepletion procedure, patients' serum was pre-incubated with the suspected native allergen (peach, walnut, or wheat) in solid phase (ImmunoCAP). The eluted serum, containing unbound IgE, was collected and samples were re-tested using Immunocap ISAC 112 and compared with baseline results. Results: All individuals were sensitized to lipid transfer proteins. The first patient was sensitized to Pru p 3, Cor a 8, Jug r 3, and Ara h 9; after pre-incubation with peach there was 100% depletion of sIgE to all components. The second patient was sensitized to Pru p 3, Cor a 8, Jug r 3, and Ara h 9; immunodepletion with walnut depleted sIgE to Ara h 9 by 67%, Pru p 3 and Pla a 3 (60%), Art v 3 (75%), Jug r 3 (88%), and Cor a 8 (100%). The third patient was sensitized to Pru p 3, Jug r 3, Ara h 9, and Tri a 14; immunodepletion with wheat depleted Tri a 14 only (100%). Conclusions: In vitro immunodepletion might be a useful diagnostic tool in food dependent exercise induced urticaria/anaphylaxis with panallergen sensitization, particularly for identifying the culprit allergen and guiding dietary elimination recommendations. [ABSTRACT FROM AUTHOR]

The available immunomethods for gluten quantitation could underestimate or overestimate the net immunoactivity of foods and beverages if the chosen analytical antibody is not specific to the relevant gluten immunogenic peptides (GIP). Accurate detection of the most active GIP is desirable to assess the potential celiac toxicity of food. We evaluated the capacity of the G12 monoclonal antibody for selectively depleting GIP in samples from two different gluteomes. Samples of hydrolyzed gliadin from wheat and a barley beer were used. The input (starting peptide digest of prolamins), the flow-through (unbound peptides), and the output (captured peptides) were analyzed by G12 and R5 competitive ELISA as well as by stimulation assays of T-cells from celiac patients. Most of the GIP were retained by the G12-agarose and represented the largest part of the immunogenicity of the gluten peptidome. G12 immunodepletion experiments with hydrolyzed gluten showed that this antibody reacted with those with the highest immunoactivity for celiac patients. [ABSTRACT FROM AUTHOR]

Background The evolution of the “gut-lymph concept” has promoted thoracic duct (TD) lymph drainage as a possible treatment to reduce systemic inflammation and end-organ dysfunction in acute illness. The aim was to review the published experience of thoracic duct interventions (TDIs) aimed at improving clinical outcomes. Methods A search of three databases (MEDLINE, EMBASE, and EMBASE CLASSIC) over the last 60 y. The indications for intervention, the technique, and clinical outcomes were reviewed. Results There were a wide range of indications for TDI. These included reducing rejection after transplantation, treating inflammatory diseases, and reducing chronic failure of the liver, kidney, and heart. The techniques included TD cannulation and lymphovenuous fistula. The outcomes were variable and often equivocal, and this appears to reflect poor design quality. There is clinical equipoise regarding a therapeutic role of (TD lymph drainage in acute pancreatitis, and probably other acute diseases. Conclusions Until well-designed clinical trials are undertaken, the clinical benefits of TDIs will remain promising, but uncertain. [ABSTRACT FROM AUTHOR]

Human biofluids, especially blood plasma or serum, hold great potential as the sources of candidate biomarkers for various diseases; however, the enormous dynamic range of protein concentrations in biofluids represents a significant analytical challenge for detecting promising low-abundance proteins. Over the last decade, various immunoaffinity chromatographic methods have been developed and routinely applied for separating low-abundance proteins from the high- and moderate-abundance proteins, thus enabling much more effective detection of low-abundance proteins. Herein, we review the advances of immunoaffinity separation methods and their contributions to the proteomic applications in human biofluids. The limitations and future perspectives of immunoaffinity separation methods are also discussed. [ABSTRACT FROM AUTHOR]

