Proteomic Analyses of Cysteine Redox in High-Fat-Fed and Fasted Mouse Livers: Implications for Liver Metabolic Homeostasis

Beyond glucose: The crucial role of redox signaling in β-cell metabolic adaptation

OBJECTIVE

Redox signaling mediated by reversible oxidative cysteine thiol modifications is crucial for driving cellular adaptation to dynamic environmental changes, maintaining homeostasis, and ensuring proper function. This is particularly critical in pancreatic β-cells, which are highly metabolically active and play a specialized role in whole organism glucose homeostasis. Glucose stimulation in β-cells triggers signals leading to insulin secretion, including changes in ATP/ADP ratio and intracellular calcium levels. Additionally, lipid metabolism and reactive oxygen species (ROS) signaling are essential for β-cell function and health.

METHODS

We employed IodoTMT isobaric labeling combined with tandem mass spectrometry to elucidate redox signaling pathways in pancreatic β-cells.

RESULTS

Glucose stimulation significantly increases ROS levels in β-cells, leading to targeted reversible oxidation of proteins involved in key metabolic pathways such as glycolysis, the tricarboxylic acid (TCA) cycle, pyruvate metabolism, oxidative phosphorylation, protein processing in the endoplasmic reticulum (ER), and insulin secretion. Furthermore, the glucose-induced increase in reversible cysteine oxidation correlates with the presence of other post-translational modifications, including acetylation and phosphorylation.

CONCLUSIONS

Proper functioning of pancreatic β-cell metabolism relies on fine-tuned regulation, achieved through a sophisticated system of diverse post-translational modifications that modulate protein functions. Our findings demonstrate that glucose induces the production of ROS in pancreatic β-cells, leading to targeted reversible oxidative modifications of proteins. Furthermore, protein activity is modulated by acetylation and phosphorylation, highlighting the complexity of the regulatory mechanisms in β-cell function.

Unlocking the molecular modifications of plasma-activated water-induced oxidation through redox proteomics: In the case of duck myofibrillar protein (Anas platyrhynchos)

Plasma-activated water (PAW) contains multiple active species that alter the structure of myofibrillar protein (MP) to enhance their gel properties. This work investigated the impact of PAW on the oxidation of cysteine in MP by label-free quantitative proteomics. PAW treatment caused the oxidation of 8241 cysteine sites on 2815 proteins, and structural proteins such as nebulin, myosin XVIIIB, myosin XVIIIA, and myosin heavy chain were susceptible to oxidation by PAW. Bioinformatics analysis, including Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway, subcellular localization, and STRING analysis, indicated that these proteins with differential oxidation sites were mainly derived from the cytoplasm and membrane, and were involved in multiple GO terms and KEGG pathways. This is one of the first reports of the redox proteomic changes induced by PAW treatment, and the results are useful for understanding the possible mechanism of PAW-induced oxidation of MP.

Therapy-induced senescence through the redox lens

Therapy-induced senescent tumor cells have emerged as significant drivers of tumor recurrence and disease relapse. Interestingly, reactive oxygen species (ROS) production and its associated redox signaling networks are intertwined with initiation and establishment of therapy-induced senescence. Therapy-induced senescent cells influence neighboring cells and the tumor microenvironment via their bioactive secretome known as the senescence-associated secretory phenotype (SASP). The intracellular effects of ROS are dose and context-dependent. Under normal physiological conditions, ROS is involved in various signalling pathways and cellular processes important for maintenance of cellular homeostasis, such as redox balance, stress response, inflammatory signalling, cell proliferation and cell death among others. However excess ROS accompanied by a pro-oxidant microenvironment can engender oxidative DNA damage, triggering cellular senescence. In this review, we discuss the role of ROS and the redox state dynamics in fine-tuning homeostatic processes that drive therapy-induced cell fate towards senescence establishment, as well as their influence in stimulating inflammatory signalling and SASP production. We also offer insights into interventional strategies, specifically senotherapeutics, that could potentially leverage on modulation of redox and antioxidant pathways. Lastly, we evaluate possible implications of redox rewiring during escape from therapy-induced senescence, an emerging area of research. We envision that examining therapy-induced senescence through the redox lens, integrated with time-resolved single-cell RNA sequencing combined with spatiotemporal multi-omics, could further enhance our understanding of its functional heterogeneity. This could aid identification of targetable signalling nodes to reduce disease relapse, as well as inform strategies for development of broad-spectrum senotherapeutics. Overall, our review aims to delineate redox-driven mechanisms which contribute to the biology of therapy-induced senescence and beyond, while highlighting implications for tumor initiation and recurrence.

