Oxidative Stress Response Genes Research Articles

Sex- and age-associated factors drive the pathophysiology of MASLD.

Metabolic dysfunction-associated steatotic liver disease (MASLD) is strongly associated with obesity. Sex and age affect MASLD prevalence and pathophysiology. The use of animal models fed Western-style diets is vital for investigating the molecular mechanisms contributing to metabolic dysregulation and for facilitating novel drug target identification. However, the sex-associated and age-associated mechanisms underlying the pathophysiology remain poorly understood. This knowledge gap limits the development of personalized sex-specific and age-specific drug treatments. Young (7wk) and aged (52wk) male and female mice were fed a high-fat diet (HFD) or low-fat diet. Liver metabolome (>600 molecules) and transcriptome profiles were analyzed. Male and female mice fed an HFD developed obesity, glucose intolerance, and hepatic steatosis. However, fasting blood glucose, insulin, and serum alanine aminotransferase levels were higher in males fed an HFD, indicating a more severe metabolic disease. In addition, males showed significant increases in liver diacylglycerides and glycosylceramides (known mediators of insulin resistance and fibrosis), and more changes in the transcriptome: extracellular matrix organization and proinflammatory genes were elevated only in males. In contrast, no major increase in damaging lipid classes was observed in females fed an HFD. However, aging affected the liver to a greater extent in females. Acylcarnitine levels were significantly reduced, suggestive of changes in fatty acid oxidation, and broad changes in the transcriptome were observed, including reduced oxidative stress response gene expression and alterations in lipid partitioning genes. Here, we show distinct responses to an HFD between males and females. Our study underscores the need for using both sexes in drug target identification studies, and characterizing the molecular mechanisms contributing to the MASLD pathophysiology in aging animals.

Single-cell and spatial transcriptome assays reveal heterogeneity in gliomas through stress responses and pathway alterations.

Glioma is a highly heterogeneous malignancy of the central nervous system. This heterogeneity is driven by various molecular processes, including neoplastic transformation, cell cycle dysregulation, and angiogenesis. Among these biomolecular events, inflammation and stress pathways in the development and driving factors of glioma heterogeneity have been reported. However, the mechanisms of glioma heterogeneity under stress response remain unclear, especially from a spatial aspect. This study employed single-cell RNA sequencing (scRNA-seq) and spatial transcriptomics (ST) to explore the impact of oxidative stress response genes in oligodendrocyte precursor cells (OPCs). Our analysis identified distinct pathways activated by oxidative stress in two different types of gliomas: high- and low- grade (HG and LG) gliomas. In HG gliomas, oxidative stress induced a metabolic shift from oxidative phosphorylation to glycolysis, promoting cell survival by preventing apoptosis. This metabolic reprogramming was accompanied by epithelial-to-mesenchymal transition (EMT) and an upregulation of stress response genes. Furthermore, SCENIC (Single-Cell rEgulatory Network Inference and Clustering) analysis revealed that oxidative stress activated the AP1 transcription factor in HG gliomas, thereby enhancing tumor cell survival and proliferation. Our findings provide a novel perspective on the mechanisms of oxidative stress responses across various grades of gliomas. This insight enhances our comprehension of the evolutionary processes and heterogeneity within gliomas, potentially guiding future research and therapeutic strategies.

Mechanisms of Cadmium stress response in watermelon: Insights from physiological, transcriptomic, and metabolic analyses

Cadmium (Cd) contamination of soil may lead to Cd stress for plants, which significantly hinders plant growth and development, posing a risk to human health through the consumption of Cd-contaminated foods. Watermelon (Citrullus lanatus), a widely consumed fruit, is particularly affected by Cd stress globally, yet the mechanisms underlying its response are not well understood. Here, we subjected watermelon seedlings to simulated Cd stress treatment and explored the physiological, transcriptomic, and metabolic response. Our findings revealed that Cd stress treatment led to increased accumulation of reactive oxygen species (ROS) in watermelon leaves. Transcriptome sequencing unveiled a multitude of osmotic and oxidative stress-responsive genes, including peroxidase (POD), MYB, voltage-dependent anion channel (SLAC1), and ABC transporter. KEGG enrichment analysis highlighted the predominant enrichment of Cd stress-responsive genes in pathways such as glutathione (GSH) metabolism, MAPK signaling, and biosynthesis of secondary metabolites. Within the GSH metabolism pathway, several glutathione S-transferase (GST) genes were up-regulated, alongside phytochelatin synthetase (PCS) genes involved in phytochelatin synthesis. In the MAPK signaling pathway, genes associated with ABA and ethylene signal transduction showed up-regulation following Cd stress. Metabolomic analysis demonstrated that Cd stress enhanced the production of amino acids, phenolamines, and esters. Overall, our study elucidates that watermelon responds to Cd stress by activating its antioxidant system, GSH metabolism pathway, MAPK signal pathway, and biosynthesis of key metabolites. These findings offer valuable insights for the remediation of heavy metal pollution in soil affecting plant life.

