Single-cell transcriptomic and epigenomic analysis of young and elder mouse gastric mucosa infected by Helicobacter pylori

Research Project

Project/Area Number	20K16347
Research Category	Grant-in-Aid for Early-Career Scientists
Allocation Type	Multi-year Fund
Review Section	Basic Section 50010:Tumor biology-related
Research Institution	National Cancer Center Japan
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)
Project Period (FY)	2020-04-01 – 2024-03-31
Project Status	Granted (Fiscal Year 2021)
Budget Amount *help	¥3,640,000 (Direct Cost: ¥2,800,000、Indirect Cost: ¥840,000) Fiscal Year 2023: ¥130,000 (Direct Cost: ¥100,000、Indirect Cost: ¥30,000) Fiscal Year 2022: ¥390,000 (Direct Cost: ¥300,000、Indirect Cost: ¥90,000) Fiscal Year 2021: ¥390,000 (Direct Cost: ¥300,000、Indirect Cost: ¥90,000) Fiscal Year 2020: ¥2,730,000 (Direct Cost: ¥2,100,000、Indirect Cost: ¥630,000)
Keywords	Helicobacter pylori / DNA methylation / Gastric cancer / Single-cell analysis / Stem cell epigenetics
Outline of Research at the Start	We aim to explain the mechanism in the gastric mucosa where there is a differential targeting for DNA methylation between youngs ter and elderly, and between age-related and inflammation-induced. We hypothesized that there are differences in i) stem and pro genitor cell populations and ii) the epigenome in stem cells. We plan to conduct organoid and single-cell analysis to confirm ou r hypothesis.
Outline of Annual Research Achievements	This year, all samples have been gathered for 3- and 20-week-old mice, control or infected with PMSS1 for 2 or 12 weeks. Infinium BeadChip was performed with gastric mucosa, fibroblasts, PBMCs, splenocytes, and bone marrow cells. RNA-seq was performed with gastric mucosa and fibroblasts. DNA methylation analysis revealed that inflammatory response against H.pylori induced more aberrant methylation in 3-week-old mice gastric mucosa but more aberrant methylation in 20-week-old mice fibroblasts after 12 weeks of infection. RNA-seq data also revealed a different set of up-regulated genes between 3- and 20-week-old mice gastric mucosa and fibroblasts after H.pylori infection. Single-cell RNA-seq confirmed that the fibroblast subpopulations are different between 3- and 20-week-old mice.
Current Status of Research Progress	Current Status of Research Progress 1: Research has progressed more than it was originally planned. Reason Once the samples are collected, we performed all the planned experiments. However, we also added extra samples that we think could provide informative results, such as the DNA methylation profiles of splenocytes and bone marrow.
Strategy for Future Research Activity	We collected a large amount of samples and performed multiple high-throughput analysis with the samples. We will then need time for analysis and to link and observe the correlation between all the results.