Identification and validation of hub genes for diabetic retinopathy

Background Diabetic retinopathy (DR) is characterized by a gradually progressive alteration in the retinal microvasculature that leads to middle-aged adult acquired persistent blindness. Limited research has been conducted on DR pathogenesis at the gene level. Thus, we aimed to reveal novel key genes that might be associated with DR formation via a bioinformatics analysis. Methods The GSE53257 dataset from the Gene Expression Omnibus was downloaded for gene co-expression analysis. We identified significant gene modules via the Weighted Gene Co-expression Network Analysis, which was conducted by the Protein-Protein Interaction (PPI) Network via Cytoscape and from this we screened for key genes and gene sets for particular functional and pathway-specific enrichments. The hub gene expression was verified by real-time PCR in DR rats modeling and an external database. Results Two significant gene modules were identified. Significant key genes were predominantly associated with mitochondrial function, fatty acid oxidation and oxidative stress. Among all key genes analyzed, six up-regulated genes (i.e., SLC25A33, NDUFS1, MRPS23, CYB5R1, MECR, and MRPL15) were highly and significantly relevant in the context of DR formation. The PCR results showed that SLC25A33 and NDUFS1 expression were increased in DR rats modeling group. Conclusion Gene co-expression network analysis highlights the importance of mitochondria and oxidative stress in the pathophysiology of DR. DR co-expressing gene module was constructed and key genes were identified, and both SLC25A33 and NDUFS1 may serve as potential biomarker and therapeutic target for DR.

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Targeting ROS/NF-κB sigaling pathway by the seedless black Vitis vinifera polyphenols in CCl4-intoxicated kidney, lung, brain, and spleen in rats

Scientific Reports ◽

10.1038/s41598-021-96008-0 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Noha H. Habashy ◽

Ahmad S. Kodous ◽

Marwa M. Abu-Serie

Keyword(s):

Oxidative Stress ◽

Gene Expression ◽

Vitis Vinifera ◽

Rat Kidney ◽

Environmental Pollutant ◽

Enhancing Effect ◽

Tnf Α ◽

Cox 2 ◽

Histopathological Studies ◽

And Oxidative Stress

AbstractCarbon tetrachloride (CCl4) is an abundant environmental pollutant that can generate free radicals and induce oxidative stress in different human and animal organs like the kidney, lung, brain, and spleen, causing toxicity. The present study evaluated the alleviative mechanism of the isolated polyphenolic fraction from seedless (pulp and skin) black Vitis vinifera (VVPF) on systemic oxidative and necroinflammatory stress in CCl4-intoxicated rats. Here, we found that the administration of VVPF to CCl4-intoxicated rats for ten days was obviously ameliorated the CCl4-induced systemic elevation in ROS, NO and TBARS levels, as well as MPO activity. Also, it upregulated the cellular activities of the enzymatic (SOD, and GPx) and non-enzymatic (TAC and GSH) antioxidants. Furthermore, the gene expression of the ROS-related necroinflammatory mediators (NF-κB, iNOS, COX-2, and TNF-α) in the kidney, brain, and spleen, as well as IL-1β, and IL-8 in the lung were greatly restored. The histopathological studies confirmed these biochemical results and showed a noticeable enhancing effect in the architecture of the studied organs after VVPF intake. Thus, this study indicated that VVPF had an alleviative effect on CCl4-induced necroinflammation and oxidative stress in rat kidney, lung, brain, and spleen via controlling the ROS/NF-κB pathway.

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Alteration of Gene Expression Profile in Niemann-Pick Type C Mice Correlates with Tissue Damage and Oxidative Stress

PLoS ONE ◽

10.1371/journal.pone.0028777 ◽

2011 ◽

Vol 6 (12) ◽

pp. e28777 ◽

Cited By ~ 45

Author(s):

Mary C. Vázquez ◽

Talía del Pozo ◽

Fermín A. Robledo ◽

Gonzalo Carrasco ◽

Leonardo Pavez ◽

...