Dual species transcriptomics reveals conserved metabolic and immunologic processes in interactions between human neutrophils and Neisseria gonorrhoeae.

Neisseria gonorrhoeae (the gonococcus, Gc) causes the sexually transmitted infection gonorrhea. Gc is a prominent threat to human health by causing severe lifelong sequelae, including infertility and chronic pelvic pain, which is amplified by the emergence of "superbug" strains resistant to all current antibiotics. Gc is highly adapted to colonize human mucosal surfaces, where it survives despite initiating a robust inflammatory response and influx of polymorphonuclear leukocytes (PMNs, neutrophils) that typically clear bacteria. Here, dual-species RNA-sequencing was used to define Gc and PMN transcriptional profiles alone and after infection. Core host and bacterial responses were assessed for two strains of Gc and three human donors' PMNs. Comparative analysis of Gc transcripts revealed overlap between Gc responses to PMNs, iron, and hydrogen peroxide; 98 transcripts were differentially expressed across both Gc strains in response to PMN co-culture, including iron-responsive and oxidative stress response genes. We experimentally determined that the iron-dependent TbpB is suppressed by PMN co-culture, and iron-limited Gc have a survival advantage when cultured with PMNs. Analysis of PMN transcripts modulated by Gc infection revealed differential expression of genes driving cell adhesion, migration, inflammatory responses, and inflammation resolution pathways. Production of pro-inflammatory cytokines, including IL1B and IL8, the adhesion factor ICAM1, and prostaglandin PGE2 were induced in PMNs in response to Gc. Together, this study represents a comprehensive and experimentally validated dual-species transcriptomic analysis of two isolates of Gc and primary human PMNs that gives insight into how this bacterium survives innate immune onslaught to cause disease.

Expression of mitochondrial oxidative stress response genes in muscle is associated with mitochondrial respiration, physical performance, and muscle mass in the Study of Muscle, Mobility, and Aging.

Gene expression in skeletal muscle of older individuals may reflect compensatory adaptations in response to oxidative damage that preserve tissue integrity and maintain function. Identifying associations between oxidative stress response gene expression patterns and mitochondrial function, physical performance, and muscle mass in older individuals would further our knowledge of mechanisms related to managing molecular damage that may be targeted to preserve physical resilience. To characterize expression patterns of genes responsible for the oxidative stress response, RNA was extracted and sequenced from skeletal muscle biopsies collected from 575 participants (≥70 years old) from the Study of Muscle, Mobility, and Aging. Expression levels of 21 protein-coding RNAs related to the oxidative stress response were analyzed in relation to six phenotypic measures, including maximal mitochondrial respiration from muscle biopsies (Max OXPHOS), physical performance (VO2 peak, 400-m walking speed, and leg strength), and muscle size (thigh muscle volume and whole-body D3Cr muscle mass). The mRNA level of the oxidative stress response genes most consistently associated across outcomes are preferentially expressed within the mitochondria. Higher expression of mRNAs that encode generally mitochondria located proteins SOD2, TRX2, PRX3, PRX5, and GRX2 were associated with higher levels of mitochondrial respiration and VO2 peak. In addition, greater SOD2, PRX3, and GRX2 expression was associated with higher physical performance and muscle size. Identifying specific mechanisms associated with high functioning across multiple performance and physical domains may lead to targeted antioxidant interventions with greater impacts on mobility and independence.

Functional characterization of Fur from the strict anaerobe Clostridioides difficile provides insight into its redox-driven regulatory capacity.

