Nitration of H2B histone elicits an immune response in experimental animals

Oxidative stress and central metabolism pathways impact epigenetic modulation in inflammation and immune response

Oxidative stress, metabolism, and epigenetics are deeply interconnected processes that collectively influence cellular function, health status, and contribute to disease progression. This review highlights the critical role of metabolic intermediates in epigenetic regulation, focusing on lactate, glutathione (GSH), and S-adenosylmethionine (SAM). Beyond its traditional role in energy metabolism, lactate modulates epigenetic mechanisms, influencing gene expression and cellular adaptation. Meanwhile, GSH and SAM serve as key regulators of DNA methylation and histone post-translational modifications, maintaining epigenetic homeostasis. These processes are tightly controlled by redox balance and oxidative stress, underscoring the intricate interplay between metabolism and epigenetic regulation. GSH depletion disrupts methylation homeostasis, while oxidative post-translational modifications (oxPTMs) on histones-including S-glutathionylation, carbonylation, and nitrosylation-alter chromatin architecture and transcriptional regulation. Additionally, we focus on histone lactylation, particularly its role in regulating innate and adaptive immune responses. We also explore how GSH and oxidative stress influence lactate levels, potentially inducing histone lactylation or S-glutathionylation through S,D-lactoylglutathione (LGSH), thereby impacting epigenetic regulation. By integrating insights into metabolic-epigenetic crosstalk, this review underscores the role of oxidative stress and central metabolic pathways in regulating epigenetic mechanisms, a concept known as "redox epigenetics." Understanding these intricate interactions offers new perspectives for therapeutic strategies aimed at restoring redox homeostasis and metabolic integrity to counteract disturbances in the epigenetic landscape.

Significance of co-positivity for anti-dsDNA, -nucleosome, and -histone antibodies in patients with lupus nephritis

OBJECTIVE

The aim of this study was to define the clinical, histopathologic, and prognostic features associated with simultaneous positivity for anti-dsDNA, -nucleosome, and -histone antibodies (3-pos) in Korean patients with biopsy-proven lupus nephritis (LN).

METHODS

The 102 patients included in the study had undergone kidney biopsy prior to the start of induction treatment, were treated with immunosuppressives, and followed-up for >12 months.

RESULTS

In total, 44 (43.1%) of the 102 LN patients were 3-pos. Patients with 3-pos had a higher SLEDAI-2K score (p = .002), lower lymphocyte count (p = .004), and higher rates of proteinuria > 3.5 g/24 h (p = .039) and positivity for urinary sediments (p = .005) at the time of renal biopsy than non-3-pos patients. 3-pos patients had a more proliferative form of LN (p = .045) in the renal histopathologic findings, and as co-positivity gradually increased from 0 to 3, the total activity score in the renal biopsy findings increased significantly (p = .033). In addition, 3-pos patients had a more rapid eGFR decline than non-3-pos patients after a follow-up of 83.2 months (p = .016).

CONCLUSIONS

Our findings suggest that 3-pos is related to severe LN and that 3-pos patients are more likely to experience a rapid decline of renal function than non-3-pos patients.KEY MESSAGEPatients with co-positivity for anti-dsDNA, -nucleosome, and -histone antibodies (3-pos) had higher disease activity and a worse renal histopathology than those without co-positivity.3-pos patients had a more rapid decline of renal function than non-3-pos patients.

Post-translational modifications of histone and non-histone proteins in epigenetic regulation and translational applications in alcohol-associated liver disease: Challenges and research opportunities