Redox proteomics of PANC-1 cells reveals the significance of HIF-1 signaling protein oxidation in pancreatic ductal adenocarcinoma pathogenesis

BACKGROUND

Protein cysteine oxidation is substantially involved in various biological and pathogenic processes, but its implications in pancreatic cancer development remains poorly understood.

METHODS AND RESULTS

In this study, we performed a global characterization of protein oxidation targets in PDAC cells through iodoTMT-based quantitative proteomics, which identified over 4300 oxidized cysteine sites in more than 2100 proteins in HPDE6c7 and PANC-1 cells. Among them, 1715 cysteine residues were shown to be differentially oxidized between HPDE6c7 and PANC-1 cells. Also, charged amino acids including aspartate, glutamate and lysine were significantly overrepresented in flanking sequences of oxidized cysteines. Differentially oxidized proteins in PANC-1 cells were enriched in multiple cancer-related biological processes and signaling pathways. Specifically, the HIF-1 signaling proteins exhibited significant oxidation alterations in PANC-1 cells, and the reduced PHD2 oxidation in human PDAC tissues was correlated with lower survival time in pancreatic cancer patients.

CONCLUSION

These investigations provided new insights into protein oxidation-regulated signaling and biological processes during PDAC pathogenesis, which might be further explored for pancreatic cancer diagnosis and treatment.

A red-emitting ultrasensitive fluorescent probe for specific detection and biological visualization of cysteine in vitro and in vivo

Developing efficient strategies for specific detection of cysteine (Cys) is of great importance for identifying complicated biological roles in physiological and pathological processes. Herein, an ultrasensitive red-emission fluorescent probe (termed 1) is constructed for specific detection and biological visualization of Cys. The linked-anthocyanin fluorophore modified with a twisted N, N-diethylamino moiety shows improved red-shifted emission (642 nm) and absolute quantum yield (0.224 in dimethyl sulfoxide), as well as minimal fluorescence background signal and good water solubility. Meanwhile, utilizing acryloyl chloride as recognition group endows the probe 1 with excellent sensitivity and selectivity towards Cys (limit of detection: 2.93 nM). More importantly, the in vitro and in vivo results confirm that the probe 1 has the capacity of fluorescence imaging of Cys and good biological safety, which holds great promise for bioanalysis and biosensing of Cys.

Mechanism Analysis of Metabolic Fatty Liver on Largemouth bass (Micropterus salmoides) Based on Integrated Lipidomics and Proteomics

Metabolic fatty liver disease caused by high-starch diet restricted the intensive and sustainable development of carnivorous fish such as largemouth bass. In this study, the combination liver proteomic and lipidomic approach was employed to investigate the key signaling pathways and identify the critical biomarkers of fatty liver in largemouth bass. Joint analysis of the correlated differential proteins and lipids revealed nine common metabolic pathways; it was determined that FABP1 were significantly up-regulated in terms of transporting more triglycerides into the liver, while ABCA1 and VDAC1 proteins were significantly down-regulated in terms of preventing the transport of lipids and cholesterol out of the liver, leading to triglyceride accumulation in hepatocyte, eventually resulting in metabolic fatty liver disease. The results indicate that FABP1, ABCA1 and VDAC1 could be potential biomarkers for treating metabolic fatty liver disease of largemouth bass.