Clostridioides (formerly Clostridium) difficile is a leading cause of infectious diarrhea associated with antibiotic therapy. The ability of this anaerobic pathogen to acquire enough iron to proliferate under iron limitation conditions imposed by the host largely determines its pathogenicity. However, since high intracellular iron catalyzes formation of deleterious reactive hydroxyl radicals, iron uptake is tightly regulated at the transcriptional level by the ferric uptake regulator Fur. Several studies relate lacking a functional fur gene in C. difficile cells to higher oxidative stress sensitivity, colonization defect and less toxigenicity, although Fur does not appear to directly regulate either oxidative stress response genes or pathogenesis genes. In this work, we report the functional characterization of C. difficile Fur and describe an additional oxidation sensing Fur-mediated mechanism independent of iron, which affects Fur DNA-binding. Using electrophoretic mobility shift assays, we show that Fur binding to the promoters of fur, feoA and fldX genes, identified as iron and Fur-regulated genes in vivo, is specific and does not require co-regulator metal under reducing conditions. Fur treatment with H2O2 produces dose-dependent soluble high molecular weight species unable to bind to target promoters. Moreover, Fur oligomers are dithiotreitol sensitive, highlighting the importance of some interchain disulfide bond(s) for Fur oligomerization, and hence for activity. Additionally, the physiological electron transport chain NADPH-thioredoxin reductase/thioredoxin from Escherichia coli reduces inactive oligomerized C. difficile Fur that recovers activity. In conjunction with available transcriptomic data, these results suggest a previously underappreciated complexity in the control of some members of the Fur regulon that is based on Fur redox properties and might be fundamental for the adaptive response of C. difficile during infection.

Mapping Interindividual Variability of Toxicodynamics Using High-Throughput Transcriptomics and Primary Human Hepatocytes from Fifty Donors.

Understanding the variability across the human population with respect to toxicodynamic responses after exposure to chemicals, such as environmental toxicants or drugs, is essential to define safety factors for risk assessment to protect the entire population. Activation of cellular stress response pathways are early adverse outcome pathway (AOP) key events of chemical-induced toxicity and would elucidate the estimation of population variability of toxicodynamic responses. We aimed to map the variability in cellular stress response activation in a large panel of primary human hepatocyte (PHH) donors to aid in the quantification of toxicodynamic interindividual variability to derive safety uncertainty factors. High-throughput transcriptomics of over 8,000 samples in total was performed covering a panel of 50 individual PHH donors upon 8 to 24 h exposure to broad concentration ranges of four different toxicological relevant stimuli: tunicamycin for the unfolded protein response (UPR), diethyl maleate for the oxidative stress response (OSR), cisplatin for the DNA damage response (DDR), and tumor necrosis factor alpha () for signaling. Using a population mixed-effect framework, the distribution of benchmark concentrations (BMCs) and maximum fold change were modeled to evaluate the influence of PHH donor panel size on the correct estimation of interindividual variability for the various stimuli. Transcriptome mapping allowed the investigation of the interindividual variability in concentration-dependent stress response activation, where the average of BMCs had a maximum difference of 864-, 13-, 13-, and 259-fold between different PHHs for UPR, OSR, DDR, and signaling-related genes, respectively. Population modeling revealed that small PHH panel sizes systematically underestimated the variance and gave low probabilities in estimating the correct human population variance. Estimated toxicodynamic variability factors of stress response activation in PHHs based on this dataset ranged between 1.6 and 6.3. Overall, by combining high-throughput transcriptomics and population modeling, improved understanding of interindividual variability in chemical-induced activation of toxicity relevant stress pathways across the human population using a large panel of plated cryopreserved PHHs was established, thereby contributing toward increasing the confidence of in vitro-based prediction of adverse responses, in particular hepatotoxicity. https://doi.org/10.1289/EHP11891.

A photoheterotrophic bacterium from Iceland has adapted its photosynthetic machinery to the long days of polar summer.

