Oxidative Stress-related Genes Research Articles

Retracted: The Risk Model Based on the Three Oxidative Stress-Related Genes Evaluates the Prognosis of LAC Patients.

[This retracts the article DOI: 10.1155/2022/4022896.].

Production with Fermentation Culture and Antioxidant Activity of Polysaccharides from Morchella esculenta

Morchella esculenta is a precious edible and medicinal fungus rich in protein, polysaccharides, polyphenols, amino acids, triterpenes, and other active components. In this study, MS-1 was isolated from the fruiting body of M. esculenta. Through conducting single-factor experiments and the response surface analysis of the culture conditions, the optimal culture components of an M. esculenta fermentation broth for extracellular polysaccharide production were determined, namely, 3.7% glucose, 2% yeast extract, and 0.15% sodium chloride. The polysaccharides MSF and MSL were extracted from the fruiting body of M. esculenta and the fermentation broth, respectively, and analyzed with gel permeation chromatography (GPC), monosaccharide composition, scanning electron microscopy (SEM), Fourier-transform infrared spectroscopy (FTIR), thermogravimetric analysis (TGA), and in vivo and in vitro antioxidant and anti-inflammatory activity analyses. The research results show that the calculated MW of MSF is 2.34 × 105 Da, and the calculated MW of MSL is 1.40 × 105 Da. MSF is composed of three monosaccharides: D-galactose, D-glucose, and D-mannose (molar ratio of 4.34:90.22:5.45). MSL consists of five monosaccharides: D-arabinose, D-galactose, D-glucose, D-mannose, and glucuronic acid (molar ratio of 0.31:14.71:13.03:71.43:0.53). The in vitro antioxidant test results show that MSF and MSL both have significant antioxidant activities. Activity experiments on MSF and MSL in zebrafish showed that MSF and MSL have significant repair effects on the oxidative damage caused by metronidazole in zebrafish embryos, and there were significant changes in the transcriptional activity levels of the oxidative stress-related genes SOD, Keap1, and Nrf2. Therefore, the polysaccharides MSF and MSL from MS-1 can be used as important raw materials for functional foods and drugs.

Fetal programming effect of rumen-protected methionine on primiparous Angus × Simmental offspring's performance and skeletal muscle gene expression.

Primiparous Angus × Simmental dams (n = 22) with an average body weight (BW) of 449 ± 32kg of BW were divided based on two nutritional treatments: control (CTRL) and rumen-protected methionine (RPM). The control group received bermudagrass hay, corn gluten, and soybean hulls pellets supplementation (base diet); whereas the RPM group received the base diet in addition to 0.07% of DM of RPM at a fixed rate during the last trimester of gestation and the first ~80d of lactation, in which calves (n = 17) were early weaned. Only male calves were included in this study. After weaning, calves born to RPM dams also received RPM from weaning (day 1) to day 100. Blood sampling and skeletal muscle biopsies for subsequent quantitative polymerase chain reaction (PCR) analysis were conducted on days 1, 25, 50, and 100 on calves. Quantitative PCR data were analyzed using GLIMMIX, and blood metabolites concentrations, BW, and body condition score (BCS) were analyzed using the MIXED procedure of SAS. There was no difference in maternal BW and BCS between treatments. Glucose and blood metabolites that served as biomarkers for liver health (e.g., aspartate transaminase, albumin, alkaline phosphatase, and alanine transaminase) were in the normal levels for all calves (P > 0.40). Calves in the RPM group had a greater expression of adipogenic genes (e.g., PPARG, LPL, and CEBPD) at day 100 compared with CTRL (P < 0.01). In addition, DNA methylation (DNMT1) and oxidative stress-related genes (SOD2 and NOS3) in the RPM group were upregulated at day 100 compared with CTRL (P < 0.01). These results may suggest that calves born to primiparous dams exposed to RPM supplementation are more prone to develop greater adipose tissue than CTRL calves. Furthermore, RPM supplementation may improve methylation processes, as shown by the upregulation of DNMT1. The results shown in our study aim at expanding the knowledge on fetal programming and early-life growth and development of beef cattle under supplementation with RPM.