A reactive oxygen species burst causes haploid induction in maize

Haploid induction (HI) is an important tool in crop breeding. Phospholipase A1 (ZmPLA1)/NOT LIKE DAD (NLD)/MATRILINEAL (MTL) is a key gene controlling HI in maize; however, the underlying molecular mechanism remains unclear. In this study, to dissect why loss of ZmPLA1 function could mediate HI we performed a comprehensive multiple omics analysis of zmpla1 mutant anthers by integrating transcriptome, metabolome, quantitative proteome, and protein modification data. Functional classes of significantly enriched or differentially abundant molecular entities were found to be associated with the oxidative stress response, suggesting that a reactive oxygen species (ROS) burst plays a critical role in HI. In support of this, we further discovered that a simple chemical treatment of pollen with ROS reagents could lead to HI. Moreover, we identified ZmPOD65, which encodes a sperm-specific peroxidase, as a new gene controlling HI. Taken together, our study revealed a likely mechanism of HI, discovered a new gene controlling HI, and created a new method for HI in maize, indicating the importance of ROS balance in maintaining normal reproduction and providing a potential route to accelerate crop breeding.

Peroxiredoxin 6 protects irradiated cells from oxidative stress and shapes their senescence-associated cytokine landscape

Cellular senescence is a complex stress response defined as an essentially irreversible cell cycle arrest mediated by the inhibition of cell cycle-specific cyclin dependent kinases. The imbalance in redox homeostasis and oxidative stress have been repeatedly observed as one of the hallmarks of the senescent phenotype. However, a large-scale study investigating protein oxidation and redox signaling in senescent cells in vitro has been lacking. Here we applied a proteome-wide analysis using SILAC-iodoTMT workflow to quantitatively estimate the level of protein sulfhydryl oxidation and proteome level changes in ionizing radiation-induced senescence (IRIS) in hTERT-RPE-1 cells. We observed that senescent cells mobilized the antioxidant system to buffer the increased oxidation stress. Among the antioxidant proteins with increased relative abundance in IRIS, a unique 1-Cys peroxiredoxin family member, peroxiredoxin 6 (PRDX6), was identified as an important contributor to protection against oxidative stress. PRDX6 silencing increased ROS production in senescent cells, decreased their resistance to oxidative stress-induced cell death, and impaired their viability. Subsequent SILAC-iodoTMT and secretome analysis after PRDX6 silencing showed the downregulation of PRDX6 in IRIS affected protein secretory pathways, decreased expression of extracellular matrix proteins, and led to unexpected attenuation of senescence-associated secretory phenotype (SASP). The latter was exemplified by decreased secretion of pro-inflammatory cytokine IL-6 which was also confirmed after treatment with an inhibitor of PRDX6 iPLA2 activity, MJ33. In conclusion, by combining different methodological approaches we discovered a novel role of PRDX6 in senescent cell viability and SASP development. Our results suggest PRDX6 could have a potential as a drug target for senolytic or senomodulatory therapy.

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SILAC-iodoTMT is a powerful tool to quantify redox imbalance in IRIS.

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Senescence in hTERT-RPE-1 cells is not accompanied by bulk cysteine oxidation.

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Antioxidant proteins are upregulated in senescent hTERT-RPE-1 cells.

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PRDX6 silencing affects redox homeostasis and viability of senescent cells.

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PRDX6 silencing alters secretome of senescent RPE-1 cells and suppresses IL-6.

Redox Proteomic Analysis Reveals Microwave-Induced Oxidation Modifications of Myofibrillar Proteins from Silver Carp (Hypophthalmichthys molitrix)

To provide an insight into the oxidation behavior of cysteines in myofibrillar proteins (MPs) during microwave heating (MW), a quantitative redox proteomic analysis based on the isobaric iodoacetyl tandem mass tag technology was applied in this study. MPs from silver carp muscles were subjected to MW and water bath heating (WB) with the same time-temperature profiles to eliminate the thermal differences caused by an uneven energy input. Altogether, 422 proteins were found to be differentially expressed after thermal treatments as compared to that with no heat treatment. However, MW triggered a larger number of proteins and cysteine sites for oxidation. Myosin heavy chain, myosin-binding protein C, nebulin, α-actinin-3-like, and titin were found to be highly susceptible to oxidation under microwave irradiation. Notably, MW caused such modifications at cysteine site 9 in the head of myosin, revealing the enhancement mechanism of MP gelation by excess cysteine cross-linking during microwave processing. Furthermore, Gene Ontology and functional enrichment analyses suggested that the two thermal treatments resulted in some differences in ion binding, muscle cell development, and protein-containing complex assembly. Overall, this study is the first to report the redox proteomic changes caused by MW and WB treatments, thus providing a further understanding of the microwave-induced oxidative modifications of MPs.