Keyword(s):

Oxidative Stress ◽

Gene Expression ◽

Gene Expression Profile ◽

Expression Profile ◽

Tissue Damage ◽

Type C ◽

Niemann Pick ◽

And Oxidative Stress

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Gene expression and oxidative stress markers profile associated with toxic metals in patients with renal cell carcinoma

Molecular Biology Reports ◽

10.1007/s11033-021-06944-3 ◽

2021 ◽

Author(s):

Heba H. Tarabay ◽

Hassan Abol-Enein ◽

Amira Awadalla ◽

Wael I. Mortada ◽

A. F. Abdel-Aziz

Keyword(s):

Oxidative Stress ◽

Gene Expression ◽

Renal Cell Carcinoma ◽

Cell Carcinoma ◽

Toxic Metals ◽

Renal Cell ◽

Oxidative Stress Markers ◽

Stress Markers ◽

And Oxidative Stress

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Assessment of Human Skin Gene Expression by Different Blends of Plant Extracts with Implications to Periorbital Skin Aging

International Journal of Molecular Sciences ◽

10.3390/ijms19113349 ◽

2018 ◽

Vol 19 (11) ◽

pp. 3349 ◽

Cited By ~ 3

Author(s):

Jin Namkoong ◽

Dale Kern ◽

Helen Knaggs

Keyword(s):

Oxidative Stress ◽

Gene Expression ◽

Human Skin ◽

Barrier Function ◽

Skin Barrier ◽

Skin Aging ◽

Skin Barrier Function ◽

Oxidative Stress Biomarkers ◽

Stress Biomarkers ◽

And Oxidative Stress

Since the skin is the major protective barrier of the body, it is affected by intrinsic and extrinsic factors. Environmental influences such as ultraviolet (UV) irradiation, pollution or dry/cold air are involved in the generation of radical oxygen species (ROS) and impact skin aging and dermal health. Assessment of human skin gene expression and other biomarkers including epigenetic factors are used to evaluate the biological/molecular activities of key compounds in cosmetic formulas. The objective of this study was to quantify human gene expression when epidermal full-thickness skin equivalents were exposed to: (a) a mixture of betaine, pentylene glycol, Saccharomyces cerevisiae and Rhodiola rosea root extract (BlendE) for antioxidant, skin barrier function and oxidative stress (with hydrogen peroxide challenge); and (b) a mixture of Narcissus tazetta bulb extract and Schisandra chinensis fruit extract (BlendIP) for various biomarkers and microRNA analysis. For BlendE, several antioxidants, protective oxidative stress biomarkers and many skin barrier function parameters were significantly increased. When BlendE was evaluated, the negative impact of the hydrogen peroxide was significantly reduced for the matrix metalloproteinases (MMP 3 and MMP 12), the skin aging and oxidative stress biomarkers, namely FBN2, ANXA1 and HGF. When BlendIP was tested for cell proliferation and dermal structural components to enhance the integrity of the skin around the eyes: 8 growth factors, 7 signaling, 7 structural/barrier function and 7 oxidative stress biomarkers were significantly increased. Finally, when BlendIP was tested via real-time RT-PCR for microRNA expression: miR-146a, miR-22, miR155, miR16 and miR21 were all significantly increased over control levels. Therefore, human skin gene expression studies are important tools to assess active ingredient compounds such as plant extract blends to advance dermal hypotheses toward validating cosmetic formulations with botanical molecules.

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Gene Expression Profiles of Cultured Rat Cardiomyocytes (H9C2 Cells) in Response to Arsenic Trioxide at Subcytotoxic Level and Oxidative Stress

JOURNAL OF HEALTH SCIENCE ◽

10.1248/jhs.52.512 ◽

2006 ◽

Vol 52 (5) ◽

pp. 512-521 ◽

Cited By ~ 8

Author(s):

Eun-Jung Park ◽

Kwangsik Park

Keyword(s):

Oxidative Stress ◽

Gene Expression ◽

Arsenic Trioxide ◽

Expression Profiles ◽

Gene Expression Profiles ◽

H9c2 Cells ◽

Rat Cardiomyocytes ◽

And Oxidative Stress

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Simultaneous miRNA and mRNA Transcriptome Profiling of Differentiating Equine Satellite Cells Treated with Gamma-Oryzanol and Exposed to Hydrogen Peroxide