Prognostic value of oxidative stress-related genes in colorectal cancer and its correlation with tumor immunity

Oxidative stress (OS) plays an essential role in chronic diseases such as colorectal cancer (CRC). In this study, we aimed to explore the relation between oxidative stress-related genes and CRC prognosis and their involvement in the immune microenvironment. Totally 101 OS-related genes were selected from the MsigDB database. Then, univariate Cox regression was used to explore the prognostic value of the selected genes correlated with the CRC patient survival in the TCGA database. A total of 9 prognostic OS-related genes in CRC were identified. Based on consensus clustering, CRC patients were then categorized into two molecular subtypes. A prognostic risk model containing 8 genes was established using Lasso regression, and CRC patients were divided into high or low-risk groups based on the median risk scores. The predictive value of the 8 genes in CRC prognosis was validated using ROC curves, which indicate that CTNNB1, STK25, RNF112, SFPQ, MMP3, and NOL3 were promising prognostic biomarkers in CRC. Furthermore, the immune cell infiltration levels in different risk groups or CRC subtypes were analyzed. We found that the high-risk or C1 subtype had immunosuppressive microenvironment, which might explain the unfavorable prognosis in the two groups of CRC patients. Additionally, functional experiments were conducted to investigate the effects of OS-related genes on CRC cell proliferation, stemness, and apoptosis. We found that CTNNB1, HSPB1, MMP3, and NOL3 were upregulated in CRC tissues and cells. Knockdown of CTNNB1, HSPB1, MMP3, and NOL3 significantly suppressed CRC cell proliferation, stemness and facilitated CRC cell apoptosis. In conclusion, we established prognostic CRC subtypes and an eight-gene risk model, which may provide novel prognostic indicators and benefit the design of individualized therapeutic strategies for CRC patients.

Bioinformatics analysis of oxidative stress genes in the pathogenesis of ulcerative colitis based on a competing endogenous RNA regulatory network.

Ulcerative colitis (UC) is a common chronic disease associated with inflammation and oxidative stress. This study aimed to construct a long noncoding RNA (lncRNA)-microRNA (miRNA)-messenger RNA (mRNA) network based on bioinformatics analysis and to explore oxidative stress-related genes underlying the pathogenesis of UC. The GSE75214, GSE48959, and GSE114603 datasets were downloaded from the Gene Expression Omnibus database. Following differentially expressed (DE) analysis, the regulatory relationships among these DERNAs were identified through miRDB, miRTarBase, and TargetScan; then, the lncRNA-miRNA-mRNA network was established. The Molecular Signatures Database (MSigDB) was used to search oxidative stress-related genes. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses were performed for functional annotation and enrichment analyses. Based on the drug gene interaction database DGIdb, drugs that interact with oxidative stress-associated genes were explored. A dextran sulfate sodium (DSS)-induced UC mouse model was used for experimental validation. A total of 30 DE-lncRNAs, 3 DE-miRNAs, and 19 DE-mRNAs were used to construct a lncRNA-miRNA-mRNA network. By comparing these 19 DE-mRNAs with oxidative stress-related genes in MSigDB, three oxidative stress-related genes (CAV1, SLC7A11, and SLC7A5) were found in the 19 DEM sets, which were all negatively associated with miR-194. GO and KEGG analyses showed that CAV1, SLC7A11, and SLC7A5 were associated with immune inflammation and steroid hormone synthesis. In animal experiments, the results showed that dexamethasone, a well-known glucocorticoid drug, could significantly decrease the expression of CAV1, SLC7A11, and SLC7A5 as well as improve UC histology, restore antioxidant activities, inhibit inflammation, and decrease myeloperoxidase activity. SLC7A5 was identified as a representative gene associated with glucocorticoid therapy resistance and thus may be a new therapeutic target for the treatment of UC in the clinic.

Identification of histone acetylation modification sites in the striatum of subchronically manganese-exposed rats.