Comprehensive analysis of the translatome reveals the relationship between the translational and transcriptional control in high fat diet-induced liver steatosis

Translational regulation plays a critical role in gene expression. However, there are few genome-wide studies on translational regulation in non-alcoholic fatty liver disease (NAFLD), which is a severe non-communicable epidemic worldwide. In this study, we performed RNC-mRNA (mRNAs bound to ribosome-nascent chain complex) sequencing and mRNA sequencing to probe the translation status of high-fat-diet (HFD) induced mouse fatty liver. Generally, in the HFD group compared to the control group, changes of translation ratios and changes in mRNA abundance had a negative correlation. The relative abundance of RNC-mRNAs and mRNAs were positively correlated, yet the former changed more slowly than the latter. However, the rate of change became more balanced when it came to the livers of mice that were fed the HFD plus lycopene, an antioxidant. This indicated relatively independent roles of translational modulation and transcriptional regulation. Furthermore, many genes were differentially regulated at the transcriptional or translational levels, suggesting a new screening strategy for functional genes. In conclusion, our analysis revealed the different and correlated role of translational control with transcriptional regulation in the HFD-induced mouse fatty liver relative to the control, which indicates critical roles of translational control for liver steatosis; thus, adding a new dimension towards a better understanding and improvement of treatment for NAFLD.

Assessment of the mechanism of drug resistance in Trichophyton mentagrophytes in response to various substances

BACKGROUND

Trichophyton mentagrophyte (TM), a zoonotic pathogen, has been endangering public health due to emerging drug resistance. Although increased attention is paid to this issue, there is very limited research available on drug resistance in TM. In this study, we studied the gene and proteomic changes, morphological changes, cellular fat localization, fat content changes, and biofilm of TM treated with different substances.

RESULTS

The TM growth curve showed a positive correlation with the concentration of Fenarimol (FE), genistein (GE), clotrimazole (KM), and Miconazole nitrate salt (MK). The morphology of TM cells changed in different degrees after treatment with different substances as observed by TEM and SEM. The results showed that under KM and berberine hydrochloride (BB) treatment, a total of 3305 differentially expressed genes were detected, with the highest number in the KM-treated group (578 up-regulated and 615 down-regulated). A total of 847 proteins and 1850 peptides were identified in TM proteomics. Nile red staining showed that the fat content of TM was significantly higher in the BB-, ethidium bromide- (EB), FE-, KM-, Adriamycin hydrochloride- (YA), and MK-treated group compared to the control group. Results of the biofilm thickness showed that it gradually increased under treatment with specific concentrations of KM or BB, which may be related to the up-regulation of ERG25 and CYP related gene proteins.

CONCLUSIONS

It is suggested that in order to effectively deal with dermatomycosis caused by TM, it is necessary to inhibit the expression of ERG25 and CYP related genes and fat metabolism, which can result in the inhibition of the production of biofilm by the fungus and solve the problem of fungal drug resistance in clinical settings.

Stoichiometric Thiol Redox Proteomics for Quantifying Cellular Responses to Perturbations

Post-translational modifications regulate the structure and function of proteins that can result in changes to the activity of different pathways. These include modifications altering the redox state of thiol groups on protein cysteine residues, which are sensitive to oxidative environments. While mass spectrometry has advanced the identification of protein thiol modifications and expanded our knowledge of redox-sensitive pathways, the quantitative aspect of this technique is critical for the field of redox proteomics. In this review, we describe how mass spectrometry-based redox proteomics has enabled researchers to accurately quantify the stoichiometry of reversible oxidative modifications on specific cysteine residues of proteins. We will describe advancements in the methodology that allow for the absolute quantitation of thiol modifications, as well as recent reports that have implemented this approach. We will also highlight the significance and application of such measurements and why they are informative for the field of redox biology.

