Comparison analysis of 2 week old C57BL6J lung exposed to 2 weeks of cigarette smoke compared to age-matched controls
Ontology highlight
ABSTRACT:
ORGANISM(S): Mus musculus
PROVIDER: GSE7310 | GEO | 2008/01/01
SECONDARY ACCESSION(S): PRJNA97967
REPOSITORIES: GEO
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Project description:We hypothesize that gene expression in the cigarette smoke (CS) exposed neonatal lung and age-matched controls will be divergent. CS exposed lung will have divergence of immune response genes and structural genes. The lungs of (6) 2 week old neonatal mice exposed to 2 weeks of CS were compared to the lung of (4) 2 week old age-matched control mice. We utilized microarray analysis to examine transcriptional differences between smoke exposed neonatal lung and age-matched controls. Experiment Overall Design: This study utilizes microarray analysis to test these hypotheses. Six sets of lungs were harvested from CS exposed mice and four sets of lungs were harvested from age-matched control mice. RNA was isolated and used for global gene expression profiling (Affymetrix Mouse 430 2.0 array). Statistically significant gene expression was determined as a minimum 6 counts of 9 pairwise comparisons, minimum 1.5-fold change, and p < 0.05. Further, Absolute | FC - FC SEM | >= 1.5.
2008-06-15 | E-GEOD-7310 | biostudies-arrayexpress
Project description:Here, we report a multi OMIC (transcriptome, proteome, and metabolome) approach to investigate molecular changes in lens fiber cells (FC) of mice exposed to cigarette smoke (CS). Pregnant mice were placed in a whole-body smoke chamber and a few days later pups were born, which were exposed to CS for 5 hours/day, 5 days/week for a total of 3½ months. We examined the mice exposed to CS for CS-related cataractogenesis after completion of the CS exposure but no cataracts were observed. Lenses of CS-exposed and age-matched, untreated control mice were extracted and lens FC were subjected to multi OMIC profiling. We identified 348 genes, 130 proteins, and 14 metabolites exhibiting significant (p < 0.05) differential levels in lens FC of mice exposed to CS, corresponding to 3.6%, 4.3%, and 5.0% of the total genes, protein, and metabolites, respectively identified in this study. Our multi OMIC approach confirmed that only a small fraction of the transcriptome, the proteome, and the metabolome was perturbed in the lens FC of mice exposed to CS, which suggests that exposure of CS had a minimal effect on the mouse lens. It is worth noting that while our results confirm that CS exposure does not have a substantial impact on the molecular landscape of the mouse lens FC, we cannot rule out that CS exposure for longer durations and/or in combination with other morbidities or environmental factors would have a more robust effect and/or result in cataractogenesis.
2024-03-24 | MTBLS207 | MetaboLights
Project description:We adopted an omics (transcriptome, proteome, and metabolome) approach to characterize the lens fiber cells extracted from control (CT) and cigarette smoke (CS) exposed mouse (C57BL/6) eyes. The eight pregnant female mice (gestation days 19-20) were placed in a whole-body exposure smoking chamber and served as a CS-exposed group. The mothers and newborn pups were exposed to CS for five hours/day, five days/week for 110 days. In parallel, age-matched mice were kept in normal cages and served as a control group. The ophthalmic examination revealed no sign of cataracts in CS-exposed and aged-matched CT mice. The ocular lenses were extracted and fiber cells (FC) were separated from the lens epithelium under a microscope. The CT and CS fiber cells were maintained in four biological replicates each consisting of a pool of lens fiber cells from four eyes. The eight biological replicates including four CT and four CS-exposed fiber cells were used for the next-generation-based transcriptome (RNA-Seq), mass-spectrometry-based proteome, and metabolome profiling. RNA-Seq analysis identified the expression (≥1.0 FPKM) of 9,590 and 9,531 genes in CT and CS-exposed fiber cells, respectively. The analysis identified 348 differentially expressed genes, including 186 downregulated and 162 upregulated genes in CS-exposed fiber cells. Proteome profiling revealed a total of 2,424 proteins in CT and CS exposed fiber cells. The analysis identified 42 downregulated and 59 upregulated proteins in CS exposed fiber cells. Metabolome profiling identified a total of 280 metabolites, marked with decreased levels of branched-chain amino acids (BCAAs)-related metabolites in CS exposed fiber cells. In conclusion, we have established a comprehensive omics profile of fiber cells from CS-exposed mice. To the best of our knowledge, this is the first report investigating a comprehensive omics profile of fiber cells from CS-exposed mice.
