Impact of inhibition of the autophagy-lysosomal pathway on biomolecules carbonylation and proteome regulation in rat cardiac cells

Autophagy mediates an amplification loop during ferroptosis

Ferroptosis, a programmed cell death, has been identified and associated with cancer and various other diseases. Ferroptosis is defined as a reactive oxygen species (ROS)-dependent cell death related to iron accumulation and lipid peroxidation, which is different from apoptosis, necrosis, autophagy, and other forms of cell death. However, accumulating evidence has revealed a link between autophagy and ferroptosis at the molecular level and has suggested that autophagy is involved in regulating the accumulation of iron-dependent lipid peroxidation and ROS during ferroptosis. Understanding the roles and pathophysiological processes of autophagy during ferroptosis may provide effective strategies for the treatment of ferroptosis-related diseases. In this review, we summarize the current knowledge regarding the regulatory mechanisms underlying ferroptosis, including iron and lipid metabolism, and its association with the autophagy pathway. In addition, we discuss the contribution of autophagy to ferroptosis and elucidate the role of autophagy as a ferroptosis enhancer during ROS-dependent ferroptosis.

Analytical Toolbox to Unlock the Diversity of Oxidized Lipids

ConspectusLipids are diverse class of small biomolecules represented by a large variety of chemical structures. In addition to the classical biosynthetic routes, lipids can undergo numerous modifications via introduction of small chemical moieties forming hydroxyl, phospho, and nitro derivatives, among others. Such modifications change the physicochemical properties of a parent lipid and usually result in new functionalities either by mediating signaling events or by changing the biophysical properties of lipid membranes. Over the last decades, a large body of evidence indicated the involvement of lipid modifications in a variety of physiological and pathological events. For instance, lipid (per)oxidation for a long time was considered as a hallmark of oxidative stress and related proinflammatory signaling. Recently, however, with the burst in the development of the redox biology field, oxidative modifications of lipids are also recognized as a part of regulatory and adaptive events that are highly specific for particular cell types, tissues, and conditions.The initial diversity of lipid species and the variety of possible lipid modifications result in an extremely large chemical space of the epilipidome, the subset of the natural lipidome formed by enzymatic and non-enzymatic lipid modifications occurring in biological systems. Together with their low natural abundance, structural annotation of modified lipids represents a major analytical challenge limiting the discovery of their natural variety and functions. Furthermore, the number of available chemically characterized standards representing various modified lipid species remains limited, making analytical and functional studies very challenging. Over the past decade we have developed and implemented numerous analytical methods to study lipid modifications and applied them in the context of different biological conditions. In this Account, we outline the development and evolution of modern mass-spectrometry-based techniques for the structural elucidation of modified/oxidized lipids and corresponding applications. Research of our group is mostly focused on redox biology, and thus, our primary interest was always the analysis of lipid modifications introduced by redox disbalance, including lipid peroxidation (LPO), oxygenation, nitration, and glycation. To this end, we developed an array of analytical solutions to measure carbonyls derived from LPO, oxidized and nitrated fatty acid derivatives, and oxidized and glycated complex lipids. We will briefly describe the main analytical challenges along with corresponding solutions developed by our group toward deciphering the complexity of natural epilipdomes, starting from in vitro-oxidized lipid mixtures, artificial membranes, and lipid droplets, to illustrate the diversity of lipid modifications in the context of metabolic diseases and ferroptotic cell death.

Combined effect of microplastic, salinomycin and heating on Unio tumidus

Microplastic (MP) and heating (T) suspected to modulate biological effects of aquatic contaminants. Salinomycin (Sal) is veterinary antibiotic and anticancer agent. The goal of this study was to examine the multistress effect of MP, Sal and T on the bioindicator bivalve mollusc. The Unio tumidus were treated with MP (1 mg L^-1), Sal (0.6 µg L^-1), their combination under 18° C (Mix) and 25° C (MixT) for 14 days. The digestive glands were analyzed. MP and Sal did not cause changes of Mn- and Cu,Zn-SOD, lipid peroxidation and Cyp-450-depended EROD levels, whereas catalase, GST and protein carbonyls (Sal-group) increased compared to control. In the Mix-group, enzymes, particularly EROD and GST (by 34% and 115% respectively) were up-regulated. However, in the MixT-group, they were corresponding to control or lesser (EROD, catalase). Our findings emphasize the need to take into account multistress interactions in the MP environmental risk assessment.

