2020 Fiscal Year Research-status Report
Single-cell transcriptomic and epigenomic analysis of young and elder mouse gastric mucosa infected by Helicobacter pylori
| Project/Area Number |
20K16347
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| Research Institution | National Cancer Center Japan |
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Principal Investigator |
Liu Yuyu 国立研究開発法人国立がん研究センター, 研究所, 特任研究員 (10870462)
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| Project Period (FY) |
2020-04-01 – 2024-03-31
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| Keywords | Helicobacter pylori / DNA methylation / Gastric cancer |
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| Outline of Annual Research Achievements |
After documentation on correspondence between the age of mouse and human, we modified our model by using 3-week-old and 20-week-old mice which represent young and old individuals, respectively. Each group is infected by Helicobacter pylori PMSS1 strain by oral gavage at 3-week-old or 20-week-old. The mice are then sacrificed 2 weeks or 12 weeks after infection. We collected samples by freezing tissues from stomach, thymus, blood (plasma and buffy coat), liver, bone marrow, and heart. In order to compare the stem/progenitor cell population between young and old individuals, we performed single-cell RNA-seq using uninfected 3-week-old and 20-week-old mice. Additionally, we performed Mouse Infinium BeadChip using fibroblasts to compare the basal DNA methylation between young and elderly.
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| Current Status of Research Progress |
Current Status of Research Progress
1: Research has progressed more than it was originally planned.
Reason
Collection of samples from control and infected mice were planned for the first half of year 1. However, we decided to increase the number of mice and to collect samples from organs other than the stomach. Therefore, we are still collecting samples from additional mice. Meanwhile, we performed experiments planned for the second half of year 1, such as single-cell RNA-seq. In the future, as we might replace ATAc-seq analysis by Infinium BeadChip, we analyzed methylation data from fibroblasts obtained from the infected mice. A differential methylation profile was shown between young infected mice and adult infected mice. We will add control samples to confirm our results.
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| Strategy for Future Research Activity |
We will proceed as planned for the following years. First, we will analyze the data obtained from single-cell RNA-seq and Mouse Infinium BeadChip. Then, we will increase the number of replicates and submit a publication at the same time. From the analysis results we will screen for possible target genes or epigenetic markers for the development of gastric cancer prevention method or novel therapeutic approach.
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| Causes of Carryover |
This year, we will use the rest of the grant to proceed sample collections from non-infected and infected mice. We will also perform additional single-cell RNA-seq. We will as well spend a part of the grant for the usage of supercomputer to analyze the obtained data.
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