Aim: To explore the specific histone acetylation sites and oxidative stress-related genes that are associated with the pathogenesis of manganese toxicity. Methods: We employed liquid chromatography-tandem mass spectrometry and bioinformatics analysis to identify acetylated proteins in the striatum of subchronic manganese-intoxicated rats. Results: We identified a total of 12 differentially modified histone acetylation sites: H3K9ac, H3K14ac, H3K18ac, H3K56ac and H3K79ac were upregulated and H3K27ac, H3K36ac, H4K91ac, H4K79ac, H4K31ac, H2BK16ac and H2BK20ac were downregulated. Additionally, we found that CAT, SOD1 and SOD2 might be epigenetically regulated and involved in the pathogenesis of manganism. Conclusion: This study identified histone acetylation sites and oxidative stress-related genes associated with the pathogenesis of manganese toxicity, and these findings are useful in the search for potential epigenetic targets for manganese toxicity.

Effect of cinnamaldehyde on Rhizopus stolonifer and on the conservation of sweet potato

Abstract Objectives Rhizopus stolonifer, which causes soft rot of sweet potato, has resulted in substantial loss of economy postharvest. Materials and Methods The antifungal effect and mechanism of cinnamaldehyde (CIN) against R. stolonifer were explored by biochemical analysis and RNA-sequencing in this research, and the edible quality of CIN-treated sweet potato was evaluated. Results The results showed that CIN inhibited the growth of R. stolonifer and reduced the incidence of soft rot in sweet potato at a minimum inhibitory concentration of 1000 μL/L. The damage of the cell walls of R. stolonifer by CIN was associated with the upregulation of CHT1. Cytosolic leakage and malondialdehyde content increased following CIN-treatment, which was correlated with increased reactive oxygen species levels and decreased catalase activity. Upregulation of ERG genes and oxidative stress-related genes following CIN treatment was associated with impaired cell membrane integrity. The mitochondrial structure of R. stolonifer was damaged by CIN treatment resulting in decreased respiration rates and ATP production, which was correlated with lower expression levels of IDH1, COX4, and QCR7. Conclusions Our research suggests that the inhibition of CIN on R. stolonifer was related to the disruption of its normal gene expression network, and CIN maintained the nutritional and edible quality of sweet potato. This study provides valuable insights into the antifungal mechanism of CIN on R. stolonifer and the maintenance of root quality, which contributes to the efficient use of CIN for controlling soft rot in sweet potato.

An Oxidative Stress-Related Prognostic Signature Predicts Treatment Response and Outcomes for Hepatocellular Carcinoma After Transarterial Chemoembolization.

Oxidative stress plays a critical role in promoting tumor resistance to hypoxia and chemotherapeutic drugs. However, the prognostic role of oxidative stress-related genes (OSRGs) in hepatocellular carcinoma (HCC) treated with transarterial chemoembolization (TACE) has not been fully explored. We used transcriptome data from the GSE104580 cohort containing patients marked as responders or nonresponders to TACE therapy to identify differentially expressed OSRGs associated with TACE response (TR-OSRGs). We created a TR-OSRG prognostic signature based on TR-OSRGs using least absolute shrinkage and selection operator Cox and stepwise Cox regression analyses in a training cohort of patients with HCC (TCGA-LIHC). We verified this prognostic signature in two external cohorts of patients who received TACE for HCC (GSE14520-TACE and ZS-TACE-37). Finally, we constructed a prognostic nomogram model for predicting survival probability of patients with HCC based on Cox regression analysis. The TR-OSRG prognostic signature was created and shown to be a robust independent prognostic factor for treatment response and outcomes for HCC after TACE therapy. Risk scores based on this signature correlated with tumor stage and grade. Tumor samples from patients with higher risk scores exhibited more infiltration of immune cells and significantly increased expression of immune checkpoint genes. We also developed a nomogram for patients with HCC based on the TR-OSRG prognostic signature and clinical parameters; this nomogram was a useful quantitative analysis tool for predicting patient survival. The TR-OSRGs signature exhibited good performance in predicting treatment response and outcomes in patients with HCC treated with TACE.

Identification of oxidative stress-related genes associated with immune cells in Aortic Valve Stenosis based on bioinformatics analysis.

