Lung cancer is the second most common cancer in the world. The aim of this study is to identify biomarkers for lung cancer that can aid in its diagnosis and treatment. The gene expression profiles from GEO database were analyzed by GEO2R to identify Differentially Expressed Genes (DEGs) and further analyzed using Cytoscape. The data was divided into two categories: non-treatment and treatment groups. A total of 407 DEGs (254 upregulated and 153 downregulated) and 259 DEGs (124 upregulated and 135 downregulated) were isolated for non-treatment and treatment studies respectively. The significant Gene Ontologies and pathways enriched with DEGS were identified using Cytoscape apps, BiNGO and ReactomeFIPlugIn, respectively. Hub genes based on network parameters - Degree, Closeness and Betweenness - were isolated using CytoHubba. In conclusion, DEGs identified in this study may play an important role in early diagnosis or as biomarkers of lung cancer.
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Transcriptomic Evidence That Switching from Tobacco to Electronic Cigarettes Does Not Reverse Damage to the Respiratory Epithelium
The health benefits of switching from tobacco to electronic cigarettes (ECs) are neither confirmed nor well characterized. To address this problem, we used RNA-seq analysis to compare the nasal epithelium transcriptome from the following groups (n = 3 for each group): (1) former smokers who completely switched to second generation ECs for at least 6 months, (2) current tobacco cigarette smokers (CS), and (3) non-smokers (NS). Group three included one former cigarette smoker. The nasal epithelial biopsies from the EC users vs. NS had a higher number of differentially expressed genes (DEGs) than biopsies from the CS vs. NS and CS vs. EC sets (1817 DEGs total for the EC vs. NS, 407 DEGs for the CS vs. NS, and 116 DEGs for the CS vs. EC comparison). In the EC vs. NS comparison, enriched gene ontology terms for the downregulated DEGs included cilium assembly and organization, whereas gene ontologies for upregulated DEGs included immune response, keratinization, and NADPH oxidase. Similarly, ontologies for cilium movement were enriched in the downregulated DEGs for the CS vs. NS group. Reactome pathway analysis gave similar results and also identified keratinization and cornified envelope in the upregulated DEGs in the EC vs. NS comparison. In the CS vs. NS comparison, the enriched Reactome pathways for upregulated DEGs included biological oxidations and several metabolic processes. Regulator effects identified for the EC vs. NS comparison were inflammatory response, cell movement of phagocytes and degranulation of phagocytes. Disease Ontology Sematic Enrichment analysis identified lung disease, mouth disease, periodontal disease and pulmonary fibrosis in the EC vs. NS comparison. Squamous metaplasia associated markers, keratin 10, keratin 13 and involucrin, were increased in the EC vs. NS comparison. Our transcriptomic analysis showed that gene expression profiles associated with EC use are not equivalent to those from non-smokers. EC use may interfere with airway epithelium recovery by promoting increased oxidative stress, inhibition of ciliogenesis, and maintaining an inflammatory response. These transcriptomic alterations may contribute to the progression of diseases with chronic EC use.
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- Award ID(s):
- 1661152
- NSF-PAR ID:
- 10351566
- Date Published:
- Journal Name:
- Toxics
- Volume:
- 10
- Issue:
- 7
- ISSN:
- 2305-6304
- Page Range / eLocation ID:
- 370
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
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Purpose To evaluate cardiovascular disease (CVD) risk factors among smokeless tobacco (ST) users. Exclusive ST users were compared to exclusive cigarette smokers and non-tobacco users.
Design Cross-sectional study
Sample Data were used from 16,336 adult males who participated in one of the National Health and Nutrition Examination Surveys (NHANES) from 2003 to 2018.
Measures Biochemically verified tobacco use, CVD risk factors (hypertension, cholesterol levels, BMI categories), physical activity, cotinine concentration, and sociodemographic variables.
Analysis Weighted analysis of the aggregate data was performed. ST users were compared with cigarette smokers and nontobacco users for their association with CVD risk factors. Associations were examined using univariate and multiple logistic regression with odds ratios (OR) and 95% confidence intervals (CI) reported.
Results Prevalence of exclusive ST use was 4.4% whereas, exclusive smoking was 22.2%. Among ST users, 36.2% were hypertensive, 24.5% had high cholesterol levels, and most of them were overweight (31.1%) or obese (52.6%). ST users were more likely to have hypertension compared to smokers (aOR = 1.48, 95%CI: 1.12, 1.95) and nontobacco users (aOR = 1.41, 95%CI: 1.09, 1.83) adjusted for other covariates. ST users were twice more likely to be obese than nontobacco users (aOR = 2.18, 95%CI: 1.52, 3.11). ST users had significantly higher cotinine concentration than smokers.
Conclusion Study findings indicate substantial association of ST use among males with hypertension and obesity which are independent risk factors of CVD.