The first sections of this review compile and discuss strategies and protocols for managing plasma/serum as a source of biomarkers relevant to human disease. In many such cases, depletion of abundant protein(s) is a crucial preliminary step to the procedure; specific conceptual and technical approaches, however, make it possible to effectively use to this purpose whole plasma/serum. The final sections focus instead on the complexity associated with each of the major serum/plasma proteins in terms of both, multiple molecular structures (existence of a number of protein species) and of multiple molecular functions (behavior as multifunctional/multitasking/moonlighting proteins). Reviewing evidence in these and some related fields (regulation of the synthetic pattern by proteins and non-protein compounds and its connection with health and disease) prompts the suggestion/recommendation that information on the abundant components of plasma/serum proteome is routinely obtained and processed/mined as a valuable contribution to the characterization of any non-physiological condition and to the understanding of its mechanisms and of its implications/sequels. [ABSTRACT FROM AUTHOR]

Background: Challenge tests for food‐dependent exercise‐induced anaphylaxis (FDEIA) carry some risk and have a high rate of false negatives. Our aim was to explore the usefulness of an in vitro immunodepletion assay and an allergen microarray test in the identification of IgE‐mediated cross‐reactive food allergens in patients with suspected FDEIA or food‐dependent exercise‐induced urticaria and panallergen sensitization. Methods: Three patients with a history of food dependent exercise induced urticaria/anaphylaxis and food panallergen sensitization in whom a food‐exercise challenge was not feasible were selected: a 25‐year‐old man with cholinergic urticaria who experienced generalized urticaria and angioedema during a soccer match after drinking a peach‐based soft drink; a 19‐year‐old woman with allergic rhinitis and controlled asthma who experienced anaphylactic shock while playing soccer, having eaten walnuts in the previous 90 min; and a 57‐year‐old man with baker's asthma who experienced four episodes of anaphylaxis during exercise after ingesting wheat‐containing food. All individuals underwent a diagnostic work‐up with skin prick tests, specific IgE (sIgE) and ImmunoCAP ISAC test. For the in vitro immunodepletion procedure, patients' serum was pre‐incubated with the suspected native allergen (peach, walnut, or wheat) in solid phase (ImmunoCAP). The eluted serum, containing unbound IgE, was collected and samples were re‐tested using Immunocap ISAC 112 and compared with baseline results. Results: All individuals were sensitized to lipid transfer proteins. The first patient was sensitized to Pru p 3, Cor a 8, Jug r 3, and Ara h 9; after pre‐incubation with peach there was 100% depletion of sIgE to all components. The second patient was sensitized to Pru p 3, Cor a 8, Jug r 3, and Ara h 9; immunodepletion with walnut depleted sIgE to Ara h 9 by 67%, Pru p 3 and Pla a 3 (60%), Art v 3 (75%), Jug r 3 (88%), and Cor a 8 (100%). The third patient was sensitized to Pru p 3, Jug r 3, Ara h 9, and Tri a 14; immunodepletion with wheat depleted Tri a 14 only (100%). Conclusions: In vitro immunodepletion might be a useful diagnostic tool in food dependent exercise induced urticaria/anaphylaxis with panallergen sensitization, particularly for identifying the culprit allergen and guiding dietary elimination recommendations. [ABSTRACT FROM AUTHOR]

Liquid chromatography/mass spectrometry (LC/MS) has become a routine powerful technology in clinical proteomic studies for protein identification, protein characterization, and the discovery of biomarkers. In this chapter, we describe two protocol methods to analyze clinical patient samples using a resin-based depletion column followed by either protein In-Gel enzymatic digestion or protein In-Solution enzymatic digestion using a simple kit-based approach (i.e., using the PreOmics iST sample preparation kit), followed by analysis using one-dimensional reverse-phase chromatography (RPC) or high pH reversed-phase peptide fractionation., (© 2023. The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature.)