During their long evolution, anoxygenic phototrophic bacteria have inhabited a wide variety of natural habitats and developed specific strategies to cope with the challenges of any particular environment. Expression, assembly, and safe operation of the photosynthetic apparatus must be regulated to prevent reactive oxygen species generation under illumination in the presence of oxygen. Here, we report on the photoheterotrophic Sediminicoccus sp. strain KRV36, which was isolated from a cold stream in north-western Iceland, 30 km south of the Arctic Circle. In contrast to most aerobic anoxygenic phototrophs, which stop pigment synthesis when illuminated, strain KRV36 maintained its bacteriochlorophyll synthesis even under continuous light. Its cells also contained between 100 and 180 chromatophores, each accommodating photosynthetic complexes that exhibit an unusually large carotenoid absorption spectrum. The expression of photosynthesis genes in dark-adapted cells was transiently downregulated in the first 2 hours exposed to light but recovered to the initial level within 24 hours. An excess of membrane-bound carotenoids as well as high, constitutive expression of oxidative stress response genes provided the required potential for scavenging reactive oxygen species, safeguarding bacteriochlorophyll synthesis and photosystem assembly. The unique cellular architecture and an unusual gene expression pattern represent a specific adaptation that allows the maintenance of anoxygenic phototrophy under arctic conditions characterized by long summer days with relatively low irradiance.IMPORTANCEThe photoheterotrophic bacterium Sediminicoccus sp. KRV36 was isolated from a cold stream in Iceland. It expresses its photosynthesis genes, synthesizes bacteriochlorophyll, and assembles functional photosynthetic complexes under continuous light in the presence of oxygen. Unraveling the molecular basis of this ability, which is exceptional among aerobic anoxygenic phototrophic species, will help to understand the evolution of bacterial photosynthesis in response to changing environmental conditions. It might also open new possibilities for genetic engineering of biotechnologically relevant phototrophs, with the aim of increasing photosynthetic activity and their tolerance to reactive oxygen species.

Newcastle disease virus regulates its replication by instigating oxidative stress-driven Sirtuin 7 production.

Reactive oxygen species (ROS) accumulation inside the cells instigates oxidative stress, activating stress-responsive genes. The viral strategies for promoting stressful conditions and utilizing the induced host proteins to enhance their replication remain elusive. The present work investigates the impact of oxidative stress responses on Newcastle disease virus (NDV) pathogenesis. Here, we show that the progression of NDV infection varies with intracellular ROS levels. Additionally, the results demonstrate that NDV infection modulates the expression of oxidative stress-responsive genes, majorly sirtuin 7 (SIRT7), a NAD+-dependent deacetylase. The modulation of SIRT7 protein, both through overexpression and knockdown, significantly impacts the replication dynamics of NDV in DF-1 cells. The activation of SIRT7 is found to be associated with the positive regulation of cellular protein deacetylation. Lastly, the results suggested that NDV-driven SIRT7 alters NAD+ metabolism in vitro and in ovo. We concluded that the elevated expression of NDV-mediated SIRT7 protein with enhanced activity metabolizes the NAD+ to deacetylase the host proteins, thus contributing to high virus replication.

Bacterial community distribution and functional potentials provide key insights into their role in the ecosystem functioning of a retreating Eastern Himalayan glacier.

Himalayan glaciers are receding at an exceptional rate, perturbing the local biome and ecosystem processes. Understanding the microbial ecology of an exclusively microbe-driven biome provides insights into their contributions to the ecosystem functioning through biogeochemical fluxes. Here, we investigated the bacterial communities and their functional potential in the retreating East Rathong Glacier (ERG) of Sikkim Himalaya. Amplicon-based taxonomic classification revealed the dominance of the phyla Proteobacteria, Bacteroidota, and candidate Patescibacteria in the glacial sites. Further, eight good-quality metagenome-assembled genomes (MAGs) of Proteobacteria, Patescibacteria, Acidobacteriota, and Choloflexota retrieved from the metagenomes elucidated the microbial contributions to nutrient cycling. The ERG MAGs showed aerobic respiration as a primary metabolic feature, accompanied by carbon fixation and complex carbon degradation potentials. Pathways for nitrogen metabolism, chiefly dissimilatory nitrate reduction and denitrification, and a complete sulphur oxidation enzyme complex for sulphur metabolism were identified in the MAGs. We observed that DNA repair and oxidative stress response genes complemented with osmotic and periplasmic stress and protein chaperones were vital for adaptation against the intense radiation and stress conditions of the extreme Himalayan niche. Current findings elucidate the microbiome and associated functional potentials of a vulnerable glacier, emphasizing their significant ecological roles in a changing glacial ecosystem.

Transcriptome Analysis and Identification of Cadmium-Induced Oxidative Stress Response Genes in Different Meretrix meretrix Developmental Stages.