Aortic valve stenosis (AS) is the most common clinical valvular heart disease. Without effective pharmaceutical therapy at present, identifying effective therapeutic targets is critical. However, the pathological and molecular mechanisms of aortic stenosis are complex, including inflammatory infiltration, oxidative stress and so on. In this study, we investigated how oxidative stress interacts with immune cell infiltration in aortic stenosis using bioinformatics analysis, and provide a better understanding of aortic valve stenosis at the pathophysiologic level. After obtaining the datasets, including GSE153555, GSE51472 and GSE12644, from the Gene Expression Omnibus (GEO) database, the package 'limma' was applied to identify the differentially expressed genes (DEGs) in GSE153555. The GeneCards database searched for oxidative stress-related genes. We evaluated the expression of 22 immune cells using Cibersort. Clustering differentially expressed genes into different modules via Weighted gene correlation network analysis (WGCNA) and exploring the relationship among modules and immune cell types. The genes in modules intersected with oxidative stress-related genes to find oxidative stress genes related to immune infiltration. Finally, the GSE51472 and GSE12644 datasets were used to initially verify oxidative stress-related genes in aortic valve stenosis. A total of 1213 differentially expressed genes were identified in the GSE153555 dataset, and 279 of them were oxidative stress-related genes. Increased infiltration of B cell navie and Macrophages M1 in aortic stenosis was found. Using WGCNA, we clustered 15 modules. The brown module was identified as the most significant template positively correlated with T-cell regulatory Treg, and the magenta module was identified as a critical module associated with M1 macrophages with the highest negative correlation coefficient. The results verified by other datasets showed that in comparison to normal people, the aortic stenosis patients exhibited dramatically high IGFBP2 and SPHK1 expression. Both IGFBP2 and SPHK1 may be significantly involved in the mechanism of aortic stenosis pathophysiologically and can be used for aortic stenosis early detection, therapy, and therapeutic targets.

A novel oxidative stress-related gene signature as an indicator of prognosis and immunotherapy responses in HNSCC.

To identify molecular subtypes of oxidative stress-related genes in head and neck squamous cell carcinoma (HNSCC) and to construct a scoring model of oxidative stress-related genes. R language based scRNA-seq and bulk RNA-seq analyses were used to identify molecular isoforms of oxidative stress-related genes in HNSCC. An oxidative stress-related gene scoring (OSRS) model was constructed, which were verified through online data and immunohistochemical staining of clinical samples. Using TCGA-HNSCC datasets, nine predictive genes for overall patient survival, rarely reported in previous similar studies, were screened. AREG and CES1 were identified as prognostic risk factors. CSTA, FDCSP, JCHAIN, IFFO2, PGLYRP4, SPOCK2 and SPINK6 were identified as prognostic factors. Collectively, all genes formed a prognostic risk signature model for oxidative stress in HNSCC, which were validated in GSE41613, GSE103322 and PRJEB23709 datasets. Immunohistochemical staining of SPINK6 in nasopharyngeal cancer samples validated the gene panel. Subsequent analysis indicated that subgroups of the oxidative stress prognostic signature played important roles during cellular communication, the immune microenvironment, the differential activation of transcription factors, oxidative stress and immunotherapeutic responses. The risk model might predict HNSCC prognosis and immunotherapeutic responses.

Comprehensive analysis of biological landscape of oxidative stress-related genes in diabetic erectile dysfunction.

Oxidative stress plays a pivotal role in the pathogenesis of diabetic erectile dysfunction, while specific mechanisms have not been illuminated. The study aims to reveal the genetic expression patterns of oxidative stress in diabetic erectile dysfunction. Transcriptome data of diabetic erectile dysfunction and oxidative stress-related genes (OSRGs) in the Gene Expression Omnibus database were downloaded and analyzed based on differential expression. Functional enrichment analyses were conducted to clarify the biological functions. A protein interaction framework was established, and significant gene profiles were validated in the cavernous endothelial cells, clinical patients, and rat models. A miRNA-OSRGs network was predicted and validated. The results were analyzed using Student's t-test. The analysis screened 203 differentially expressed OSRGs (p < 0.05), which had a close association with oxidoreductase activities, glutathione metabolism, and autophagy. A four-gene signature comprised of EPS8L2 (p = 0.044), GSTA3 (p = 0.015), LOX (p < 0.001) and MGST1 (p = 0.002) was well validated and regarded as the hub OSRGs. Compared with the control group, notable increases and decreases were observed in the expressions of GSTA3 (3.683 ± 0.636 vs. 0.416 ± 0.507) and LOX (2.104 ± 1.895 vs. 18.804 ± 2.751) in the validated diabetic erectile dysfunction group. The hub OSRGs-related miRNAs participated in smooth muscle cell proliferation. Besides, miR-125a-3p (p = 0.034) and miR-138-2-3p (p = 0.012) were validated as promising oxidative stress-related miRNA biomarkers. Our findings revealed the genetic alternations of oxidative stress in diabetic erectile dysfunction. These results will be instructive to explore the molecular landscape and the potential treatment for diabetic erectile dysfunction.