This chapter focuses on upstream immunodepletion of high-abundance proteins from plasma samples and subsequent analysis by fluorescence two-dimensional difference gel electrophoresis (2D-DIGE). The abundances of proteins in biofluid proteomes, such as serum, plasma, saliva, and bronchoalveolar lavage fluid (BALF), can exceed ten orders of magnitude. This substantial dynamic range is problematic for the detection of medium and low-abundance proteins by 2D-DIGE analysis. To increase the detection, quantification, and identification of medium-low-abundance proteins, the targeted depletion of known abundant proteins with antibody columns has been successfully employed. From the literature, it is clear that the performance of abundant protein depletion with immunodepletion columns has been successful in broadening the coverage of the biofluid proteome and facilitating the identification of disease-specific biomarkers. The task for a successful biomarker strategy involves the combination of a reproducible and robust fractionation method, coupled with a highly accurate quantitative method, a task that is exemplified by combining both immunodepletion and 2D-DIGE together to discover significant proteins associated with the disease phenotype., (© 2023. The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature.)

Extracellular vesicles (EVs) are released naturally in vivo and in vitro from cells and tissues into biological fluids such as plasma, urine, saliva and amniotic fluid, and into culture medium. EV may contain proteins, lipids, mRNA and miRNA significant of the physiological status or of their cellular origin and affect the functions of neighboring cells. The characterization of EVs present in HIV-1-infected individuals provides insight into pathogenesis, inflammation and disease progression. However, the potential of EVs to become reliable research or diagnostic tools is currently limited by the difficulty of distinguishing apoptotic and plasma membrane EVs, exosomes and virions. In spite of this methodological limitation, EVs are expected to become highly useful tools in biomedicine and uncover a research area expected to lead to innovative R&D. [ABSTRACT FROM AUTHOR]

Background Prostate cancer (PCa) is the second cause of mortality in men worldwide. The prostate-specific antigen (PSA) test is routinely adopted in diagnosis; nevertheless more reliable biomarkers are continuously under investigation by monitoring the release of molecules into the bloodstream. The serum protein profiles appear to provide cancer-specific fingerprints that help to discriminate patients (especially with low PSA level) from controls, improving the performance of existing clinical tests. Methods Samples from healthy controls and PCa patients with low (≤ 4 ng/mL) and high PSA (> 4 ng/mL) levels were analyzed by MALDI profiling, and by a multi fractionation approach coupled to ESI-MS for peaks identification. Results MALDI profiling achieved to detect 10 and 14 changed peaks ( p -value < 0.05), respectively, in PCa patients with low and high PSA versus controls. In particular, a peak identified as C3f fragment, resulted overexpressed in low PSA PCa patients. Conclusions PSA test, coupled to MALDI profiling, is able to detect changes, specifically related to PCa, in low molecular weight protein range. Furthermore, for the first time in prostate cancer research, the identification and quantification of the small peptide C3f appears to be relevant for the detection of false negatives, providing an additive diagnostic power to PSA ( p < 0.01) and suggesting its use in clinical tests. [ABSTRACT FROM AUTHOR]

Bispecific monoclonal IgG antibodies offer increased efficacy by antagonizing two different targets. Assessing drug mechanisms, target engagement and biomarker features, the quantification of free target levels is essential. The anti-Ang2/VEGF-CrossMab (anti-A2V) recognizes soluble vascular endothelial growth factor-A (VEGF-A) and soluble angiopoietin-2 (Ang2). However, an assay for reliable free Ang2 determination is missing. Here, we describe an immunodepletion procedure that allows for selective quantification of free Ang2 target levels by taking into advantage the bispecificity of the therapeutic antibody. The specificity for VEGF was utilized to efficiently eliminate drug-bound Ang2 from plasma samples prior to an established Ang2 measurement. The magnetic bead-based depletion procedure used an anti-idiotypic monoclonal antibody (mAb) specific for the VEGF binding site of anti-A2V (anti-Id-anti-VEGF mAb) to capture the drug along with drug-bound Ang2. High efficiencies of 99.9% were obtained for anti-A2V depletion (concentration range 300 ng/mL to 10 6 ng/mL) reflecting a 1000-fold reduction of drug-bound Ang2. A significant impact of the interaction of anti-Id-anti-VEGF mAb with anti-A2V on the Ang2 binding could be excluded. Moreover, reliable quantification of free Ang2 concentrations in plasma samples was assured by interference testing. Performing advanced free Ang2 determination including the immunodepletion step in parallel to established Ang2 measurement without immunodepletion, we compared free with total Ang2 concentrations in human plasma samples obtained from an anti-A2V Phase 1 clinical study. Samples from untreated patients displayed rather low and equal values for both free and total Ang2. In contrast, samples from drug-treated patients showed a significant reduction of free Ang2 accompanied by an accumulation in total Ang2. These results underline the value of the novel immunodepletion procedure for reliable discrimination of free vs. total target quantification with particular importance for pre-clinical and clinical development of anti-A2V. Moreover, this approach may serve as universal concept for the determination of free target levels of bispecific therapeutic antibodies. [ABSTRACT FROM AUTHOR]