Cadmium (Cd) is one of the major pollutants in the aquatic environment, and it can easily accumulate in aquatic animals and result in toxic effects by changing the metabolism of the body, causing a serious impact on the immune system, reproductive system, and the development of offspring. The clam Meretrix meretrix is one of the commercially important species that is cultivated in large-scale aquaculture in China. To elucidate the underlying molecular mechanisms of Cd2+ in the developmental processes, fertilized eggs and larvae of M. meretrix at different developmental stages were exposed to Cd2+ (27.2 mg L-1 in natural seawater) or just natural seawater without Cd2+ (control), and high-throughput transcriptome sequencing and immunohistochemistry techniques were used to analyze the toxic effects of Cd on larvae at different early developmental stages. The results revealed 31,914 genes were differentially expressed in the different stages of M. meretrix development upon treatment with Cd2+. Ten of these genes were differentially expressed in all stages of development examined, but they comprised only six unigenes (CCO, Ndh, HPX, A2M, STF, and pro-C3), all of which were related to the oxidative stress response. Under Cd exposure, the expression levels of CCO and Ndh were significantly upregulated in D-shaped and pediveliger larvae, while pro-C3 expression was significantly upregulated in the fertilized egg, D-shaped larva, and pediveliger. Moreover, HPX, A2M, and STF expression levels in the fertilized egg and pediveliger larvae were also significantly upregulated. In contrast, CCO, Ndh, HPX, A2M, STF, and pro-C3 expression levels in the postlarva were all downregulated under Cd exposure. Besides the genes with changes in expression identified by the transcriptome, the expression of two other oxidative stress-related genes (MT and Nfr2) was also found to change significantly in the different developmental stages of M. meretrix upon Cd exposure, confirming their roles in combating oxidative stress. Overall, the findings of this study indicated that Cd would interfere with cellular respiration, ion transport, and immune response through inducing oxidative stress, and changes in the expression of oxidative stress-related genes might be an important step for M. meretrix to deal with the adverse effects of Cd at different stages of its development.

Unravelling the key steps impairing the metabolic state of Xanthomonas cells undergoing programmed cell death.

Programmed cell death (PCD) has been reported in Xanthomonas axonopodis pv. glycines (Xag) wild type earlier and was indirectly shown to be induced by metabolic stress; however, deciphering the key proteins regulating the metabolic stress remained unrevealed. In this study, transcriptomic and proteomic analyses were performed to investigate the prominent pathways, having a role in the induction of metabolic stress in Xag cells undergoing PCD. A comprehensive analysis of transcriptome and proteome data revealed the major involvement of metabolic pathways related to branched chain amino acid degradation, such as acyl-CoA dehydrogenase and energy-yielding, ubiquinol:cytochrome c oxidoreductase complex, in Xag cells undergoing PCD. Consequently, oxidative stress response genes showed major upregulation in Xag cells in PCD-inducing medium; however, no such upregulation was observed at the protein level, indicative of depleted protein levels under excessive stress conditions. Activation of stress response and DNA repair proteins was also observed in Xag cells grown in PCD-inducing medium, which is indicative of excessive cellular damage. Thus, the findings indicate that programmed cell death in Xag is an outcome of metabolic stress in nutrient condition not suitable for a plant pathogen like Xanthomonas, which is more acclimatised with altogether a different nutritional requirement predominantly having an enriched carbohydrate source.

Comparative transcriptomic effects of Harpephyllum caffrum extracts and sodium metabisulphite on hydrogen peroxide stressed Saccharomyces cerevisiae cells using RNA-seq

Plant extracts intended for application as natural food antioxidants are largely touted as safe antioxidants without mechanistic interpretation of their in vivo efficacy or tangible proof of their toxicological effects. The study used RNA-Seq analysis to evaluate the transcriptomic effects of Harpephyllum caffrum Berhn. Fruit peel extracts (HCP) at 250, 450 and 650 ppm in Saccharomyces cerevisiae and their ability to attenuate in vivo H2O2-induced oxidative stress in comparison with sodium metabisulphite (SMB) at 450 ppm. The HCP were influenced ribosome biogenesis and spliceosome relative to SMB. Additionally, HCP treatments primed cells for oxidative stress response and recovery with HCP-450 application being optimal, while SMB induced differential upregulation of thioredoxin, peroxiredoxin, glutathione peroxidase and catalase oxidative stress response genes. There were signs of mitochondrial damage in stressed HCP-650, while the proteasomal system and pro-apoptotic genes were induced in the stressed SMB treatment. Overall, the study demonstrates the antioxidant efficacy of HCP, especially at 450 ppm, and its potential to induce epitranscriptomic modifications beneficial for a healthful diet as opposed to SMB.