Nitric oxide affects seed oil accumulation and fatty acid composition through protein S-nitrosation

Nitric oxide (NO) is a key signaling molecule regulating several plant developmental and stress responses. Here, we report that NO plays an important role in seed oil content and fatty acid composition. RNAi silencing of Arabidopsis S-nitrosoglutathione reductase 1 (GSNOR1) led to reduced seed oil content. In contrast, nitrate reductase double mutant nia1nia2 had increased seed oil content, compared with wild-type plants. Moreover, the concentrations of palmitic acid (C16:0), linoleic acid (C18:2), and linolenic acid (C18:3) were higher, whereas those of stearic acid (C18:0), oleic acid (C18:1), and arachidonic acid (C20:1) were lower, in seeds of GSNOR1 RNAi lines. Similar results were obtained with rapeseed embryos cultured in vitro with the NO donor sodium nitroprusside (SNP), and the NO inhibitor NG-Nitro-L-arginine Methyl Ester (L-NAME). Compared with non-treated embryos, the oil content decreased in SNP-treated embryos, and increased in L-NAME-treated embryos. Relative concentrations of C16:0, C18:2 and C18:3 were higher, whereas C18:1 concentration decreased in rapeseed embryos treated with SNP. Proteomics and transcriptome analysis revealed that three S-nitrosated proteins and some key genes involved in oil synthesis, were differentially regulated in SNP-treated embryos. Therefore, regulating NO content could be a novel approach to increasing seed oil content in cultivated oil crops.

The duration of food withdrawal affects the intestinal structure, nutrients absorption, and utilization in broiler chicken

Food withdrawal is usually used for accurate feed metabolizable energy (ME) assessment in poultry, but its effects on intestinal structure and the absorption of nutrients are unclear. In this study, broilers were fed ad libitum (CT) or withdrew food for 12 (FH12), 24 (FH24), 36 (FH36), or 48 hours (FH48). We showed that food withdrawal increased the energy assimilation when compared with the CT. Food withdrawal improved the digestibility of ether extract and the level of lipid substances and fatty acid-derived β-hydroxybutyrate in serum. Compared to the CT, food withdrawal did not influence the digestibility of starch. Due to 12 hours or longer food withdrawal duration increased glutamate oxidation and uric acid excretion, the analyzed digestibility of crude protein was underestimated, although the upregulated amino acid transporter genes. In addition, histological analysis showed that short-term food withdrawal (12 hours) increased intestinal villus height, crypt depth, and proliferative cell, whereas prolonged food withdrawal (more than 24 hours) impaired villus structure due to the decreased cell proliferation. Moreover, proteomics analysis revealed upregulated pathways in birds withdrawn food for 36 hours involved in nutrient absorption and amino acid oxidation. In conclusion, food withdrawal changes nutrient absorption and utilization, especially for amino acid and ether extract, and results in increased ME. Both glutamate oxidation and fatty acid incomplete oxidation are involved in energy supply after refeeding. In contrast to short-term food withdrawal, prolonged food withdrawal impairs the intestinal structure and villus renewal. Our findings deserve attention from nutritionists who are analyzing food digestibility.

Comparative Proteomic Analysis Reveals Complex Responses to Bordetella bronchiseptica Infections in the Spleen of Rabbits

Bordetella bronchiseptica (B. bronchiseptica) causes a respiratory disease in rabbits. To determine the proteins of B. bronchiseptica in rabbits related to the disease, differentially accumulated proteins in B. bronchiseptica-infected cells are identified by comparative proteomic analysis. Comparative proteomic analysis detects 5814 proteins and quantifies 4854 of these. Fifty eight upregulated and 38 downregulated proteins are identified in spleen tissue after B. bronchiseptica infection of rabbits (both p < 0.05). The significantly enriched Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways are ribosome, biosynthesis of amino acids, biosynthesis of amino acids, protein export, and carbon metabolism etc. (all p < 0.01). Significantly enriched KEGG pathways include 'ocu03010 ribosome' (a); 'ocu00260 glycine, serine threonine metabolism'. Analyses of control and infected spleen cells detect responses to B. bronchiseptica infection. Many differentially affected proteins are evident, and reflect different biological changes and diverse subcellular localizations between control and infected spleen cells. Infection markedly alters the expressions of proteins linked to the serine protease system, with the 'phagosome,' 'biosynthesis of amino acids,' 'glycine, serine threonine metabolism,' 'intestinal immune network for IgA production', and 'amino sugar and nucleotide sugar metabolism' associated with B. bronchiseptica infection. The result will inform studies of responses to B. bronchiseptica infections in rabbits.