Highlights: [•] Differences in the porcine and piscine heparin binding pattern were detected by 2D-electrophoresis. [•] Seventeen fibrinogen isomers were identified as heparin-binding. [•] Heparin chromatography and adapted immunodepletion resulted in the identification of 76 candidate biomarkers. [•] Fourteen previously undescribed heparin-binding proteins were identified. [•] Low abundance plasma proteins were identified. [Copyright &y& Elsevier]

A second generation antivenomics protocol, based on affinity chromatography, was compared with a previously (first generation) immunodepletion protocol using as a proof of principle the pan-African EchiTAb-Plus-ICP ® IgG antivenom and the venoms of Echis ocellatus , Bitis arietans , and African spitting cobras. The antivenom showed qualitatively similar immunoreactivity patterns using either antivenomic approach. Quantitative departures were noticed between both methods, which may be ascribed to differences in calculating the relative amounts of the non-recognized venom proteins. The smoother baseline in chromatograms of the affinity column allowed better resolution and more accurate quantification of the antivenomic outcome than the original immunodepletion protocol. Our results indicate that both methods can be used interchangeably to investigate the in vitro immunoreactivity of antivenoms. However, advantages of the second generation antivenomics are the possibility of analyzing F(ab′) 2 antivenoms and the reusability of the affinity columns. These features contribute to the generalization, economy and reproducibility of the method. [ABSTRACT FROM AUTHOR]

Purpose: Breast cancer is the most frequent malignancy in women. However, no useful serum markers with high sensitivity and specificity for the detection of early breast cancer have been identified. The search for biological markers of early breast cancer is of continual interest in experimental and clinical breast cancer research. We recently described a simple and highly reproducible three-step proteome analysis for identifying potential disease-marker candidates among the low-abundance serum proteins. Methods: Serum samples from breast ductal carcinoma in situ (DCIS) patients and normal controls were subjected to a three-step serum proteome analysis. The steps were the following: first, immunodepletion of most abundant proteins; second, fractionation using reverse-phase high-performance liquid chromatography; and third, separation using two-dimensional electrophoresis (2-DE). Differences revealed by protein staining were further confirmed by Western blotting, immunohistochemical staining, and enzyme-linked immunosorbent assays (ELISA). Results: Twenty-two upregulated and 26 downregulated spots were detected on the 2-DE gels, and a total of 33 proteins were identified by liquid chromatography and tandem mass spectrometry. Western blotting confirmed that the level of vitronectin was significantly increased in DCIS patients compared with that of normal controls. Immunohistochemical staining of vitronectin in breast cancer tissue revealed high expression in small vessel walls surrounding cancer cells and the extracellular matrix of stroma. Moreover, vitronectin serum concentrations, as measured by ELISA, were significantly increased in patients with DCIS or more advanced breast cancer compared with those of normal controls. Conclusions: Vitronectin could serve as a promising serum marker for the detection of primary breast cancer. [ABSTRACT FROM AUTHOR]

