Time-Course Transcriptome Analysis of Lungs From Mice Infected With Hypervirulent Klebsiella pneumoniae via Aerosolize Intratracheal Inoculation
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PROVIDER: PRJNA820708 | ENA |
REPOSITORIES: ENA
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Project description:Purpose:Investigated transcriptome profile changes in the lungs of infected mice at different time points, to increase our understanding of hvKp pulmonary infection and to screen for genes or targets of research value. microarray and quantitative reverse transcription polymerase chain reaction (qRT–PCR) methods and to evaluate protocols for optimal high-throughput data analysis Methods: Animals were randomly divided into four infection groups and one control group (five mice per group), and the infected mice were euthanized at 12, 24, 48 and 60 h post-infection (hpi), respectively, while the control group mice were euthanized immediately after delivery of PBS at the 0 h time point. The lungs of the mice were isolated and divided into two parts for subsequent histopathologic examination or total RNA extraction. Results: Using the control group (0 hpi) as a reference, 6247 DEGs were identified across four time points after hvKp infection. At 12 hpi, 939 upregulated DEGs and 439 downregulated DEGs were detected, and by 60 hpi, 2647 upregulated DEGs and 2806 downregulated DEGs were detected. Overall, the number of upregulated and downregulated DEGs increased over time and a total of 688 genes were upregulated and 240 genes downregulated in common for all time points. And 12 of these were validated with qRT–PCR. RNA-seq data had a linear relationship with qRT–PCR for more than four orders of magnitude and a goodness of fit (R2) of 0.9548. To get a more holistic view, DEGs were clustered into nine clusters according to their temporal expression patterns.WGCNA was performed with the detected DEGs. The dynamic tree cutting algorithm in the WGCNA package was used to process the hierarchical clustering tree, and a total of 28 different modules were finally obtained. Conclusions: Our work both validates the results of previous studies on K. pneumoniae pulmonary infections and provides new additions and insights on hvKp pulmonary infections, which may contribute to the development of therapeutic approaches to reduce hvKp lung inflammation.
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Project description:Csf2ra deletion attenuates acute lung injuries induced by intratracheal inoculation of aerosolized ricin in mice
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Project description:Carbon black nanoparticles (CBNP) are the most widely produced nanomaterial and are thus a concern for occupational exposures. CBNPs are known to cause inflammation upon inhalation; however, detailed time course data to evaluate the changing nature of inflammatory responses have not been evaluated. In this study, we investigate the short- and longer-term effects of CBNP following a single intratracheal exposure. Female C57BL/6BomTac mice were exposed to CBNPs (printex 90) via a single intratracheal instillation of 162 µg/mouse alongside vehicle controls. Mice were examined 3 hours (hrs), and 1, 2, 3, 4, 5, 14, and 42 days (d) post-exposure. Global gene expression was assessed using DNA microarrays in parallel with analysis of pulmonary inflammation assessed as bronchoalveolar lavage (BAL) cell counts and DNA strand breaks assessed by the comet assay. Pulmonary inflammation in terms of increased neutrophil influx was obverved at all time points. Increased levels of DNA strand breaks were observed in BAL cells 3 hrs post exposure and in lung tissue 2-5 d post exposure. Approximately 2600 significant differentially expressed genes (±1.5 fold; p ≤0.05) across all of the time-points in the lungs of exposed mice were identified upon comparison to time-matched controls. Transcriptional alterations were enriched for genes involved in common respiratory infectious diseases. The perturbed biological processes and pathways were primarily related to immune-inflammatory responses and acute phase responses, consistent with the BAL inflammatory profiles. Gene and pathway analysis revealed a biphasic inflammatory response, with changes occurring as early as 3 hrs post-exposure and declining to base-levels by 3 d post-exposure, but with inflammatory pathways increasing in response again at 14 d and persisting to 42 d post-exposure. Other perturbed pathways included DNA repair and apoptosis, cell cycle regulation, and muscle contraction. Single CBNP exposure induced a biphasic inflammatory response that lasted until 42 d post-exposure. Such persistent inflammatory response raises concerns over the chronic effects of CBNP exposure since the administered dose corresponds to pulmonary deposition in mice during nine 8-hour working days at the current occupational exposure limit for carbon black.
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Project description:Gene expression profiling of the rat lung following intratracheal instillation with C60 fullerene particles was employed to gain insights into these molecular events. Groups of nine-week-old male Wistar rats (n= 4-6 per group/ time point) were intratracheally instilled with C60 fullerene suspended in 0.4 ml distilled water including 0.8% Tween-80 as a single injection (0.1 mg, 0.2 mg (LD: low doses) and 1.0 mg (HD: high dose) C60 fullerene/ rat). Control groups received 0.8 % Tween-80 (vehicle control). After intratracheal instillation treatment, rats were housed within polycarbonate cages at a controlled temperature of 22 °C with a chow diet ad libitum, and dissected at 3 days, 1 week, 1 month, 3 month, and 6 month post-instillation. Right lungs of anesthetized rats were perfused with physiological saline, excised, and used for DNA microarray analysis.
2009-08-26 | E-GEOD-17747 | biostudies-arrayexpress
Project description:Gene expression profiling of the rat lung following intratracheal instillation with SWCNTs was employed to gain insights into these molecular events. We attempted to characterize time-dependent changes in the gene expression until 754 days after intratracheal instillation with SWCNTs suspensions at 0.2 mg (L-SWCNT) and 0.4 mg (H-SWCNT) injected dose per rat, and to identify the shift from the acute-phase to the chronic-phase phase on the basis of evaluation at the molecular level. Groups of nine-week-old male Wistar rats (n= 6 per group/ time point) were intratracheally instilled with single-wall carbon nanotubes (SWCNTs) suspended in 0.4 ml distilled water including 0.1% Triton X-100 as a single injection 0.1 mg (L-SWCNT) and 0.4 mg (H-SWCNT) SWCNTs/ rat). Control groups received 0.1% Triton X-100 (vehicle control). After intratracheal instillation treatment, rats were housed within polycarbonate cages at a controlled temperature of 22 M-BM-0C with a chow diet ad libitum, and dissected at 3 days, 7 days, 30 days, 90 days, 180 days, 365 days and 754 days post-instillation. Right lungs of anesthetized rats were perfused with physiological saline, excised, and used for DNA microarray analysis.
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Project description:In this work we study the pulmonary toxicological properties of Mitsui-7 and NM-403 using molecular toxicological approach. For this, we exposed Sprague Dawley rats by intratracheal instillation. Lung samples have been collected 3 days after the end of exposure and transcriptomics analysis were performed.
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