Protein tyrosine nitration of aldolase in mast cells: a plausible pathway in nitric oxide-mediated regulation of mast cell function

Cellular Energetics of Mast Cell Development and Activation

Mast cells are essential first responder granulocytes in the innate immune system that are well known for their role in type 1 immune hypersensitivity reactions. Although mostly recognized for their role in allergies, mast cells have a range of influences on other systems throughout the body and can respond to a wide range of agonists to properly prime an appropriate immune response. Mast cells have a dynamic energy metabolism to allow rapid responsiveness to their energetic demands. However, our understanding of mast cell metabolism and its impact on mast cell activation and development is still in its infancy. Mast cell metabolism during stimulation and development shifts between both arms of metabolism: catabolic metabolism-such as glycolysis and oxidative phosphorylation-and anabolic metabolism-such as the pentose phosphate pathway. The potential for metabolic pathway shifts to precede and perhaps even control activation and differentiation provides an exciting opportunity to explore energy metabolism for clues in deciphering mast cell function. In this review, we discuss literature pertaining to metabolic environments and fluctuations during different sources of activation, especially IgE mediated vs. non-IgE mediated, and mast cell development, including progenitor cell types leading to the well-known resident mast cell.

On the Liquid Chemistry of the Reactive Nitrogen Species Peroxynitrite and Nitrogen Dioxide Generated by Physical Plasmas

Cold physical plasmas modulate cellular redox signaling processes, leading to the evolution of a number of clinical applications in recent years. They are a source of small reactive species, including reactive nitrogen species (RNS). Wound healing is a major application and, as its physiology involves RNS signaling, a correlation between clinical effectiveness and the activity of plasma-derived RNS seems evident. To investigate the type and reactivity of plasma-derived RNS in aqueous systems, a model with tyrosine as a tracer was utilized. By high-resolution mass spectrometry, 26 different tyrosine derivatives including the physiologic nitrotyrosine were identified. The product pattern was distinctive in terms of plasma parameters, especially gas phase composition. By scavenger experiments and isotopic labelling, gaseous nitric dioxide radicals and liquid phase peroxynitrite ions were determined as dominant RNS. The presence of water molecules in the active plasma favored the generation of peroxynitrite. A pilot study, identifying RNS driven post-translational modifications of proteins in healing human wounds after the treatment with cold plasma (kINPen), demonstrated the presence of in vitro determined chemical pathways. The plasma-driven nitration and nitrosylation of tyrosine allows the conclusion that covalent modification of biomolecules by RNS contributes to the clinically observed impact of cold plasmas.

Nonenzymatic post-translational modifications in peptides by cold plasma-derived reactive oxygen and nitrogen species

Cold physical plasmas are emerging tools for wound care and cancer control that deliver reactive oxygen species (ROS) and nitrogen species (RNS). Alongside direct effects on cellular signaling processes, covalent modification of biomolecules may contribute to the observed physiological consequences. The potential of ROS/RNS generated by two different plasma sources (kINPen and COST-Jet) to introduce post-translational modifications (PTMs) in the peptides angiotensin and bradykinin was explored. While the peptide backbone was kept intact, a significant introduction of oxidative PTMs was observed. The modifications cluster at aromatic (tyrosine, histidine, and phenylalanine) and neutral amino acids (isoleucine and proline) with the introduction of one, two, or three oxygen atoms, ring cleavages of histidine and tryptophan, and nitration/nitrosylation predominantly observed. Alkaline and acidic amino acid (arginine and aspartic acid) residues showed a high resilience, indicating that local charges and the chemical environment at large modulate the attack of the electron-rich ROS/RNS. Previously published simulations, which include only OH radicals as ROS, do not match the experimental results in full, suggesting the contribution of other short-lived species, i.e., atomic oxygen, singlet oxygen, and peroxynitrite. The observed PTMs are relevant for the biological activity of peptides and proteins, changing polarity, folding, and function. In conclusion, it can be assumed that an introduction of covalent oxidative modifications at the amino acid chain level occurs during a plasma treatment. The introduced changes, in part, mimic naturally occurring patterns that can be interpreted by the cell, and subsequently, these PTMs allow for prolonged secondary effects on cell physiology.