Viperid snakes of the genus Atropoides are distributed in Mexico and Central America and, owing to their size and venom yield, are capable of provoking severe envenomings in humans. This study evaluated, using an 'antivenomics' approach, the ability of a polyspecific (polyvalent) antivenom manufactured in Costa Rica to recognize the proteins of Atropoides mexicanus and A. picadoi venoms, which are not included in the immunization mixture. In addition, the neutralization of lethal, hemorrhagic, myotoxic, coagulant, proteinase and phospholipase A2 (PLA2) activities of these venoms by the antivenom was assessed. The antivenom was highly2 effective in immunodepleting many venom components, particularly high molecular mass P-III metalloproteinases (SVMPs), L-amino acid oxidases, and some serine proteinases and P-I SVMPs. In contrast, PLA2s, certain serine proteinases and P-I SVMPs, and a C type lectin-like protein were only partially immunodepleted, and two PLA2 molecules were not depleted at all. The antivenom was able to neutralize all toxic and enzymatic activities tested, although neutralization of lethality by A. nummifer venom was achieved when a challenge dose of 3 LD50s of venom was used, but was iffective when 4 LD50s were used. These results, and previously obtained evidence on the immunoreactivity of this antivenom towards homologous and heterologous venoms, revealed the low immunogenicity of a number of venom components (PLA2s, CRISPs, P-I SVMPs, and some serine proteinases), underscoring the need to search for innovative immunization protocols to improve the immune response to these antigens. [ABSTRACT FROM AUTHOR]

Abstract: New biomarkers are urgently needed to accelerate efforts in developing new drugs and treatments of known diseases. New clinical and translational proteomics studies emerge almost every day. However, discovery of new diagnostic biomarkers lags behind because of variability at every step in proteomics studies (e.g., assembly of a cohort of patients, sample preparation and the nature of body fluids, selection of a profiling method and uniform protocols for data analysis). Quite often, the validation step that follows the discovery phase does not reach desired levels of sensitivity, specificity or reproducibility between laboratories. Mass spectrometry and gel-based methods do not provide enough throughput for screening thousands of clinical samples. Further development of protein arrays may address this issue. Despite many obstacles, proteomics delivers vast amounts of information useful for understanding the molecular mechanisms underlying diseases. [Copyright &y& Elsevier]

Abstract: Introduction: Increase of serum alanine aminotransferase (ALT) activity is widely used as a surrogate marker for tissue damage. Two ALT isoforms, ALT1 and ALT2, have been cloned recently in mammals. The study investigated the source of elevated ALT activity in serum of dogs treated with a hepatotoxic compound. Methods: ALT activity was measured by enzyme assay. Immunoblot analysis was performed using generated specific peptide antibodies against dog ALTs. LC-MS/MS-based proteomics analysis was conducted to independently identify dog ALT peptides. Serum samples immunodepleted of major serum components by Seppro IgY-D11 microbead spin column were evaluated by the immunoblot analysis, and compared with those of the ALT activity. Results: Involvement of ALT enzyme(s) is consistent with the following observations: 1) all the substrates (l-alanine and α-ketoglutarate) were required for serum ALT activity as purified porcine ALT1 needed for activity, 2) serum ALT activity was inhibited by l-cycloserine, a known ALT inhibitor, and 3) apparent Km value for the ALT reaction catalyzed by the serum, liver, and skeletal muscle was roughly similar. Immunoblot analysis showed that ALT1 was detected in liver and both ALTs were detected in the skeletal muscle. The relative expression level of ALTs was —: liver ALT1>skeletal muscle ALT1>skeletal muscle ALT2. LC-MS/MS-based proteomics analysis gave similar results. Immunoblot analysis of the depleted serum samples revealed the presence of ALT1 in compound-treated dogs. Intensity of the ALT1 band detected in the sera correlated well with the ALT activity measured by the enzyme assay. Discussion: Based on these findings, we conclude that the elevation of serum ALT activity in dogs with liver injury is attributed to elevation of ALT1 protein level in serum. The methodology to directly detect ALT proteins in serum could be a tool to facilitate our understanding of biological and toxicological significance of the ALT isoenzymes. [Copyright &y& Elsevier]