Epigenetic regulation is a process that takes place through adaptive cellular pathways influenced by environmental factors and metabolic changes to modulate gene activity with heritable phenotypic variations without altering the DNA sequences of many target genes. Epigenetic regulation can be facilitated by diverse mechanisms: many different types of post-translational modifications (PTMs) of histone and non-histone nuclear proteins, DNA methylation, altered levels of noncoding RNAs, incorporation of histone variants, nucleosomal positioning, chromatin remodeling, etc. These factors modulate chromatin structure and stability with or without the involvement of metabolic products, depending on the cellular context of target cells or environmental stimuli, such as intake of alcohol (ethanol) or Western-style high-fat diets. Alterations of epigenetics have been actively studied, since they are frequently associated with multiple disease states. Consequently, explorations of epigenetic regulation have recently shed light on the pathogenesis and progression of alcohol-associated disorders. In this review, we highlight the roles of various types of PTMs, including less-characterized modifications of nuclear histone and non-histone proteins, in the epigenetic regulation of alcohol-associated liver disease (ALD) and other disorders. We also describe challenges in characterizing specific PTMs and suggest future opportunities for basic and translational research to prevent or treat ALD and many other disease states.

Fast and biphasic 8-nitroguanine production from guanine and peroxynitrite

Guanine (Gua), among purines, is a preferred oxidation/nitration target because of its low one-electron redox potential. The reactive oxygen/nitrogen species peroxynitrite (ONOO^-), produced in vivo by the reaction between nitric oxide (^•NO) and superoxide radical (O₂^•‒), is responsible for several oxidative modifications in biomolecules, including nitration, nitrosation, oxidation, and peroxidation. In particular, the nitration of Gua, although detected, as well as its reaction kinetics have been seldom investigated. Thus, we studied the concentration- and temperature-dependent formation of 8-nitroguanine (8-NitroGua) in phosphate buffer (pH 7.40) using stopped-flow spectrophotometry. Traces showed a biexponential behavior, with best-fit rate constants: k_fast = 4.4 s^-1 and k_slow = 0.41 s^-1 (30 °C, 400 μM both Gua and ONOO^-). k_fast increased linearly with the concentration of both reactants whereas k_slow was concentration-independent. Linear regression analysis of k_fast as a function of Gua and ONOO^- concentration yielded values of 2.5-6.3 × 10³ M^-1s^-1 and 1.5-3.5 s^-1 for the second-order (slope) and first-order (ordinate) rate constants, respectively (30 °C). Since ONOO^- is a short-lived species, its decay kinetics was also taken into account for this analysis. The 8-NitroGua product was stable for at least 4 h, so no spontaneous denitration was observed. Stopped-flow assays using antioxidants and free-radical scavengers suggested a mixed direct/indirect reaction mechanism for 8-NitroGua formation. Gua nitration by ONOO^- was also observed in the presence of physiologically relevant CO₂ concentrations. The reaction product identity, its yield (∼4.2%, with 400 μM ONOO^- and 200 μM Gua), and the reaction mechanism were unequivocally determined by HPLC-MS/MS experiments. In conclusion, 8-NitroGua production at physiologic pH reached significant levels in a few hundred milliseconds, suggesting that the process might be kinetically relevant in vivo and can likely cause permanent nitrative damage to DNA bases.

Clinical use of anti-histone antibodies in idiopathic and drug-induced lupus

Anti-histone antibodies (AHAs) make their appearance in a number of systemic autoimmune diseases including systemic lupus erythematosus (SLE) and drug-induced lupus erythematosus (DILE). Although being known for over 50 years, they are poorly studied and understood. There is emerging evidence for their use in predicting clinical features of SLE, diversifying their clinical use. AHAs, however, are probably less prevalent in DILE than once thought owing to a move away from older DILE drugs to modern biological agents which do not appear to elicit AHAs. This review examines the historical studies that have defined AHAs and looks at some of the recent work with these autoantibodies.

Creating a Selective Nanobody Against 3-Nitrotyrosine Containing Proteins

A critical step in developing therapeutics for oxidative stress-related pathologies is the ability to determine which specific modified protein species are innocuous by-products of pathology and which are causative agents. To achieve this goal, technologies are needed that can identify, characterize and quantify oxidative post translational modifications (oxPTMs). Nanobodies (Nbs) represent exquisite tools for intracellular tracking of molecules due to their small size, stability and engineerability. Here, we demonstrate that it is possible to develop a selective Nb against an oxPTM protein, with the key advance being the use of genetic code expansion (GCE) to provide an efficient source of the large quantities of high-quality, homogenous and site-specific oxPTM-containing protein needed for the Nb selection process. In this proof-of-concept study, we produce a Nb selective for a 3-nitrotyrosine (nitroTyr) modified form of the 14-3-3 signaling protein with a lesser recognition of nitroTyr in other protein contexts. This advance opens the door to the GCE-facilitated development of other anti-PTM Nbs.