Dysregulated autophagy-related genes in septic cardiomyopathy: Comprehensive bioinformatics analysis based on the human transcriptomes and experimental validation

Septic cardiomyopathy (SCM) is severe organ dysfunction caused by sepsis that is associated with poor prognosis, and its pathobiological mechanisms remain unclear. Autophagy is a biological process that has recently been focused on SCM, yet the current understanding of the role of dysregulated autophagy in the pathogenesis of SCM remains limited and uncertain. Exploring the molecular mechanisms of disease based on the transcriptomes of human pathological samples may bring the closest insights. In this study, we analyzed the differential expression of autophagy-related genes in SCM based on the transcriptomes of human septic hearts, and further explored their potential crosstalk and functional pathways. Key functional module and hub genes were identified by constructing a protein–protein interaction network. Eight key genes (CCL2, MYC, TP53, SOD2, HIF1A, CTNNB1, CAT, and ADIPOQ) that regulate autophagy in SCM were identified after validation in a lipopolysaccharide (LPS)-induced H9c2 cardiomyoblast injury model, as well as the autophagic characteristic features. Furthermore, we found that key genes were associated with abnormal immune infiltration in septic hearts and have the potential to serve as biomarkers. Finally, we predicted drugs that may play a protective role in SCM by regulating autophagy based on our results. Our study provides evidence and new insights into the role of autophagy in SCM based on human septic heart transcriptomes, which would be of great benefit to reveal the molecular pathological mechanisms and explore the diagnostic and therapeutic targets for SCM.

Extracellular vesicle miR-32 derived from macrophage promotes arterial calcification in mice with type 2 diabetes via inhibiting VSMC autophagy

Background

The development of diabetes vascular calcification (VC) is tightly associated with the inhibition of vascular smooth muscle cell (VSMC) autophagy. Previously, our team found that miR-32-5p (miR-32) promotes macrophage activation, and miR-32 is expressed at higher level in the plasma of patients with coronary calcification. However, whether miR-32 mediates the function of macrophages in type 2 diabetes (T2D) VC is still unclear.

Methods

Wild-type (WT) and miR-32−/− mice were used in this study. qRT-PCR and western blotting were used to analyze gene expression. Flow cytometry was used to analyze the influence of glucose concentration on macrophage polarization. Nanoparticle tracking analysis (NTA), transmission electron microscopy, and confocal microscopy were used to identify macrophage extracellular vehicles (EVs). Immunofluorescence, in situ hybridization (ISH), immunohistochemistry, and alizarin red staining were used to analyze the influence of macrophage EVs on autophagy and calcification of the aorta of miR-32−/− mice. A luciferase assay was used to analyze the effect of miR-32 on myocyte enhancer factor 2D (Mef2d) expression. Co-IP combined with mass spectrometry (MS) and transcriptome sequencing was used to analyze the signalling pathway by which Mef2d acts in VSMC autophagy.

Results

We found that high glucose conditions upregulate miR-32 expression in macrophages and their EVs. Importantly, macrophages and their EVs promote VSMC osteogenic differentiation and upregulate miR-32 expression in VSMCs. Moreover, miR-32 mimics transfection promoted osteogenic differentiation and inhibited autophagy in VSMCs. In vitro and in vivo experiments showed that Mef2d is the key target gene of miR-32 that inhibits VSMC autophagy. Furthermore, MS and transcriptome sequencing found that cGMP-PKG is an important signalling pathway by which Mef2d regulates VSMC autophagy. In addition, after T2D miR-32−/− mice were injected with macrophage EVs via the caudal vein, miR-32 was detected in aortic VSMCs of miR-32−/− mice. Moreover, autophagy was significantly inhibited, and calcification was significantly enhanced in aorta cells.

Conclusions

These results reveal that EVs are the key pathway by which macrophages promote T2D VC, and that EVs miR-32 is a key cause of autophagy inhibition in VSMCs.

Oxidative distress in aging and age-related diseases: Spatiotemporal dysregulation of protein oxidation and degradation

The concept of oxidative distress had arisen from the assessment of cellular response to high concentrations of reactive species that result from an imbalance between oxidants and antioxidants and cause biomolecular damage. The intracellular distribution and flux of reactive species dramatically change in time and space contributing to the remodeling of the redox landscape and sensitivity of protein residues to oxidants. Here, we hypothesize that compromised spatiotemporal control of generation, conversions, and removal of reactive species underlies protein damage and dysfunction of protein degradation machineries. This leads to the accumulation of oxidatively damaged proteins resulted in an age-dependent decline in the organismal adaptability to oxidative stress. We highlight recent data obtained with the use of various cell cultures, animal models, and patients on irreversible and non-repairable oxidation of key redox-sensitive residues. Multiple reaction products include peptidyl hydroperoxides, alcohols, carbonyls, and carbamoyl moieties as well as Tyr-Tyr, Trp-Tyr, Trp-Trp, Tyr-Cys, His-Lys, His-Arg, and Tyr-Lys cross-links. These lead to protein fragmentation, misfolding, covalent cross-linking, oligomerization, aggregation, and ultimately, causing impaired protein function and turnover. 20S proteasome and autophagy-lysosome pathways are two major types of machinery for the degradation and elimination of oxidatively damaged proteins. Spatiotemporal dysregulation of these pathways under oxidative distress conditions is implicated in aging and age-related disorders such as neurodegenerative and cardiovascular diseases and diabetes. Future investigations in this field allow the discovery of new drugs to target components of dysregulated cell signaling and protein degradation machinery to combat aging and age-related chronic diseases.