Abstract: In the present study we describe type 1 cystatin, a cysteine protease inhibitor, as a major released antigen of the tropical liver fluke Fasciola gigantica (FgStefin-1). Immunohistochemical analysis showed that FgStefin-1 is abundant in (a) tissue of tegumental type, including oral and ventral sucker, pharynx, genital atrium, metraterm, cirrus and (b) the intestinal epithelium. Faint staining was observed in the epithelia of ovary and proximal uterus. Immunoblots showed the presence of FgStefin-1 in the parasite''s excretion/secretion (ES) product and immunodepletion demonstrated that FgStefin-1 herein is partially complexed with cathepsin L. Furthermore, quantitation of FgStefin-1 in comparison to cathepsin L in ES product and crude worm extract of adults supports a major external function of FgStefin-1 with an estimated 50% being released in at least equimolar amounts to cathepsin L. Sera of an experimentally infected rabbit reacted with recombinant FgStefin-1 starting 8 weeks postinfection. Activity analyses of recombinant FgStefin-1 showed nanomolar inhibition constants for mammalian cathepsin B, L, and S cysteine proteases and released cysteine proteases of the parasite. The protein is active over a wide pH range and is heat stable. Our results suggest protective functions of FgStefin-1, regulating intracellular cysteine protease activity, and possibly protection against extracellular proteolytic damage to the parasite''s intestinal and tegumental surface proteins. Considering inhibition kinetics and previously demonstrated immunomodulatory properties of cystatin in parasitic nematodes a comparable function of FgStefin-1 is suggested and is at present under investigation. [Copyright &y& Elsevier]

Given that proteomic analysis of complex protein mixtures may be restricted by the presence of highly abundant proteins, sample preparation to remove abundant proteins is essential for the analysis of low abundance proteins. Chickens are effective producers of antibodies (IgY) against mammalian proteins, able to produce large quantities of antibodies that can be recovered by simple non-intrusive extraction of egg yolk. The extraction procedure described uses a modification of the water dilution method (WD) to deplete lipids and lipoproteins followed by sequential precipitation with 31% ammonium sulphate and 12% poly ethylene glycol (PEG) producing IgY antibodies with greater than 95% purity and no loss in immunoreactivity. In the present study, various cocktails of the 12 most abundant human plasma proteins were used as immunogens to produce IgY antibodies. The anti-cocktail IgY antibodies were effectively used to sequentially and selectively immunodeplete abundant proteins from plasma. Also, affinity depletion (e.g., Affi-Gel Blue) was combined with immunodepletion to sequentially deplete abundant proteins from both plasma and urine. The current approach described allows the end user to mix and match sets of IgY cocktails to deplete tailored sets of targeted proteins dependent on their end use application. [ABSTRACT FROM AUTHOR]

Abstract: Proteomic analysis can be hampered by the large concentration distribution of proteins. Immunoaffinity techniques have been applied to selectively remove high abundant proteins (HAP''s) from samples prior to analysis. Although immunodepletion of HAP''s has been shown to enable greater detection of low abundance proteins, the resulting fractions are often diluted 5–10-fold during the process. Various concentration techniques can be applied; however, many are incompatible with the high salt content of the fractions. To help overcome this limitation, a two-dimensional liquid chromatography (2D-LC) method was developed which couples an IgY immunodepletion column in the first dimension with a large pore C18 analytical column in the second. A protein trap cartridge serves as an injection loop between the columns to facilitate on-line concentration and desalting. Feasibility of this 2D-LC system was demonstrated for mammalian proteomics. Beyond depletion of interfering proteins, this instrumentation provides four advantages which make immunodepletion technology more convenient, including: (1) on-line desalting (2) automatic buffer exchange (3) facile concentration and (4) fractionation by polarity. [Copyright &y& Elsevier]