Immune Cell Metabolism in Tumor Microenvironment

Tumor microenvironment (TME) is composed of tumor cells, immune cells, cytokines, extracellular matrix, etc. The immune system and the metabolisms of glucose, lipids, amino acids, and nucleotides are integrated in the tumorigenesis and development. Cancer cells and immune cells show metabolic reprogramming in the TME, which intimately links immune cell functions and edits tumor immunology. Recent findings in immune cell metabolism hold the promising possibilities toward clinical therapeutics for treating cancer. This chapter introduces the updated understandings of metabolic reprogramming of immune cells in the TME and suggests new directions in manipulation of immune responses for cancer diagnosis and therapy.

Neural Stem Cell Death Mechanisms Induced by Amyloid Beta

Background and Purpose

Amyloid beta (Aβ) is the main component of amyloid plaques, which are deposited in the brains of patients with Alzheimer's disease (AD). Biochemical and animal studies support the central role of Aβ in AD pathogenesis. Despite several investigations focused on the pathogenic mechanisms of Aβ, it is still unclear how Aβ accumulates in the central nervous system and subsequently initiates the disease at the cellular level. In this study, we investigated the pathogenic mechanisms of Aβ using proteomics and antibody microarrays.

Methods

To evaluate the effect of Aβ on neural stem cells (NSCs), we treated primary cultured cortical NSCs with several doses of Aβ for 48 h. A 3-[4,5-dimethylthiazol-2-yl]-2,5-diphenyltetrazolium bromide assay, trypan blue staining, and bromodeoxyuridine cell proliferation assay were performed. We detected several intracellular proteins that may be associated with Aβ by proteomics and Western blotting analysis.

Results

Various viability tests showed that Aβ decreased NSCs viability and cell proliferation in a concentration-dependent manner. Aβ treatment significantly decreased lactate dehydrogenase B, high-mobility group box 1, aldolase C, Ezrin, and survival signals including phosphorylated phosphoinositide 3-kinase, Akt, and glycogen synthase kinase-3β.

Conclusions

These results suggest that several factors determined by proteomics and Western blot hold the clue to Aβ pathogenesis. Further studies are required to investigate the role of these factors.

Mass spectrometry analysis of nitrotyrosine-containing proteins

Oxidative stress plays important roles in a wide range of diseases such as cancer, inflammatory disease, neurodegenerative disorders, etc. Tyrosine nitration in a protein is a chemically stable oxidative modification, and a marker of oxidative injuries. Mass spectrometry (MS) is a key technique to identify nitrotyrosine-containing proteins and nitrotyrosine sites in endogenous and synthetic nitroproteins and nitropeptides. However, in vivo nitrotyrosine-containing proteins occur with extreme low-abundance to severely challenge the use of MS to identify in vivo nitroproteins and nitrotyrosine sites. A preferential enrichment of nitroproteins and/or nitropeptides is necessary before MS analysis. Current enrichment methods include immuno-affinity techniques, chemical derivation of the nitro group plus target isolations, followed with tandem mass spectrometry analysis. This article reviews the MS techniques and pertinent before-MS enrichment techniques for the identification of nitrotyrosine-containing proteins. This article reviews future trends in the field of nitroproteomics, including quantitative nitroproteomics, systems biological networks of nitroproteins, and structural biology study of tyrosine nitration to completely clarify the biological functions of tyrosine nitration.