PXDN reduces autophagic flux in insulin-resistant cardiomyocytes via modulating FoxO1

Autophagy, a well-observed intracellular lysosomal degradation process, is particularly important to the cell viability in diabetic cardiomyopathy (DCM). Peroxidasin (PXDN) is a heme-containing peroxidase that augments oxidative stress and plays an essential role in cardiovascular diseases, while whether PXDN contributes to the pathogenesis of DCM remains unknown. Here we reported the suppression of cell viability and autophagic flux, as shown by autophagosomes accumulation and increased expression level of LC3-II and p62 in cultured H9C2 and human AC16 cells that treated with 400 μM palmitate acid (PA) for 24 h. Simultaneously, PXDN protein level increased. Moreover, cell death, autophagosomes accumulation as well as increased p62 expression were suppressed by PXDN silence. In addition, knockdown of PXDN reversed PA-induced downregulated forkhead box-1 (FoxO1) and reduced FoxO1 phosphorylation, whereas did not affect AKT phosphorylation. Not consistent with the effects of si-PXDN, double-silence of PXDN and FoxO1 significantly increased cell death, suppressed autophagic flux and declined the level of FoxO1 and PXDN, while the expression of LC3-II was unchanged under PA stimulation. Furthermore, inhibition of FoxO1 in PA-untreated cells induced cell death, inhibited autophagic flux, and inhibited FoxO1 and PXDN expression. Thus, we come to conclusion that PXDN plays a key role in PA-induced cell death by impairing autophagic flux through inhibiting FoxO1, and FoxO1 may also affect the expression of PXDN. These findings may develop better understanding of potential mechanisms regarding autophagy in insulin-resistant cardiomyocytes.

Lipid composition dictates the rate of lipid peroxidation in artificial lipid droplets

Cellular and organismal redox imbalance leading to the accumulation of reactive oxygen species significantly enhances lipid peroxidation (LPO). LPO is relatively well studied for phospholipid membranes and to some extent for circulating lipoproteins. However, it is rarely addressed for intracellular lipid droplets (LDs). Here we optimized an in vitro model system to investigate oxidizability of different lipid classes within artificial LDs (aLDs). To this end, aLDs were reconstructed using differential centrifugation and characterized by a variety of analytical methods. Influence of different lipid compositions on aLDs size was studied and showed opposing effects of unsaturated phospholipids (PLs), triacyclglycerols (TAGs) and cholesteryl esters (CEs). To address aLDs oxidizability, the LPO sensitive ratiometric probe BODIPY-C11 was infused into aLDs, and lipid peroxidation kinetics, upon LPO activation either by copper/ascorbate or 2,2'-azobis(2-methylpropionamidine), was followed up by fluorescence spectroscopy. Generated lipid peroxidation products were additionally identified and relatively quantified by high-resolution LC-MS/MS. It was demonstrated that lipid composition is detrimental to aLD's oxidation sensitivity. Increasing unsaturation levels in the PL monolayer or the TAG core increases oxidation sensitivity, whereas the presence of CEs in the LD core has a dual effect depending on the acylated fatty acid. Moreover, not only the total level of lipid unsaturation, but also the ratio between different lipid species was shown to play a significant role in LPO propagation. This shows that the lipid composition of aLD's determines their sensitivity to LPO. As LDs lipidome reflects and is dynamically influenced by cellular and organismal metabolic status, our findings provide an important observation linking LD lipid composition and their redox sensitivity.

Fundamental Mechanisms of the Cell Death Caused by Nitrosative Stress

Nitrosative stress, as an important oxygen metabolism disorder, has been shown to be closely associated with cardiovascular diseases, such as myocardial ischemia/reperfusion injury, aortic aneurysm, heart failure, hypertension, and atherosclerosis. Nitrosative stress refers to the joint biochemical reactions of nitric oxide (NO) and superoxide (O₂ ^-) when an oxygen metabolism disorder occurs in the body. The peroxynitrite anion (ONOO^-) produced during this process can nitrate several biomolecules, such as proteins, lipids, and DNA, to generate 3-nitrotyrosine (3-NT), which further induces cell death. Among these, protein tyrosine nitration and polyunsaturated fatty acid nitration are the most studied types to date. Accordingly, an in-depth study of the relationship between nitrosative stress and cell death has important practical significance for revealing the pathogenesis and strategies for prevention and treatment of various diseases, particularly cardiovascular diseases. Here, we review the latest research progress on the mechanisms of nitrosative stress-mediated cell death, primarily involving several regulated cell death processes, including apoptosis, autophagy, ferroptosis, pyroptosis, NETosis, and parthanatos, highlighting nitrosative stress as a unique mechanism in cardiovascular diseases.