Abstract C051: Deciphering the role of stress-survival pathway genes and mutations in Hispanic colorectal cancer disparities

Abstract This study aims to determine the role of stress-survival pathway (SSP) genes and the associated mutations in Hispanic colorectal cancer (CRC) disparities, particularly in young and late-stage Hispanic CRC. CRC is the second most-deadliest among all cancers and the third leading cause of cancer in the United States (US). An overall reduction in CRC cases among individuals aged 50 and older has been reported, albeit there is an alarming rise in the incidence of early-onset (patients under the age of 50) CRC. The increase in the early onset of CRC is concerning as these cases tend to appear with higher pathologic grades and have a higher risk of recurrence and metastasis. The incidence of early-onset CRC is almost two times in Hispanics (16.5%) when compared to that in non-Hispanic White (NHWs; 8.7%). Access to health care for Hispanics is limited, as a result, they also tend to present with later-stage CRC when compared to NHWs (32% versus 19% of Stage IV), which likely accounts for their inferior age-adjusted survival after CRC diagnosis. Since Hispanics have the highest percentage of young people and comprise ~18% of the US population, the rising incidence of early-onset and late-stage detection of CRC among Hispanics coupled with the rapid growth in this segment of the population makes it imperative to correctly assess the causes behind the observed disparities in Hispanics with early-onset and late-stage CRC. Our previous study, using in-silico analyses of CRC datasets, helped us identify twenty-eight oxidative stress-response and apoptosis-associated genes that are expressed differently in CRC when compared to normal colon tissues. Expressions of these SSP genes (mRNA and protein levels) were validated in CRC cell lines, cDNA arrays, and human colon cancer tissue microarrays (TMAs). Finally, we have confirmed the differential expression of all twenty-eight transcripts in Hispanic and NHW CRC, and corresponding normal adjacent to the tumor (NAT) tissues. Interestingly, we have identified distinct transcripts that are differentially expressed in Hispanics with early-onset (PDCD2L, CDK1, and PRDX4) and late-stage (CCNB1, CDK4, CHEK1, and MCM10) CRC. We have also identified the mutations associated with the SSP genes by analyzing the ClinVar and NHGRI-EBI GWAS databases. These findings have laid the foundation to characterize further, the roles played by these genes in the molecular basis for Hispanic CRC disparities at early-onset and late stages. Differential Expression of mRNAs in CRC tissues between the two ethnic groups (Hispanics and NHW) and corresponding NATs has been determined by RNA-seq. Ingenuity Pathway Analysis (IPA) has been performed to correlate SSP genes with the canonical CRC pathways to better understand the roles played by these genes, their effects on the downstream cancer-related pathways, and on the early-onset and late-stage Hispanic CRC. These putative ethnicity-specific biomarkers or targets could be used for developing novel prognostic tools or therapeutic interventions for Hispanic CRC patients in the future. Citation Format: Sourav Roy, Brian I. Grajeda, Md Zahirul Islam Khan, Urbashi Basnet, Soumya Nair. Deciphering the role of stress-survival pathway genes and mutations in Hispanic colorectal cancer disparities [abstract]. In: Proceedings of the 16th AACR Conference on the Science of Cancer Health Disparities in Racial/Ethnic Minorities and the Medically Underserved; 2023 Sep 29-Oct 2;Orlando, FL. Philadelphia (PA): AACR; Cancer Epidemiol Biomarkers Prev 2023;32(12 Suppl):Abstract nr C051.

Prevention of ferroptosis by the Alzheimer multifactorial therapeutic agent E2F4DN correlates with reduced neuronal tetraploidization