Cancer cell metabolism and the modulating effects of nitric oxide

Altered metabolic phenotype has been recognized as a hallmark of tumor cells for many years, but this aspect of the cancer phenotype has come into greater focus in recent years. NOS2 (inducible nitric oxide synthase of iNOS) has been implicated as a component in many aggressive tumor phenotypes, including melanoma, glioblastoma, and breast cancer. Nitric oxide has been well established as a modulator of cellular bioenergetics pathways, in many ways similar to the alteration of cellular metabolism observed in aggressive tumors. In this review we attempt to bring these concepts together with the general hypothesis that one function of NOS2 and NO in cancer is to modulate metabolic processes to facilitate increased tumor aggression. There are many mechanisms by which NO can modulate tumor metabolism, including direct inhibition of respiration, alterations in mitochondrial mass, oxidative inhibition of bioenergetic enzymes, and the stimulation of secondary signaling pathways. Here we review metabolic alterations in the context of cancer cells and discuss the role of NO as a potential mediator of these changes.

Expression of DP2 (CRTh2), a prostaglandin D₂ receptor, in human mast cells

PGD₂ has long been implicated in allergic diseases. Recent cloning of a second PGD₂ receptor, DP2 (also known as CRTh2), led to a greater understanding of the physiological and pathophysiological implications of PGD₂. PGD₂ signaling through DP1 and DP2 mediates different and often opposite effects in many cell types of the immune system. Although mast cells (MC) are the largest source of PGD₂ in the body, there is little information about their potential expression of DP2 and its functional significance. In this study, we show that tissue MC in human nasal polyps express DP2 protein, and that human MC lines and primary cultured human MC express mRNA as well as protein of DP2. By immunohistochemistry, we detected that 34% of MC in human nasal polyps expressed DP2. In addition, flow cytometry showed that 87% of the LAD2 human MC line and 98% of primary cultured human MC contained intracellular DP2. However, we could not detect surface expression of DP2 on human MC by single cell analysis using imaging flow cytometry. Blocking of endogenous PGD2 production with aspirin did not induce surface expression of DP2 in human MC. Two DP2 selective agonists, DK-PGD₂ and 15R-15-methyl PGD₂ induced dose-dependent intracellular calcium mobilization that was abrogated by pertussis toxin, but not by three DP2 selective antagonists. MC mediator release including degranulation was not affected by DP2 selective agonists. Thus, human MC express DP2 intracellularly rather than on their surface, and the function of DP2 in human MC is different than in other immune cells such as Th2 cells, eosinophils and basophils where it is expressed on the cell surface and induces Th2 cytokine and/or granule associated mediator release. Further studies to elucidate the role of intracellular DP2 in human MC may expand our understanding of this molecule and provide novel therapeutic opportunities.

Limited replication of influenza A virus in human mast cells

Mast cells are important in innate immunity and protective against certain bacterial infections. However, there is limited evidence that mast cells respond to viruses. As mast cells are abundant in mucosal tissues of the lung, they are in a prime location to detect and respond to influenza virus. In this study, we characterized for the first time the replication cycle of influenza A virus in human mast cells by measuring influenza A virus transcription, RNA replication, protein synthesis, and formation of infectious virus as compared to the replication cycle in epithelial cells. We detected the presence of influenza A viral genomic RNA transcription, replication, and protein synthesis in human mast cells and epithelial cells. However, there was no significant release of infectious influenza A virus from mast cells, whereas epithelial cells produce ~100-fold virus compared with the inoculating dose. We confirmed that influenza A virus infects human mast cells, begins to replicate, but the production of new virus is aborted. Thus, mast cells may lack critical factors essential for productive infection or there are intrinsic or inducible anti-influenza A mechanisms in mast cells.

Computational study of the effects of protein tyrosine nitrations on the catalytic activity of human thymidylate synthase