Oxidative stress mitigation by antioxidants - An overview on their chemistry and influences on health status

The present review paper focuses on the chemistry of oxidative stress mitigation by antioxidants. Oxidative stress is understood as a lack of balance between the pro-oxidant and the antioxidant species. Reactive oxygen species in limited amounts are necessary for cell homeostasis and redox signaling. Excessive reactive oxygenated/nitrogenated species production, which counteracts the organism's defense systems, is known as oxidative stress. Sustained attack of endogenous and exogenous ROS results in conformational and oxidative alterations in key biomolecules. Chronic oxidative stress is associated with oxidative modifications occurring in key biomolecules: lipid peroxidation, protein carbonylation, carbonyl (aldehyde/ketone) adduct formation, nitration, sulfoxidation, DNA impairment such strand breaks or nucleobase oxidation. Oxidative stress is tightly linked to the development of cancer, diabetes, neurodegeneration, cardiovascular diseases, rheumatoid arthritis, kidney disease, eye disease. The deleterious action of reactive oxygenated species and their role in the onset and progression of pathologies are discussed. The results of oxidative attack become themselves sources of oxidative stress, becoming part of a vicious cycle that amplifies oxidative impairment. The term antioxidant refers to a compound that is able to impede or retard oxidation, acting at a lower concentration compared to that of the protected substrate. Antioxidant intervention against the radicalic lipid peroxidation can involve different mechanisms. Chain breaking antioxidants are called primary antioxidants, acting by scavenging radical species, converting them into more stable radicals or non-radical species. Secondary antioxidants quench singlet oxygen, decompose peroxides, chelate prooxidative metal ions, inhibit oxidative enzymes. Moreover, four reactivity-based lines of defense have been identified: preventative antioxidants, radical scavengers, repair antioxidants, and those relying on adaptation mechanisms. The specific mechanism of a series of endogenous and exogenous antioxidants in particular aspects of oxidative stress, is detailed. The final section resumes critical conclusions regarding antioxidant supplementation.

Design of Fluorescent Probes for Bioorthogonal Labeling of Carbonylation in Live Cells

With the rapid development of chemical biology, many diagnostic fluorophore-based tools were introduced to specific biomolecules by covalent binding. Bioorthogonal reactions have been widely utilized to manage challenges faced in clinical practice for early diagnosis and treatment of several tumor samples. Herein, we designed a small molecule fluorescent-based biosensor, 2Hydrazine-5nitrophenol (2Hzin5NP), which reacts with the carbonyl moiety of biomolecules through bioorthogonal reaction, therefore can be utilized for the detection of biomolecule carbonylation in various cancer cell lines. Our almost non-fluorescent chemical probe has a fast covalent binding with carbonyl moieties at neutral pH to form a stable fluorescent hydrazone product leading to a spectroscopic alteration in live cells. Microscopic and fluorometric analyses were used to distinguish the exogenous and endogenous ROS induced carbonylation profile in human dermal fibroblasts along with A498 primary site and ACHN metastatic site renal cell carcinoma (RRC) cell lines. Our results showed that carbonylation level that differs in response to exogenous and endogenous stress in healthy and cancer cells can be detected by the newly synthesized bioorthogonal fluorescent probe. Our results provide new insights into the development of novel bioorthogonal probes that can be utilized in site-specific carbonylation labeling to enhance new diagnostic approaches in cancer.

Quantitative Profiling of Protein-Derived Electrophilic Cofactors in Bacterial Cells with a Hydrazine-Derived Probe

Post-translational modification of proteins can form electrophilic cofactors that serve as a catalytic center. The derived electrophilic cofactors greatly expand protein activities and functions. However, there are few studies concerning how to profile the electrophiles in bacteria. Herein, we utilized a clickable probe called propargyl hydrazine to profile the protein-derived electrophilic cofactors in Escherichia coli (E. coli) cells. Since the cofactors are mostly carbonyl groups, the hydrazine-based probe can specifically react with the cofactors to form a Schiff base. The labeled proteins were then pulled down for mass spectrometry (MS) analysis. Fourteen proteins were shown to undergo enrichment by the probe and competitive binding by its analogue, propyl hydrazine. The identified proteins were further analyzed with targeted proteomics based on parallel reaction monitoring (PRM). Using this strategy, we obtained a global portrait of protein electrophiles in bacterial cells, among which the proteins of speD and panD were previously reported to derive pyruvoyl group as an electrophilic center while lpp can retain N-terminal formyl methionine. This quantitative chemical proteomics strategy can be used to find out protein electrophiles in bacteria and holds great potential to further characterize the protein functions.