AbstractBackgroundSomatic mutations accumulate during aging in human neurons (Science 2018;359:555‐559), resembling the progressive increase of somatic tetraploid neurons that is observed in the human entorhinal cortex, which precedes the neuropathological hallmarks of Alzheimer’s disease (AD) (Neurobiol. Aging 2017;56:50‐66). Oxidative stress can trigger lipid peroxidation, which can mediate somatic mutations and ferroptosis in neurons. E2F4 is a transcription factor that regulates the expression of genes involved in the oxidative stress response (Int. J. Mol. Sci. 2022;23:12093). A modified version of E2F4, unable to become phosphorylated in two conserved Thr residues by the stress kinase p38MAPK (E2F4DN), is a multifactorial therapeutic agent against AD. This therapeutic agent prevents pathological neuronal tetraploidization (NT) (Neurotherapeutics 2021;18:2484‐2503, Mol. Neurobiol. 2022;59:3016‐3039).MethodTo study the connection between somatic mutations and neuronal tetraploidy, we performed whole exome sequencing of diploid and tetraploid neurons isolated from the parietal cortex of AD patients as well as diploid neurons from control individuals. We also studied by qPCR whether oxidative stress‐related genes are modulated by E2F4DN in the cerebral cortex of both WT and 5xFAD mice, a known AD mouse model.ResultTetraploid neurons contain a significantly higher proportion of single nucleotide variants (SNVs) as compared to diploid neurons. These SNVs, which showed a molecular signature associated to lipid peroxidation, were exacerbated in DNA repair genes involved in base excision repair. SNVs in cancer‐related genes showed high pathogenicity scores in all cases. In both WT and 5xFAD mice, neuronal expression of E2F4DN reduced the expression of molecular markers of ferroptosis, a process associated with lipid peroxidation. This correlated with reduced NT.ConclusionWe propose that oxidative stress induces somatic mutations in neurons. When this process stochastically occurs in DNA repair genes, it facilitates the accumulation of SNVs in cancer‐related genes. This would lead to a tumor‐like process triggering NT followed by delayed neuronal degeneration (Am. J. Pathol. 2010;177:15‐20), as previously shown in vitro (Sci. Rep. 2018;8:14316). This mechanism likely participates in the etiology of neurodegenerative diseases including AD. E2F4DN prevents pathological NT likely due to its capacity to regulate oxidative stress response genes even under stressful conditions.

Integrative DNA methylome and transcriptome analysis reveals DNA adenine methylation is involved in Salmonella enterica Typhimurium response to oxidative stress.

Salmonella could survive and replicate in macrophages, where it encounters multiple stresses. Deficiency of a DNA adenine methyltransferase impairs the survival of Salmonella enterica serovar Typhimurium (S. Typhimurium) in hydrogen peroxide. To investigate whether DNA methylation is involved in the expression of oxidative stress-responsive genes, we combined RNA-seq and single-molecule real-time sequencing to integrate transcriptome and methylome analysis. Here, we show that (i) the entire amount of m6A GATC remains stable during oxidative stress; (ii) no significant association is observed between DNA methylation and transcription level in most genes; (iii) coincidence of level change between transcription and m6A GATC in the regulatory regions is identified in 49 genes under oxidative stress. Some of them are known to contribute to bacterial defenses against oxidative stress through reducing H2O2 levels, directing aberrant protein product degradation and inducing outer membrane protein expression. Specifically, the transcription level of ahpCF is negatively correlated to the m6A GATC level in its regulatory region. The transcription of smpB is elevated along with the decrease in m6A level at position 2,879,954 on the minus strand. In contrast, mRNA levels of STM14_2773 and ycfR are positively correlated with m6A GATC content in their regulatory regions. Highly stable DNA methylome and coupled change of m6A GATC with gene expression in specific positions suggest that DNA methylation homeostasis at genome-wide and plasticity in specific regions are crucial for bacterial response to oxidative stress. These findings provide new insights into the epigenetic regulatory mechanisms of gene expression in S. Typhimurium in the host microenvironment.IMPORTANCEThe intracellular pathogen Salmonella enterica serovar Typhimurium (S. Typhimurium) comes across a wide variety of stresses from entry to dissemination, such as reactive oxygen species. To adapt itself to oxidative stress, Salmonella must adopt various and complex strategies. In this study, we revealed that DNA adenine methyltransferase was essential for S. Typhimurium to survive in hydrogen peroxide. We then screened out oxidative stress-responsive genes that were potentially regulated by DNA methylation in S. Typhimurium. Our results show that the DNA methylome is highly stable throughout the genome, and the coupled change of m6A GATC with gene expression is identified in only a few positions, which suggests the complexity of the DNA methylation and gene expression regulation networks. The results may shed light on our understanding of m6A-mediated gene expression regulation in bacteria.

Divergence of TORC1-mediated stress response leads to novel acquired stress resistance in a pathogenic yeast.