2022-02-15 | PXD020421 | Pride
Project description:We adopted an omics (transcriptome, proteome, and metabolome) approach to characterize the lens fiber cells extracted from control (CT) and cigarette smoke (CS) exposed mouse (C57BL/6) eyes. The eight pregnant female mice (gestation days 19-20) were placed in a whole-body exposure smoking chamber and served as a CS-exposed group. The mothers and newborn pups were exposed to CS for five hours/day, five days/week for 110 days. In parallel, age-matched mice were kept in normal cages and served as a control group. The ophthalmic examination revealed no sign of cataracts in CS-exposed and aged-matched CT mice. The ocular lenses were extracted and fiber cells (FC) were separated from the lens epithelium under a microscope. The CT and CS fiber cells were maintained in four biological replicates each consisting of a pool of lens fiber cells from four eyes. The eight biological replicates including four CT and four CS-exposed fiber cells were used for the next-generation-based transcriptome (RNA-Seq), mass-spectrometry-based proteome, and metabolome profiling. RNA-Seq analysis identified the expression (≥1.0 FPKM) of 9,590 and 9,531 genes in CT and CS-exposed fiber cells, respectively. The analysis identified 348 differentially expressed genes, including 186 downregulated and 162 upregulated genes in CS-exposed fiber cells. Proteome profiling revealed a total of 2,424 proteins in CT and CS exposed fiber cells. The analysis identified 42 downregulated and 59 upregulated proteins in CS exposed fiber cells. Metabolome profiling identified a total of 280 metabolites, marked with decreased levels of branched-chain amino acids (BCAAs)-related metabolites in CS exposed fiber cells. In conclusion, we have established a comprehensive omics profile of fiber cells from CS-exposed mice. To the best of our knowledge, this is the first report investigating a comprehensive omics profile of fiber cells from CS-exposed mice.
2022-02-15 | PXD017414 | Pride
Project description:Expression data from rats exposed to cigarette smoke (CS) at three concentrations (sham, 300µgTPM/l and 600µgTPM/l) for 13 weeks (5d/week; 2hrs/day) after three different recovery times (2hrs, 6hrs and 20hrs after last treatment); lung tissue Keywords: recovery time course and dose dependency
2006-07-28 | GSE4516 | GEO
Project description:Comparison analysis of 2 week old C57BL6J lung exposed to 2 weeks of cigarette smoke compared to age-matched controls
| PRJNA97967 | ENA
Project description:Purpose: The purpose of this study was to identify cigarette smoke (CS) induced changes in circulatory microRNA (miRNA) in the plasma and ocular fluids of the Rhesus macaque and compare them to normal age-related changes, with the ultimate goal to develop an animal model of early dry age-related macular degeneration (AMD). AMD is a blinding disease having both genetic and environmental components, with cigarette smoke exposure (CS) as the leading environmental risk factor. Methods: All Rhesus macaques were housed at the California National Primate Research Center (CNPRC) at UC Davis. We used 6 animals of the same gender per group: Group 1 (young, 2-4 years old), Group 2 (old, 20-25 years old), Group 3 (middle aged, 9-12 years old) and Group 4 (9-12 years old, exposed to smoke for 1 month). Group 4 macaques were clinically assessed prior to and following CS exposure. Ocular fluids and plasma samples were collected, miRNA isolated, and expression data obtained from Affymetrix miRNA GeneTitan Array Plates 4.0, followed by bioinformatics analysis on Affymetrix Expression Console (EC) and Transcriptome Analysis Software (TAS), and using ANOVA. Results: Statistically significant changes were seen in miRNA populations in ocular fluids and plasma. In the plasma samples, 45 miRNAs were strongly upregulated (Fold Change >+/-1.5, p<0.05) upon CS exposure, while in aging monkeys different miRNAs in plasma were affected, and downregulated. In the vitreous, 3 miRNAs were downregulated in animals exposed to CS, intriguing enough two of them (miR-6794 and miR-6790) were the same ones downregulated with age. Retinal imaging using OCT did not show any significant changes in retinal thickness. Cotinine assays showed that animals received on average dose of 50-60 ng/ml cotinine, a marker for significant CS exposure. Conclusions: One month of CS exposure of Rhesus macaques resulted in significant changes of expression of circulatory miRNAs. We identified several CS related miRNA changes that are plasma or ocular fluid-specific. Healthy aging changes of miRNAs populations were different from the CS exposure induced changes in plasma, while the ones in vitreous were similar. This data will be utilized to develop an animal model of early dry AMD, using a monkey model exposed to CS.