Studying the effects of sea cucumber ovum powder on nonalcoholic fatty liver disease by proteomics techniques in a rat model

Sea cucumber is a valuable marine food that has antioxidant, anti-diabetic, and anti-obesity functionalities. Sea cucumber ovum (SCO) may contain functional components, however, it is considered to be a waste product during industrial processing. In order to make good use of SCO, this work investigated the effects of freeze-dried SCO powder on NAFLD, using a rat model, through iBT labeling proteomics techniques, tracking changes in the hepatic protein profiles of rats whose diets were supplemented with SCO powder. Male rats were fed with standard food, a high fat diet (HFD), or a HFD supplemented with 150 mg per kg BW or 450 mg per kg BW SCO powder for 6 weeks. Compared with the HFD, low-dose SCO supplementation in the diet could significantly reduce body weight gain and liver weight. Furthermore, in total, 5922 proteins were identified, and 767 proteins were found to be significantly different proteins (p < 0.05) among all four groups. Most of the significantly different proteins were related to apoptosis and lipid metabolism. Fadd, Dci, and Aif1 have been identified as key proteins in the pathways related to apoptosis, lipid metabolism, and inflammation. The results in this study provide an overview of the SCO-induced changes in the liver proteome of NAFLD, which may help us to understand the molecular mechanism behind the effects of SCO on the alleviation of NAFLD.

Redox Systems Biology: Harnessing the Sentinels of the Cysteine Redoxome

Significance: Cellular redox processes are highly interconnected, yet not in equilibrium, and governed by a wide range of biochemical parameters. Technological advances continue refining how specific redox processes are regulated, but broad understanding of the dynamic interconnectivity between cellular redox modules remains limited. Systems biology investigates multiple components in complex environments and can provide integrative insights into the multifaceted cellular redox state. This review describes the state of the art in redox systems biology as well as provides an updated perspective and practical guide for harnessing thousands of cysteine sensors in the redoxome for multiparameter characterization of cellular redox networks. Recent Advances: Redox systems biology has been applied to genome-scale models and large public datasets, challenged common conceptions, and provided new insights that complement reductionist approaches. Advances in public knowledge and user-friendly tools for proteome-wide annotation of cysteine sentinels can now leverage cysteine redox proteomics datasets to provide spatial, functional, and protein structural information. Critical Issues: Careful consideration of available analytical approaches is needed to broadly characterize the systems-level properties of redox signaling networks and be experimentally feasible. The cysteine redoxome is an informative focal point since it integrates many aspects of redox biology. The mechanisms and redox modules governing cysteine redox regulation, cysteine oxidation assays, proteome-wide annotation of the biophysical and biochemical properties of individual cysteines, and their clinical application are discussed. Future Directions: Investigating the cysteine redoxome at a systems level will uncover new insights into the mechanisms of selectivity and context dependence of redox signaling networks.

A Quantitative Tissue-Specific Landscape of Protein Redox Regulation during Aging

Mammalian tissues engage in specialized physiology that is regulated through reversible modification of protein cysteine residues by reactive oxygen species (ROS). ROS regulate a myriad of biological processes, but the protein targets of ROS modification that drive tissue-specific physiology in vivo are largely unknown. Here, we develop Oximouse, a comprehensive and quantitative mapping of the mouse cysteine redox proteome in vivo. We use Oximouse to establish several paradigms of physiological redox signaling. We define and validate cysteine redox networks within each tissue that are tissue selective and underlie tissue-specific biology. We describe a common mechanism for encoding cysteine redox sensitivity by electrostatic gating. Moreover, we comprehensively identify redox-modified disease networks that remodel in aged mice, establishing a systemic molecular basis for the long-standing proposed links between redox dysregulation and tissue aging. We provide the Oximouse compendium as a framework for understanding mechanisms of redox regulation in physiology and aging.