Acquired stress resistance (ASR) enables organisms to prepare for environmental changes that occur after an initial stressor. However, the genetic basis for ASR and how the underlying network evolved remain poorly understood. In this study, we discovered that a short phosphate starvation induces oxidative stress response (OSR) genes in the pathogenic yeast C. glabrata and protects it against a severe H2O2 stress; the same treatment, however, provides little benefit in the low pathogenic-potential relative, S. cerevisiae. This ASR involves the same transcription factors (TFs) as the OSR, but with different combinatorial logics. We show that Target-of-Rapamycin Complex 1 (TORC1) is differentially inhibited by phosphate starvation in the two species and contributes to the ASR via its proximal effector, Sch9. Therefore, evolution of the phosphate starvation-induced ASR involves the rewiring of TORC1's response to phosphate limitation and the repurposing of TF-target gene networks for the OSR using new regulatory logics.

Oxidative stress is involved in immunosuppression and macrophage regulation in glioblastoma

Oxidative stress dually affected cancer progression, while its effect on glioblastomas remained unclear. Herein, we clustered the multicenter glioblastoma cohorts based on the oxidative-stress-responsive genes (OSS) expression. We found that cluster 2 with high OSS levels suffered a worse prognosis. Functional analyses and immune-related analyses results exhibited that M2-like pro-tumoral macrophages and neutrophils were enriched in cluster 2, while Natural killer cells' infiltration was decreased. The increased M2-like pro-tumoral macrophages in cluster 2 was confirmed by immunofluorescence. An integrated single-cell analysis validated the malignant features of cluster 2 neoplastic cells and discovered their crosstalk with M2-like pro-tumoral macrophages. Moreover, we observed that SOD3 knockdown might decrease the M2-like pro-tumoral transformation of macrophage in vitro and in vivo. Comprehensively, we revealed oxidative stress' prognostic and immunosuppressive potential in glioblastoma and discovered SOD3's potential role in regulating macrophage M2-like pro-tumoral transformation.

Kluyveromyces marxianus MTCC 1389 Augments Multi-stress Tolerance After Adaptation to Ethanol Stress.

During fermentation, yeast cells undergo various stresses that inhibit cell growth and ethanol production. Therefore, the ability to tolerate multiple stresses during fermentation is one of the important characteristics for yeast cells that can be used for commercial ethanol production. In the present study, we evaluated the multi-stress tolerance of parent and ethanol adapted Kluyveromyces marxianus MTCC1389 and their relative gene expression analysis. Multi-stress tolerance was confirmed by determining its cell viability, growth, and spot assay under oxidative, osmotic, thermal, and ethanol stress. During oxidative (0.8% H2O2) and osmotic stress (2M NaCl), there was significant cell viability of 90% and 50%, respectively, by adapted strain. On the other hand, under 45°C of thermal stress, the adapted strain was 80% viable while the parent strain was 60%. In gene expression analysis, the ethanol stress responsive gene ETP1 was significantly upregulated by 3.5 folds, the osmotic stress gene SLN1 was expressed by 3 folds, and the thermal stress responsive gene MSN2 was expressed by 7 folds. This study shows adaptive evolution for ethanol stress can develop other stress tolerances by changing relative gene expression of osmotic, oxidative, and thermal stress responsive genes.

Aqueous assembly of AgNPs with camellia seed cake polyphenols and its application as a postharvest anti-Penicillium digitatum agent via increasing reactive oxygen species generation

In this study, we developed a method for synthesizing silver nanoparticles (AgNPs) using aqueous assembly assay and anchoring them with camellia seed cake polyphenols (CPs). Zeta potential analysis demonstrated a higher binding affinity of CP-AgNPs to Penicillium digitatum, which could be attributed to the interaction between the hydroxyl group of CP-AgNPs and the polysaccharide present on the fungal cell wall. Compared to AgNPs, the CP-AgNPs outperformed conventional AgNPs in antifungal activity against P. digitatum. The mechanism underlying this antimicrobial effect involves raising the level of oxidative stress by regulating the expression levels of oxidative stress response genes. In addition, CP-AgNPs/CS showed highly effective in reducing citrus decay levels during chamber storage. In conclusion, the use of CPs as anchoring agent in the in-situ aqueous assembly of CP-AgNPs improved their biocompatibility and antimicrobial properties. CP-AgNPs hold great promise for applications in fruit preservation, especially citrus preservation.