Pillars and Gaps of S-Nitrosylation-Dependent Epigenetic Regulation in Physiology and Cancer

Nitric oxide (NO) is a diffusible signaling molecule produced by three isoforms of nitric oxide synthase, which release NO during the metabolism of the amino acid arginine. NO participates in pathophysiological responses of many different tissues, inducing concentration-dependent effect. Indeed, while low NO levels generally have protective effects, higher NO concentrations induce cytotoxic/cytostatic actions. In recent years, evidences have been accumulated unveiling S-nitrosylation as a major NO-dependent post-translational mechanism ruling gene expression. S-nitrosylation is a reversible, highly regulated phenomenon in which NO reacts with one or few specific cysteine residues of target proteins generating S-nitrosothiols. By inducing this chemical modification, NO might exert epigenetic regulation through direct effects on both DNA and histones as well as through indirect actions affecting the functions of transcription factors and transcriptional co-regulators. In this light, S-nitrosylation may also impact on cancer cell gene expression programs. Indeed, it affects different cell pathways and functions ranging from the impairment of DNA damage repair to the modulation of the activity of signal transduction molecules, oncogenes, tumor suppressors, and chromatin remodelers. Nitrosylation is therefore a versatile tool by which NO might control gene expression programs in health and disease.

Oxidative stress-mediated alterations in histone post-translational modifications

Epigenetic regulation of gene expression provides a finely tuned response capacity for cells when undergoing environmental changes. However, in the context of human physiology or disease, any cellular imbalance that modulates homeostasis has the potential to trigger molecular changes that result either in physiological adaptation to a new situation or pathological conditions. These effects are partly due to alterations in the functionality of epigenetic regulators, which cause long-term and often heritable changes in cell lineages. As such, free radicals resulting from unbalanced/extended oxidative stress have been proved to act as modulators of epigenetic agents, resulting in alterations of the epigenetic landscape. In the present review we will focus on the particular effect that oxidative stress and free radicals produce in histone post-translational modifications that contribute to altering the histone code and, consequently, gene expression. The pathological consequences of the changes in this epigenetic layer of regulation of gene expression are thoroughly evidenced by data gathered in many physiological adaptive processes and in human diseases that range from age-related neurodegenerative pathologies to cancer, and that include respiratory syndromes, infertility, and systemic inflammatory conditions like sepsis.

A chemical field guide to histone nonenzymatic modifications

Histone nonenzymatic covalent modifications (NECMs) have recently emerged as an understudied class of posttranslational modifications that regulate chromatin structure and function. These NECMs alter the surface topology of histone proteins, their interactions with DNA and chromatin regulators, as well as compete for modification sites with enzymatic posttranslational modifications. NECM formation depends on the chemical compatibility between a reactive molecule and its target site, in addition to their relative stoichiometries. Here we survey the chemical reactions and conditions that govern the addition of NECMs onto histones as a manual to guide the identification of new physiologically relevant chemical adducts. Characterizing NECMs on chromatin is critical to attain a comprehensive understanding of this new chapter of the so-called "histone code".

Oxidative post-translational modifications in histones

Epigenetic regulation is attracting much attention because it explains many of the effects that the external environment induces in organisms. Changes in the cellular redox status and even more specifically in its nuclear redox compartment is one of these examples. Redox changes can induce modulation of the epigenetic regulation in cells. Here we present a few cases where reactive oxygen or nitrogen species induces epigenetic marks in histones. Posttranslational modification of these proteins like histone nitrosylation, carbonylation, or glutathionylation together with other mechanisms not reviewed here are the cornerstones of redox-related epigenetic regulation. We currently face a new field of research with potential important consequences for the treatment of many pathologies.