Synergistic toxicity induced by the co-exposure of tenuazonic acid and patulin in Caenorhabditis elegans: Daf-16 plays an important regulatory role

Tenuazonic acid (TeA) and patulin (PAT), as the naturally occurring mycotoxins with various toxic effects, are often detected in environment and food chain, has attracted more and more attention due to their widespread and high contaminations as well as the coexistence, which leads to potential human and animals’ risks. However, their combined toxicity has not been reported yet. In our study, C. elegans was used to evaluate the type of combined toxicity caused by TeA+PAT and its related mechanisms. The results showed that TeA and PAT can induce synergistic toxic effects based on Combination Index (CI) evaluation model (Chou-Talalay method), that is, the body length, brood size as well as the levels of ROS, CAT and ATP were significantly affected in TeA+PAT-treated group compared with those in TeA- or PAT-treated group. Besides, the expressions of oxidative (daf-2, daf-16, cyp-35a2, ctl-1, ctl-3, pmk-1, jnk-1, skn-1) and intestinal (fat-5, pod-2, egl-8, pkc-3, ajm-1, nhx-2) stress-related genes were disrupted, among which daf-16 displayed the most significant alternation. Further study on daf-16 gene defective C. elegans showed that the damages to the mutant nematodes were significantly attenuated. Since daf-2, daf-16, jnk-1 and pmk-1 are evolutionarily conserved, our findings could hint synergistic toxic effects of TeA+PAT on higher organisms.

Manganese induces oxidative damage in the hippocampus by regulating the expression of oxidative stress-related genes via modulation of H3K18 acetylation.

Prolonged exposure to manganese (Mn) contributes to hippocampal Mn accumulation, which leads to neurodegenerative diseases called manganese poisoning. However, the underlying molecular mechanisms remain unclear and there are no ideal biomarkers. Oxidative stress is the essential mechanisms of Mn-related neurotoxicity. Furthermore, histone acetylation has been identified as being engaged in the onset and development of neurodegenerative diseases. Therefore, the work aims to understand the molecular mechanisms of oxidative damage in the hippocampus due to Mn exposure from the aspect of histone acetylation modification and to assess whether H3K18 acetylation (H3K18ac) modification level in peripheral blood reflect Mn-induced oxidative damage in the hippocampus. Here, we randomly divided 60 male rats into four groups and injected them intraperitoneally with sterile pure water and MnCl2 ⋅4H2 O (5, 10, and 15 mg/kg) for 16 weeks, 5 days a week, once a day. The data confirmed that Mn exposure down-regulated superoxide dismutase activity and glutathione level as well as up-regulated malondialdehyde level in the hippocampus and plasma, and that there was a positive correlation between these indicators in the hippocampus and plasma. Besides, we noted that Mn treatment upregulated H3K18ac modification levels in the hippocampus and peripheral blood and that H3K18ac modification levels correlated with oxidative stress. Further studies demonstrated that Mn treatment decreased the amounts of H3K18ac enrichment in the manganese superoxide dismutase (SOD2) and glutathione transferase omega 1 (GSTO1) gene promoter regions, contributing to oxidative damage in the hippocampus. In short, our results demonstrate that Mn induces oxidative damage in the hippocampus by inhibiting the expression of SOD2 and GSTO1 genes via modulation of H3K18ac. In assessing Mn-induced hippocampal neurotoxicity, oxidative damage in plasma may reflect hippocampal oxidative damage in Mn-exposed groups.