Abstract: Proteomic analysis of plasma is challenging because of its large dynamic range, which prevents the detection of low abundance proteins. Immunodepletion of high abundance proteins, such as albumin and IgG, has emerged as a favored technology to overcome this problem; however its suitability in quantitative expression proteomics has not yet been adequately addressed. In this study, albumin and IgG immunodepletion was evaluated by ELISAs and the reproducibility of depletion was tested with 2-DGE. Depletion of plasma resulted in removal of 62±1.2% of the total protein, 93±1.4% of the albumin (0.43μg/μL, residual), and 94±1.5% of the IgG (0.21μg/μL, residual). These results were confirmed by immunoblotting. Computerized image analysis of 2-D gels using Progenesis SameSpots software revealed an enhancement in the number of visible spots (675–1325), with 10±6% inter-gel variability in spot density. LC–ESI-MS/MS identification of newly resolved protein spots further validated the procedure. An innovative application of the software employed led to identification of 11 proteins lost non-specifically during depletion. This study demonstrates the effectiveness of immunodepletion of albumin and IgG in quantitative 2-DGE-based differential analysis of plasma proteins. [Copyright &y& Elsevier]

Abstract: Natural killer (NK) cells contribute to the initial nonspecific response to viral infection, and viruses exhibit a range of sensitivities to NK cells in vivo. We investigated the role of NK cells in infection of mice by mouse adenovirus type 1 (MAV-1) using antibody-mediated depletion and knockout mice. MAV-1 causes encephalomyelitis and replicates to highest levels in brains. NK cell-depleted mice infected with MAV-1 showed brain viral loads 8–20 days p.i. that were similar to wild-type control non-depleted mice. Mice genetically deficient for NK cells behaved similarly to wild-type control mice with respect to brain viral loads and survival. We conclude that NK cells are not required to control virus replication in the brains of MAV-1-infected mice. [Copyright &y& Elsevier]

Background Chronic venous leg ulcers are a significant cause of pain, immobility and decreased quality of life for patients with these wounds. In view of this, research efforts are focused on multiple factors in the wound environment to obtain information regarding the healing of ulcers. Objectives Chronic wound fluid (CWF), containing a complex mixture of proteins, is an important modulator of the wound environment, and therefore we hypothesized that these proteins may be indicators of the status of wounds and their potential to heal or otherwise. To explore this we developed and validated a proteomic approach to analyse CWF. Methods In this study, pooled CWF was depleted of high abundant proteins using immunoaffinity chromatography. The flow-through and bound fractions were collected, concentrated, desalted and analysed using a range of techniques. Each fraction was further separated using two-dimensional (2D) gel electrophoresis and 2D liquid chromatography and analysed using mass spectrometry (MS). Results Western blot analysis against three high abundant proteins confirmed the selective removal of these proteins from CWF. Critically, one-dimensional and 2D gel electrophoresis indicated that subsequent removal of these proteins enhanced the ability to detect proteins in low abundance in CWF. Further, MS demonstrated that depletion of these abundant proteins increased the detection of other proteins in these samples. Conclusions Results obtained indicate that this approach significantly improves separation of proteins present in low concentrations in CWF. This will facilitate the identification of biomarkers in samples collected from patients with ulcers and lead to improved patient therapies and wound care approaches. [ABSTRACT FROM AUTHOR]

Abstract: In plants, ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO) is an important enzyme in the Calvin cycle, catalyzing the first step of carbon fixation. Because of its critical role in photosynthesis, RuBisCO comprises 30–60% of the total protein content in green leaf tissue and represents a major protein which can interfere with determination of lower abundance proteins in plant proteomics. A potential solution to aid in the determination of low level proteins in plant proteomics are RuBisCO immunodepletion columns. Two formats, spin and LC, of Seppro™ IgY RuBisCO depletion columns were evaluated for cross species applicability. The spin and LC columns were found to deplete arabidopsis RuBisCO by greater than 90 and 98%, respectively, and automation could be achieved with the LC format. Canola RuBisCO was depleted to a similar extent, and there was evidence suggesting that corn and tobacco RuBisCO were also highly depleted in flow through fractions. Model proteins were spiked into samples to provide insight into the degree of non-specific binding. Finally, improved detection and identification of lower abundance proteins was demonstrated after depletion. [Copyright &y& Elsevier]