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null (Ed.)Potato virus X (PVX) belongs to genus Potexvirus. This study characterizes the cellular transcriptome responses to PVX infection in Russet potato at 2 and 3 days post infection (dpi). Among the 1242 differentially expressed genes (DEGs), 268 genes were upregulated, and 37 genes were downregulated at 2 dpi while 677 genes were upregulated, and 265 genes were downregulated at 3 dpi. DEGs related to signal transduction, stress response, and redox processes. Key stress related transcription factors were identified. Twenty-five pathogen resistance gene analogs linked to effector triggered immunity or pathogen-associated molecular pattern (PAMP)-triggered immunity were identified. Comparative analysis with Arabidopsis unfolded protein response (UPR) induced DEGs revealed genes associated with UPR and plasmodesmata transport that are likely needed to establish infection. In conclusion, this study provides an insight on major transcriptional regulatory networked involved in early response to PVX infection and establishment.more » « less
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Selenium (Se) is an essential micronutrient for growth and immune function in beef cattle. We previously showed that supranutritional maternal organic Se supplementation during late pregnancy improves immune function in their newborn calves; however, the effects of maternal organic Se-supplementation on fetal programming during different pregnancy stages have yet to be elucidated. Herein, we investigated the effects of supranutritional maternal organic Se-supplementation in different pregnancy trimesters on their beef calf’s genome-wide transcriptome profiles. Within 12 to 48 h of birth, whole blood and Longissimus dorsi (LD) muscle biopsies were collected from calves born to 40 crossbred Angus cows that received, except for the control group (CTR), Se-yeast boluses (105 mg of Se/wk) during the first (TR1), second (TR2), or third (TR3) trimester of gestation. Whole-blood Se concentrations of newborn calves increased from CTR, TR1, TR2 to TR3, whereas muscle Se concentrations of newborn calves were only increased in TR3 group. We identified 3048 unique differentially expressed genes (DEGs) across all group comparisons (FDR ≤ 0.05 and |log2FC| ≥ 1.5). Furthermore, we predicted 237 unique transcription factors that putatively regulate the DEGs. Independent of supplementation trimester, supranutritional maternal organic Se supplementation downregulated genes involved in adaptive immunity in all trimesters. Dependent on supplementation trimester, genes involved in muscle development were upregulated by TR3 Se supplementation and downregulated by TR1 Se-supplementation, and genes involved in collagen formation were downregulated by TR2 Se-supplementation. Supranutritional maternal organic Se supplementation in the last trimester of pregnancy resulted in upregulation of myosin and actin filament associated genes, potentially allowing for optimal muscle function and contraction. Our findings suggest a beneficial effect of supranutritional maternal organic Se supplementation during late gestation on Se-status and muscle development and function of newborn calves.more » « less
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Abstract Background and Aims Frequent experiences of discrimination could increase vulnerability to tobacco withdrawal and smoking lapse in populations subject to tobacco‐related health disparities. This laboratory study (2013–17) examined whether individual differences in perceived exposure to discrimination in one's daily life predicted tobacco withdrawal symptoms and smoking lapse behavior following acute tobacco deprivation in African American smokers.
Design Mixed design with the between‐subjects continuous variable of perceived discrimination crossed with the within‐subject variable of tobacco deprivation status (deprived versus non‐deprived).
Setting Academic medical center in Los Angeles, CA, USA.
Participants African American non‐treatment seeking daily cigarette smokers (
n = 607, ≥ 10 cig/day).Measurements At a baseline visit, self‐reported frequency of perceived exposure to discrimination in one's daily life was measured [everyday discrimination scale (EDDS)]. At two subsequent counterbalanced experimental visits (16‐hour tobacco deprivation versus
ad‐libitum smoking), self‐report assessments of various tobacco withdrawal symptom domains [Brief Questionnaire of Smoking Urges), Wisconsin Smoking Withdrawal Scale (WSWS), Profile of Mood States (POMS), Snaith–Hamilton Pleasure Scale (SHAPS) and Current Impulsivity Scale (CIS)) and a behavioral smoking lapse analogue task were measured.Findings Adjusted models demonstrated that greater frequency of perceived exposure to discrimination was associated with larger deprivation‐induced increases in acute urges to smoke to alleviate negative mood, several negative mood states and subjective cognitive functioning—effect sizes were small in magnitude (
β s = 0.09–0.13;P s < 0.02). Data were inconclusive for associations between perceived exposure to discrimination and deprivation‐induced changes in cravings, urges to smoke for pleasure, positive mood reduction, other symptoms or smoking reinstatement behavior.Conclusions Frequency of perceived exposure to discrimination appears to be modestly associated with increased severity of some deprivation‐induced tobacco withdrawal symptoms in African American smokers.
- Free Publicly Accessible Full Text
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Accepted Manuscript1.0
- Journal Article:
- https://doi.org/10.3390/toxics10070370