Strigolactone-mediated amelioration of salinity stress in bread wheat: Insights from phytochemical and ion channels related genes expression analyses

Foliar application of growth regulators seems to alleviate the adverse effects of abiotic stresses in plants through different mechanisms such as antioxidative and gene expression regulation. As an important abiotic stress, salinity has an enormous negative impact on crop plants such as bread wheat. In the present study, exogenous strigolactone (GR24) was considered for its potential stress-mitigating effect in two contrasting wheats cultivars (‘Arta’ and ‘Karchia’) grown under 2,053,100 mM NaCl stress (10 dS m−1). Yield-related traits, oxidative (APX, POX, CAT, H2O2, MDA, GB and Proline), ionic indices (Na+ and K+ content in leaf and root), and the expression of a selected set of oxidative stress related genes (TaAPX, TaGPX, TaP5CS, TaNHX2, TaSOS1, TaHAK, TaAKT2 and TaHKT2;1) were surveyed in the flowering stage. Strigolactone application (10 μM) had a significant effect on the induction and improvement of biochemical and ionic features such as reducing the electrolyte leakage, H2O2 and MDA or increasing the grain yield, total protein, proline, GB and antioxidant enzymes (APX, POX) activity, of salinity-stressed plants. The gene expression analysis with real-time PCR showed transcriptional variation of selected genes in response to salt stress and GR24. Improved homeostasis in Na+ and K+ and their ratio was found to be correlated with the expression of the antiporter genes and the consequent reduction of ion toxicity. The findings of this study can improve our knowledge about complex mechanism of strigolactone plant hormone during salt stress in crop plans to mitigation of salinity stress.

Seven oxidative stress-related genes predict the prognosis of hepatocellular carcinoma.

Predicting the prognosis of hepatocellular carcinoma (HCC) is a major medical challenge and of guiding significance for treatment. This study explored the actual relevance of RNA expression in predicting HCC prognosis. Cox's multiple regression was used to establish a risk score staging classification and to predict the HCC patients' prognosis on the basis of data in the Cancer Genome Atlas (TCGA). We screened seven gene biomarkers related to the prognosis of HCC from the perspective of oxidative stress, including Alpha-Enolase 1(ENO1), N-myc downstream-regulated gene 1 (NDRG1), nucleophosmin (NPM1), metallothionein-3, H2A histone family member X, Thioredoxin reductase 1 (TXNRD1) and interleukin 33 (IL-33). Among them we measured the expression of ENO1, NGDP1, NPM1, TXNRD1 and IL-33 to investigate the reliability of the multi-index prediction. The first four markers' expressions increased successively in the paracellular tissues, the hepatocellular carcinoma samples (from patients with better prognosis) and the hepatocellular carcinoma samples (from patients with poor prognosis), while IL-33 showed the opposite trend. The seven genes increased the sensitivity and specificity of the predictive model, resulting in a significant increase in overall confidence. Compared with the patients with higher-risk scores, the survival rates with lower-risk scores are significantly increased. Risk score is more accurate in predicting the prognosis HCC patients than other clinical factors. In conclusion, we use the Cox regression model to identify seven oxidative stress-related genes, investigate the reliability of the multi-index prediction, and develop a risk staging model for predicting the prognosis of HCC patients and guiding precise treatment strategy.

Evaluation of genes and molecular pathways involved in the oxidative stress in preeclampsia: A systems biology approach