Abstract: Background: The true therapeutic benefit of the use of natural products, especially acceptable dietary components such as curcumin, which can spare the normal cells and boost host immunity, has opened new horizons in cancer prevention and treatment. Methods: In our model system we used Ehrlich''s ascites carcinoma cells grown in peritoneal carity of Swiss albino mice and curcumin was fed every alternative day. Results: Here, we report that curcumin administration to tumor-bearing mice decreased tumor cell number significantly in a dose-dependent manner. Furthermore, tumor-induced depletion of immune cell number of the host, as was evidenced from the decrease in bone marrow progenitor as well as thymic and splenic mononuclear cell numbers, was reintrated by curcumin. In fact, curcumin inhibited tumor-induced apoptosis of both thymocytes and splenocytes thereby restoring immune cell numbers to normal level in treated Ehrlich''s ascites carcinoma-bearing mice. Moreover, curcumin was not toxic to the host; rather in tumor-bearing mice it inhibited hematopoietic toxicity, acted as a hepatoprotective agent and activated depressed anti-oxidant and detoxification systems. Conclusion: The ability of curcumin to regress tumor as well as to protect the host from tumor-induced immunosuppression and toxicity strongly supports the candidacy of curcumin as a potential agent for the dietary therapy of cancer. [Copyright &y& Elsevier]

The activity of the N-methyl-D-aspartate (NMDA) receptor, a subclass of ionotropic glutamate receptor, is modulated by a complex network of phosphorylation and dephosphorylation. I investigated the relative extent of tyrosine phosphorylation of NMDA receptor subunit 2A (NR2A) and 2B (NR2B) subunits in the rat forebrain postsynaptic density (PSD) fraction. Immunoblot analysis of immunoprecipitates with anti-phosphotyrosine antibodies indicated that tyrosine phosphorylation of NR2A was only 28.6% of that of NR2B. When phosphotyrosine-containing peptides were isolated by affinity-purification or immunoprecipitation, and probed for the two subunits. NR2B was detected but not NR2A. Furthermore, depletion of NR2B removed the phosphotyrosine-containing 180 kDa peptide from the solution while the converse was not true. The small extent of tyrosine phosphorylation of NR2A in the unstimulated condition may explain the dramatic increase in tyrosine phosphorylation in various physiological and pathological conditions. [ABSTRACT FROM AUTHOR]

subgroup of AAPS NBC Immunogenicity Workshop attendees met to discuss the current recommendations in white papers and guidance documents, to describe and discuss current practices, and to resolve concerns as to the biologically and statistically appropriate approaches to determining a confirmatory cut point for immunogenicity assays. This is a summary of our discussions and recommendations. [ABSTRACT FROM AUTHOR]

In the present study, we evaluated four small molecule affinity-based probes based on agarose-immobilized benzamidine (ABA), O-Phospho-L-Tyrosine (pTYR), 8-Amino-hexyl-cAMP (cAMP), or 8-Amino-hexyl-ATP (ATP) for their ability to remove high-abundant proteins such as serum albumin from plasma samples thereby enabling the detection of medium-to-low abundant proteins in plasma samples by mass spectrometry-based proteomics. We compared their performance with the most commonly used immunodepletion method, the Multi Affinity Removal System Human 14 (MARS14) targeting the top 14 most abundant plasma proteins and also the ProteoMiner protein equalization method by label-free quantitative liquid chromatography tandem mass spectrometry (LC-MSMS) analysis. The affinity-based probes demonstrated a high reproducibility for low-abundant plasma proteins, down to picomol per mL levels, compared to the Multi Affinity Removal System (MARS) 14 and the Proteominer methods, and also demonstrated superior removal of the majority of the high-abundant plasma proteins. The ABA-based affinity probe and the Proteominer protein equalization method performed better compared to all other methods in terms of the number of analyzed proteins. All the tested methods were highly reproducible for both high-abundant plasma proteins and low-abundant proteins as measured by correlation analyses of six replicate experiments. In conclusion, our results demonstrated that small-molecule based affinity-based probes are excellent alternatives to the commonly used immune-depletion methods for proteomic biomarker discovery studies in plasma. Data are available via ProteomeXchange with identifier PXD020727. [ABSTRACT FROM AUTHOR]