Tyrosine nitration is a widespread post-translational modification capable of affecting both the function and structure of the host protein molecule. Enzyme thymidylate synthase (TS), a homodimer, is a molecular target for anticancer therapy. Recently purified TS preparations, isolated from mammalian tissues, were found to be nitrated, suggesting this modification to appear endogenously in normal and tumor tissues. Moreover, human TS (hTS) nitration in vitro led to a by twofold lowered catalytic activity following nitration in average of 1 tyrosine residue per monomer (Dąbrowska-Maś et al. in Org Biomol Chem 10:323-331, 2012), with the modification identified by mass spectrometry at seven different sites (Y33, Y65, Y135, Y213, Y230, Y258 and Y301). In the present paper, combined computational approach, including molecular and essential dynamics and free energy computations, was used to predict the influence on the activity of hTS of nitration of each of the seven tyrosine residues. The simulations were based on the crystal structure of hTS ternary complex with dUMP and Tomudex (PDB code: 1I00), with the Tomudex molecule replaced by the molecule of TS cofactor analogue, tetrahydrofolate. The present results indicate that while with nitration of five out of seven residues (Y33, Y135, Y230, Y258 and Y301), single residue modification appears to have a strong reducing effect on the activity, with the remaining two, Y65 and Y213, no or a weaker influence is apparent. Taken together, these results demonstrate that tyrosine nitrations in the hTS enzyme show clear tendency to influence the structure and dynamics and, in turn, catalytic properties of the host enzyme. These effects are overall distance-dependent.

Protein tyrosine nitration of 15-hydroxy prostaglandin dehydrogenase in the human mast cell line LAD2

Mast cells (MC) play a pivotal role in allergic inflammation and nitric oxide (NO) is known to regulate MC function. One mechanism of NO mediated actions is the post-translational modification protein tyrosine nitration mediated by reactive nitrogen species. In this study we identified targets for nitration in the human mast cell line LAD2 after treatment with a nitric oxide donor and with peroxynitrite. Using two dimensional gel electrophoresis and western blot analyses with monoclonal and polyclonal antibodies we identified 15-hydroxy prostaglandin dehydrogenase (PGDH), a major prostaglandin catabolizing enzyme, as a target for nitration in LAD2. This is the first report on expression of this enzyme in MC and also the first report that PGDH is a target of protein tyrosine nitration. Since MC synthesize and metabolize many prostaglandins including prostaglandin E(2), the major substrate for PGDH, nitration of this prostaglandin catabolizing enzyme is likely functionally significant.

Peroxynitrite formation and function in plants

Peroxynitrite (ONOO(-)) is a reactive nitrogen species formed when nitric oxide (NO) reacts with the superoxide anion (O(2)(-)). It was first identified as a mediator of cell death in animals but was later shown to act as a positive regulator of cell signaling, mainly through the posttranslational modification of proteins by tyrosine nitration. In plants, peroxynitrite is not involved in NO-mediated cell death and its physiological function is poorly understood. However, it is emerging as a potential signaling molecule during the induction of defense responses against pathogens and this could be mediated by the selective nitration of tyrosine residues in a small number of proteins. In this review we discuss the general role of tyrosine nitration in plants and evaluate recent evidence suggesting that peroxynitrite is an effector of NO-mediated signaling following pathogen infection.

GPS-YNO2: computational prediction of tyrosine nitration sites in proteins

The last decade has witnessed rapid progress in the identification of protein tyrosine nitration (PTN), which is an essential and ubiquitous post-translational modification (PTM) that plays a variety of important roles in both physiological and pathological processes, such as the immune response, cell death, aging and neurodegeneration. Identification of site-specific nitrated substrates is fundamental for understanding the molecular mechanisms and biological functions of PTN. In contrast with labor-intensive and time-consuming experimental approaches, here we report the development of the novel software package GPS-YNO2 to predict PTN sites. The software demonstrated a promising accuracy of 76.51%, a sensitivity of 50.09% and a specificity of 80.18% from the leave-one-out validation. As an example application, we predicted potential PTN sites for hundreds of nitrated substrates which had been experimentally detected in small-scale or large-scale studies, even though the actual nitration sites had still not been determined. Through a statistical functional comparison with the nitric oxide (NO) dependent reversible modification of S-nitrosylation, we observed that PTN prefers to attack certain fundamental biological processes and functions. These prediction and analysis results might be helpful for further experimental investigation. Finally, the online service and local packages of GPS-YNO2 1.0 were implemented in JAVA and freely available at: .