BackgroundOxidative stress is one of the main factors in the pathogenesis of preeclampsia (PE). Many genes and molecular pathways play a role in its occurrence, however, so far no study has been conducted with a bioinformatics approach to identify genes. Therefore, we investigated this issue in this study. Material and methodsIn this study, microarray data (GSE30186 dataset) sourced from the Gene Expression Omnibus (GEO) database were analyzed. This dataset consists of 12 placental tissue samples; six was obtained from normal individuals and six from patients diagnosed with preeclampsia. Differential gene analysis was conducted with the LIMMA package in R software using the following criteria 1: absolute log fold change >1, 2: adjusted P-value <0.05. Oxidative stress-related genes were sourced from Genecard, and the overlap with DEGs was extracted via a Venn diagram. Gene ontology and KEGG pathway analysis were performed using Enrichr software. A protein-protein interaction (PPI) network was designed using the STRING database and visualized with Cytoscape. Hub genes were identified using various methods. Associations between hub genes, transcription factors, and microRNAs were assessed using the miRTarBase and TRRUST databases. Hub gene validation was conducted on the GSE75010 dataset, which comprises 80 preeclampsia and 77 control placenta samples. Differential expression analysis was performed using a two-sample t-test (P < 0.05); boxplots were also generated for visualization. ResultAnalysis of the GSE30186 dataset identified 717 DEGs in PE compared to normal samples with 448 upregulated and 269 downregulated DEGs. To investigate oxidative stress in PE, a list of 391 genes related to oxidative stress was initially collected from Genecard. Subsequently, an intersection was identified between these oxidative stress-related genes and DEGs, resulting in the identification of 26 shared genes between the DEGs and the oxidative stress-related genes. PPI network and hub gene analyses identified 8 hub genes, including STAT1, SERPINE1, CXCL8, and FN1. According to the results, hsa-miR-146a-5p has the most interactions with hub genes among miRNAs, and RELA has the most interactions among TFs. Finally, validation using the GSE75010 dataset confirmed significant differential expression of SERPINE1, CXCL8, and FN1 in PE; it suggested cited genes as hub genes, while STAT1 did not exhibit significant differences. ConclusionIdentifying pathways related to the expression of hub genes can be useful in designing appropriate treatment strategies. On the other hand, examining the pathways activated by hub genes can be effective in preventing ROS production.

Exploration of the role of oxidative stress-related genes in LPS-induced acute lung injury via bioinformatics and experimental studies

During the progression of acute lung injury (ALI), oxidative stress and inflammatory responses always promote each other. The datasets analyzed in this research were acquired from the Gene Expression Omnibus (GEO) database. The Weighted Gene Co-expression Network Analysis (WGCNA) and limma package were used to obtain the ALI-related genes (ALIRGs) and differentially expressed genes (DEGs), respectively. In total, two biological markers (Gch1 and Tnfaip3) related to oxidative stress were identified by machine learning algorithms, Receiver Operator Characteristic (ROC), and differential expression analyses. The area under the curve (AUC) value of biological markers was greater than 0.9, indicating an excellent power to distinguish between ALI and control groups. Moreover, 15 differential immune cells were selected between the ALI and control samples, and they were correlated to biological markers. The transcription factor (TF)-microRNA (miRNA)-Target network was constructed to explore the potential regulatory mechanisms. Finally, based on the quantitative reverse transcription polymerase chain reaction (qRT-PCR), the expression of Gch1 and Tnfaip3 was significantly higher in ALI lung tissue than in healthy controls. In conclusion, the differences in expression profiles between ALI and normal controls were found, and two biological markers were identified, providing a research basis for further understanding the pathogenesis of ALI.

Dimethyl Bisphenolate Ameliorates Carbon Tetrachloride-Induced Liver Injury by Regulating Oxidative Stress-Related Genes.

Liver disease accounts for millions of deaths per year all over the world due to complications from cirrhosis and liver injury. In this study, a novel compound, dimethyl bisphenolate (DMB), was synthesized to investigate its role in ameliorating carbon tetrachloride (CCl4)-induced liver injury through the regulation of oxidative stress-related genes. The structure of DMB was confirmed based on its hydrogen spectrum and mass spectrometry. DMB significantly reduced the high levels of ALT, AST, DBIL, TBIL, ALP, and LDH in a dose-dependent manner in the sera of CCl4-treated rats. The protective effects of DMB on biochemical indicators were similar to those of silymarin. The ROS fluorescence intensity increased in CCl4-treated cells but significantly weakened in DMB-treated cells compared with the controls. DMB significantly increased the content of oxidative stress-related GSH, Nrf2, and GCLC dose-dependently but reduced MDA levels in CCl4-treated cells or the liver tissues of CCl4-treated rats. Moreover, DMB treatment decreased the expression levels of P53 and Bax but increased those of Bcl2. In summary, DMB demonstrated protective effects on CCl4-induced liver injury by regulating oxidative stress-related genes.