2019-05-17 | GSE108951 | GEO
Project description:Cigarette smoke (CS) causes adverse health effects and leads to the development of respiratory disease (chronic obstructive pulmonary disease), cardiovascular disease, and cancer. To reduce the risk of smokers developing smoking-related diseases, Philip Morris International is developing modified risk tobacco products (MRTP). Within a systems toxicology study, we conducted an integrative multi-omics analysis to assess the effects of aerosols from two potential MRTPs - the Carbon Heated Tobacco Product (CHTP) 1.2 and the Tobacco Heating System (THS) 1.2 -, compared with cigarette smoke (CS) at matched nicotine concentrations, on the lung of ApoE-/- mice. Mice were exposed for up to six months and molecular exposure effects were measured by mRNA/miRNA transcriptomics, proteomics, metabolomics, and lipidomics. In addition, the impact of cessation (CESS) or switching to CHTP 1.2 (SWITCH) after three months of CS exposure was evaluated. This data set represents the lung metabolomics data obtained after 3 and 6 months of exposure. The 'Animal ID' or 'CAN' represents the unique animal identifier and allows matching of samples across the different data modalities.
2020-04-25 | MTBLS158 | MetaboLights
Project description:The lymphatic vasculature is critical for lung function, but defects in lymphatic functionin the pathogenesis of lung disease is understudied. To further assess the contribution of lymphatics to the pathogenesis of lung emphysema we used a mouse model of cigarette smoke (CS)-induced emphysema, and analyzed lung lymphatics using immunohistochemistry, functional assays, and confocal microscopy. Additionally, we further harvested thoracic lymph from CS-exposed mice for proteomic analysis. In this presented section of our research, we highlight the label free quantitative DIA proteomics approaches used to profile the proteomic and peptidomics changes in the lymph from cigarette smoke (CS)-mice as compared with the lymph proteome from mice exposed to room air. Label free quantitative DIA proteomics analysis of lymph confirmed upregulation of coagulation and inflammatory pathways in the lymphatics of CS-exposed mice compared to control mice.
2022-05-10 | PXD031413 | Pride
Project description:These studies tested the hypotheses that smoke induces changes in mRNA profiles that are dependent on sex and the health status of the lung, and that the effects of smoke are different after 1 day compared to 5 days of smoke exposure. The ways in which the lungs modulate their response to cigarette smoke after repeated exposures are important for understanding the toxicology of smoke, for developing biomarkers of chronic smoke exposure, and for understanding the therapeutic potential in regulatory signaling pathways that are beneficial or detrimental to lung health. Sex-matched 5-7-week old wildtype (WT) and Scnn1b-overexpressing (BENaC) littermates were exposed to cigarette smoke or sham (room air) exposure. Exposure occurred in a plexiglass chamber attached to a smoke delivery device using an exposure chamber and smoking machine (inExpose Exposure System, SCIREQ, Chandler, AZ). Mice were exposed to mainstream + sidestream smoke from 6 reference cigarettes with filters removed per day (3R4F research cigarettes, University of Kentucky). Each cigarette was puffed for 2 sec every 25 sec, using the standard Federal Trade Commission smoking machine protocol. The sham-exposed control mice were exposed to room air in the exposure chamber for a time equivalent to that needed for active smoke exposure. Mice were exposed to cigarette or sham smoke for 1 day or 5 consecutive days. Samples were harvested 4 hours after the completion of the final smoke exposure. The right lung was used for gene expression analysis.
2019-03-18 | GSE109776 | GEO