Nutrients ◽

10.3390/nu10121871 ◽

2018 ◽

Vol 10 (12) ◽

pp. 1871

Author(s):

Karolina Chodkowska ◽

Anna Ciecierska ◽

Kinga Majchrzak ◽

Piotr Ostaszewski ◽

Tomasz Sadkowski

Keyword(s):

Oxidative Stress ◽

Gene Expression ◽

Hydrogen Peroxide ◽

Cell Viability ◽

Satellite Cells ◽

Cell Damage ◽

Quantitative Polymerase Chain Reaction ◽

Mirna Gene ◽

Gamma Oryzanol ◽

And Oxidative Stress

Gamma-oryzanol (GO) is a popular supplement for performance horses, dogs, and humans. Previous studies indicated that GO supplementation decreases creatine kinase activity and lactate level after exercise and may affect oxidative stress in Thoroughbred horses. GO may change genes expression in equine satellite cells (ESC). The purpose of this study was to evaluate the effect of GO on miRNA, gene expression, oxidative stress, and cell damage and viability in differentiating ESC pretreated with hydrogen peroxide (H2O2). ESCs were obtained from a young horse’s skeletal muscle. ESCs were pre-incubated with GO (24 h) and then exposed to H2O2 for one hour. For the microRNA and gene expression assessment, the microarray technique was used. Identified miRNAs and genes were validated using real time-quantitative polymerase chain reaction. Several tests related to cell viability, cell damage, and oxidative stress were performed. The microarray analysis revealed differences in 17 miRNAs and 202 genes between GO-treated and control ESC. The tests related to apoptosis, cell viability, and oxidative stress showed that GO affects these processes to varying degrees. Our results suggest that GO can change miRNA and gene expression and may impact the processes involved in tissue repairing after an injury.

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Coumestrol mitigates retinal cell inflammation, apoptosis, and oxidative stress in a rat model of diabetic retinopathy via activation of SIRT1

Aging ◽

10.18632/aging.202467 ◽

2021 ◽

Author(s):

Yanchao Xu ◽

Yusong Zhang ◽

Hongwei Liang ◽

Xiaomeng Liu

Keyword(s):

Oxidative Stress ◽

Diabetic Retinopathy ◽

Rat Model ◽

Retinal Cell ◽

And Oxidative Stress

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The Identification of Stemness-Related Genes in the Risk of Head and Neck Squamous Cell Carcinoma

Frontiers in Oncology ◽

10.3389/fonc.2021.688545 ◽

2021 ◽

Vol 11 ◽

Author(s):

Guanying Feng ◽

Feifei Xue ◽

Yingzheng He ◽

Tianxiao Wang ◽

Hua Yuan

Keyword(s):

Gene Expression ◽

Squamous Cell Carcinoma ◽

Network Analysis ◽

Cell Carcinoma ◽

Head And Neck ◽

Risk Score ◽

Squamous Cell ◽

Neck Squamous Cell Carcinoma ◽

Potential Biomarker ◽

Score Model

ObjectivesThis study aimed to identify genes regulating cancer stemness of head and neck squamous cell carcinoma (HNSCC) and evaluate the ability of these genes to predict clinical outcomes.Materials and MethodsThe stemness index (mRNAsi) was obtained using a one-class logistic regression machine learning algorithm based on sequencing data of HNSCC patients. Stemness-related genes were identified by weighted gene co-expression network analysis and least absolute shrinkage and selection operator analysis (LASSO). The coefficient of LASSO was applied to construct a diagnostic risk score model. The Cancer Genome Atlas database, the Gene Expression Omnibus database, Oncomine database and the Human Protein Atlas database were used to validate the expression of key genes. Interaction network analysis was performed using String database and DisNor database. The Connectivity Map database was used to screen potential compounds. The expressions of stemness-related genes were validated using quantitative real‐time polymerase chain reaction (qRT‐PCR).ResultsTTK, KIF14, KIF18A and DLGAP5 were identified. Stemness-related genes were upregulated in HNSCC samples. The risk score model had a significant predictive ability. CDK inhibitor was the top hit of potential compounds.ConclusionStemness-related gene expression profiles may be a potential biomarker for HNSCC.

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