Differential cardiomyocyte transcriptomic remodeling during in vitro Trypanosoma cruzi infection using laboratory strains provides implications on pathogenic host responses

BackgroundChagas disease can lead to life-threatening cardiac manifestations. Regional factors, including genetic characteristics of circulating Trypanosoma cruzi (T. cruzi), have attracted attention as likely determinants of Chagas disease phenotypic expression and Chagas cardiomyopathy (CCM) progression. Our objective was to elucidate the differential transcriptomic signatures of cardiomyocytes resulting from infection with genetically discrete T. cruzi strains and explore their relationships with CCM pathogenesis and progression.MethodsHL-1 rodent cardiomyocytes were infected with T. cruzi trypomastigotes of the Colombian, Y, or Tulahuen strain. RNA was serially isolated post-infection for microarray analysis. Enrichment analyses of differentially expressed genes (fold-change ≥ 2 or ≤ 0.5) highlighted over-represented biological pathways. Intracellular levels of reactive oxygen species (ROS) were compared between T. cruzi-infected and non-infected HL-1 cardiomyocytes.ResultsWe found that oxidative stress-related gene ontology terms (GO terms), ‘Hypertrophy model’, ‘Apoptosis’, and ‘MAPK signaling’ pathways (all with P < 0.01) were upregulated. ‘Glutathione and one-carbon metabolism’ pathway, and ‘Cellular nitrogen compound metabolic process’ GO term (all with P < 0.001) were upregulated exclusively in the cardiomyocytes infected with the Colombian/Y strains. Mean intracellular levels of ROS were significantly higher in the T. cruzi-infected cardiomyocytes compared to the non-infected (P < 0.0001).ConclusionsThe upregulation of oxidative stress-related and hypertrophic pathways constitutes the universal hallmarks of the cardiomyocyte response elicited by T. cruzi infection. Nitrogen metabolism upregulation and glutathione metabolism imbalance may implicate a relationship between nitrosative stress and poor oxygen radicals scavenging in the unique pathophysiology of Chagas cardiomyopathy.

Construction of a 5-gene prognostic signature based on oxidative stress related genes for predicting prognosis in osteosarcoma.

The understanding of the complex biological scenario of osteosarcoma will open the way to identifying new strategies for its treatment. Oxidative stress is a cancer-related biological scenario. At present, it is not clear the oxidative stress genes in affecting the prognosis and progression of osteosarcoma, the underlying mechanism as well as their impact on the classification of osteosarcoma subtypes. We selected samples and sequencing data from TARGET data set and GSE21257 data set, and downloaded oxidative stress related-genes (OSRGs) from MsigDB. Univariate Cox analysis of OSRG was conducted using TARGET data, and the prognostic OSRG was screened to conduct unsupervised clustering analysis to identify the molecular subtypes of osteosarcoma. Through least absolute shrinkage and selection operator (LASSO) regression analysis and COX regression analysis of differentially expressed genes (DEGs) between subgroups, a risk assessment system for osteosarcoma was developed. 45 prognosis-related OSRGs genes were acquired, and two molecular subtypes of osteosarcoma were clustered. C2 cluster displayed prolonged overall survival (OS) accompanied with high degree of immune infiltration and enriched immune pathways. While cell cycle related pathways were enriched in C2 cluster. Based on DEGs between subgroups and Lasso analysis, 5 hub genes (ZYX, GJA5, GAL, GRAMD1B, and CKMT2) were screened to establish a robust prognostic risk model independent of clinicopathological features. High-risk group had more patients with cancer metastasis and death as well as C1 subtype with poor prognosis. Low-risk group exhibited favorable OS and high immune infiltration status. Additionally, the risk assessment system was optimized by building decision tree and nomogram. This study defined two molecular subtypes of osteosarcoma with different prognosis and tumor immune microenvironment status based on the expression of OSRGs, and provided a new risk assessment system for the prognosis of osteosarcoma.