2013 Fiscal Year Research-status Report
喫煙によって引き起こされる慢性炎症の発症メカニズムの解明
| Project/Area Number |
25430182
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| Research Category |
Grant-in-Aid for Scientific Research (C)
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| Research Institution | Osaka University |
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Principal Investigator |
ディエス ディエゴ 大阪大学, 免疫学フロンティア研究センター, 特任助教 (90597741)
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| Project Period (FY) |
2013-04-01 – 2016-03-31
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| Keywords | Systems biology / Bioinformatics / Regulatory network / Immune system / Differentiation |
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| Research Abstract |
1. Introduction
Chronic obstructive inflammatory disease (COPD) is predicted to become the third cause of death by 2020. COPD is caused by exposure to cigarette smoke and other environmental toxics, including silica. Risk of developing COPD remains even after stopping exposure to the toxics, suggesting irreversible changes in the airways. The aim of this project is to identify regulatory networks associated with the induction of irreversible changes leading to airways inflammation and chronic disease.
2. Systems biology methods
We have developed a computational method (rTRM) for the identification of transcriptional regulatory modules (TRMs). TRMs are complexes of proteins called transcription factors (TFs) that regulate gene expression and are important in many diseases. We applied rTRM to global expression patterns on the hematopoietic lineage and identified TRMs determining differentiation into the different types of immune cells. rTRM is applicable to any biological scenario and will help delineate the transcriptional programs that determine cell behavior in health and disease. rTRM will be applied on experimental data obtained from a mouse model of airways inflammation.
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| Current Status of Research Progress |
Current Status of Research Progress
3: Progress in research has been slightly delayed.
Reason
The main goal of this project is to identify irreversible changes in the airways upon exposure to environmental toxics that may explain the development of chronic inflammatory diseases like COPD, even when the exposure to toxics is stopped. The original plan was to perform experiments on cigarette smoke exposure in mice. These experiments require specialized equipment. In particular, a closed cabinet for the mice cages to which smoke is injected from a device that burns cigarettes automatically. Current machines collect the fumes for analysis of toxics and others. Unfortunately, the cost of this equipment was largely underestimated- being currently over 7 million yen. Consequently, it was not possible to purchase the required equipment. Finding a suitable solution delayed the starting of the experiments.
Since we could not implement the cigarette smoke model, we decided to change it. Instead, we will use a model of silica exposure. Silica produces irreversible changes in the airways. Mice exposed to 4 acute doses of silica during 4 weeks develop silicosis in six months. Furthermore, exposure to silica has been associated with development of COPD without development of silicosis, in humans. Finally, exposure to silica can be easily performed in the laboratory without requiring expensive equipment.
Note: the development of systems biology and bioinformatics methods has not been delayed.
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| Strategy for Future Research Activity |
Experiments for the silicosis model have started in April 2014. Mice will be exposed to silica by intranasal injection. Each exposure will be performed for 0 (control group) 1, 2, 3 and 4 weeks. Mice will be monitored at 1, 3 and 6 months after the start of the experiment. Tissue will be obtained for genomic studies. Whole lung lysates be obtained and collected for transcriptomic (RNA-seq) and cistromic (FAIRE-seq) analysis. FAIRE-seq analysis will be performed instead of DNase-seq analysis as initially planned, as FAIRE-seq gives similar (and also complementary) results to DNase-seq but it is cheaper and easier to perform.
This genomic data will be analyzed using bioinformatics tools to identify changes in the signaling and regulatory networks associated with the development of silicosis. The transcriptome and cistrome data will be combined with information about protein-protein interactions (rTRM method) in order to identify regulatory modules associated with the development of chronic inflammation.
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| Expenditure Plans for the Next FY Research Funding |
Because the starting of the experiments was delayed, the amount of money destined to it was not used. The experiments have started in April and the money will be used during the next fiscal year.
As planed genomic experiments will be performed in a mouse model of airways inflammation. For this, RNA-seq and FAIRE-seq expereriments will be performed.
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