Spatial and temporal alterations in protein structure by EGF regulate cryptic cysteine oxidation

Stimulation of plasma membrane receptor tyrosine kinases (RTKs), such as the epidermal growth factor receptor (EGFR), locally increases the abundance of reactive oxygen species (ROS). These ROS then oxidize cysteine residues in proteins to potentiate downstream signaling. Spatial confinement of ROS is an important regulatory mechanism of redox signaling that enables the stimulation of different RTKs to oxidize distinct sets of downstream proteins. To uncover additional mechanisms that specify cysteines that are redox regulated by EGF stimulation, we performed time-resolved quantification of the EGF-dependent oxidation of 4200 cysteine sites in A431 cells. Fifty-one percent of cysteines were statistically significantly oxidized by EGF stimulation. Furthermore, EGF induced three distinct spatiotemporal patterns of cysteine oxidation in functionally organized protein networks, consistent with the spatial confinement model. Unexpectedly, protein crystal structure analysis and molecular dynamics simulations indicated widespread redox regulation of cryptic cysteine residues that are solvent exposed only upon changes in protein conformation. Phosphorylation and increased flux of nucleotide substrates served as two distinct modes by which EGF specified the cryptic cysteine residues that became solvent exposed and redox regulated. Because proteins that are structurally regulated by different RTKs or cellular perturbations are largely unique, these findings suggest that solvent exposure and redox regulation of cryptic cysteine residues contextually delineate redox signaling networks.

Deletion of the Mitochondrial Protein VWA8 Induces Oxidative Stress and an HNF4α Compensatory Response in Hepatocytes

von Willebrand A domain-containing protein 8 (VWA8) is a poorly characterized, mitochondrial matrix-targeted protein with an AAA ATPase domain and ATPase activity that increases in livers of mice fed a high-fat diet. This study was undertaken to use CRISPR/Cas9 to delete VWA8 in cultured mouse hepatocytes and gain insight into its function. Unbiased omics techniques and bioinformatics were used to guide subsequent assays, including the assessment of oxidative stress and the determination of bioenergetic capacity. Metabolomics analysis showed VWA8 null cells had higher levels of oxidative stress and protein degradation; assays of hydrogen peroxide production revealed higher levels of production of reactive oxygen species (ROS). Proteomics and transcriptomics analyses showed VWA8 null cells had higher levels of expression of mitochondrial proteins (electron transport-chain Complex I, ATP synthase), peroxisomal proteins, and lipid transport proteins. The pattern of higher protein abundance in the VWA8 null cells could be explained by a higher level of hepatocyte nuclear factor 4 α (HNF4α) expression. Bioenergetic assays showed higher rates of carbohydrate oxidation and mitochondrial and nonmitochondrial lipid oxidation in intact and permeabilized cells. Inhibitor assays localized sites of ROS production to peroxisomes and NOX1/4. The rescue of VWA8 protein restored the wild-type phenotype, and treatment with antioxidants decreased the level of HNF4α expression. Thus, loss of VWA8 produces a mitochondrial defect that may be sensed by NOX4, leading to an increase in the level of ROS that results in a higher level of HNF4α. The compensatory HNF4α response results in a higher oxidative capacity and an even higher level of ROS production. We hypothesize that VWA8 is an AAA ATPase protein that plays a role in mitochondrial protein quality.

Biological Activities, Health Benefits, and Therapeutic Properties of Avenanthramides: From Skin Protection to Prevention and Treatment of Cerebrovascular Diseases

Oat (Avena sativa) is a cereal known since antiquity as a useful grain with abundant nutritional and health benefits. It contains distinct molecular components with high antioxidant activity, such as tocopherols, tocotrienols, and flavanoids. In addition, it is a unique source of avenanthramides, phenolic amides containing anthranilic acid and hydroxycinnamic acid moieties, and endowed with major beneficial health properties because of their antioxidant, anti-inflammatory, and antiproliferative effects. In this review, we report on the biological activities of avenanthramides and their derivatives, including analogs produced in recombinant yeast, with a major focus on the therapeutic potential of these secondary metabolites in the treatment of aging-related human diseases. Moreover, we also present recent advances pointing to avenanthramides as interesting therapeutic candidates for the treatment of cerebral cavernous malformation (CCM) disease, a major cerebrovascular disorder affecting up to 0.5% of the human population. Finally, we highlight the potential of foodomics and redox proteomics approaches in outlining distinctive molecular pathways and redox protein modifications associated with avenanthramide bioactivities in promoting human health and contrasting the onset and progression of various pathologies. The paper is dedicated to the memory of Adelia Frison.