RIKEN Center for Advanced Intelligence Project Cancer Translational Research Team

Team Leader: Ryuji Hamamoto (Ph.D.)

Japanese Page

Research Summary

We are conducting multimodal analysis of the omics data such as genome data, epigenome data, medical imaging data [CT, MRI, PET, endoscopy, pathology], proteome data, micro RNA data, cell line data, PDX [Patient-Derived Xenografts] data and clinical information in various types of cancers by machine learning and deep learning to clarify the nature of cancer. On the basis of our findings, we plan to develop novel diagnostic and therapeutic methods for cancer, and will also use them to develop novel anti-cancer drugs.

Research Subjects:

Analysis of histone modification status in cancer tissues by machine learning and deep learning
Analysis of medical imaging data by machine learning and deep learning
Multi-omics analysis of cancer by machine learning and deep learning

Main Research Fields

Molecular Biology & Genetics

Related Research Fields

Biology & Biochemistry
Immunology
Clinical Medicine
Computer Science

Selected Publications

Papers with an asterisk(*) are based on research conducted outside of RIKEN.

1. Ryuji Hamamoto, Masaaki Komatsu, Ken Takasawa, Ken Asada, Syuzo Kaneko.:
"Epigenetics Analysis and Integrated Analysis of Multiomics Data, Including Epigenetic Data, Using Artificial Intelligence in the Era of Precision Medicine."
Biomolecules 10, 62 (2020)
2. Masayoshi Yamada, Yutaka Saito, Hitoshi Imaoka, Masahiro Saiko, Shigemi Yamada, Hiroko Kondo, Hiroyuki Takamaru, Taku Sakamoto, Jun Sese, Aya Kuchiba, Taro Shibata, Ryuji Hamamoto.:
"Development of a real-time endoscopic image diagnosis support system using deep learning technology in colonoscopy."
Scientific Reports 9, 14465 (2019)
3. Yusuke Matsuno, Yuko Atsumi, Atsuhiro Shimizu, Kotoe Katayama, Haruka Fujimori, Mai Hyodo, Yusuke Minakawa, Yoshimichi Nakatsu, Syuzo Kaneko, Ryuji Hamamoto, Teppei Shimamura, Satoru Miyano, Teruhisa Tsuzuki, Fumio Hanaoka, Ken-ichi Yoshioka.:
"Replication stress triggers microsatellite destabilization and hypermutation leading to clonal expansion in vitro."
Nature Communications 10, 3925 (2019)
4. *Ryuji Hamamoto, Vassiliki Saloura, Yusuke Nakamura.:
"Critical roles of non-histone protein lysine methylation in human tumorigenesis."
Nature Reviews Cancer, 15, 110-124 (2015)
5. *Kenbun Sone, Lianhua Piao, Makoto Nakakido, Koji Ueda, Thomas Jenuwein, Yusuke Nakamura, Ryuji Hamamoto.:
"Critical role of lysine 134 methylation on histone H2AX for γ-H2AX production and DNA repair."
Nature Communications, 5, 5691 (2014)
6. *Hyun-Soo Cho, Tadahiro Shimazu, Gouji Toyokawa, Yataro Daigo, Yoshihiko Maehara, Shinya Hayami, Akihiro Ito, Ken Masuda, Noriko Ikawa, Helen I. Field, Eiju Tsuchiya, Shin-ichi Ohnuma, Bruce A.J. Ponder, Minoru Yoshida, Yusuke Nakamura, Ryuji Hamamoto.:
"Enhanced HSP70 lysine methylation promotes proliferation of cancer cells through activation of aurora kinase B."
Nature Communications, 3, 1072 (2012)
7. *Kyohei Arita, Shin Isogai, Takashi Oda, Motoko Unoki, Kazuya Sugita, Naotaka Sekiyama, Keiko Kuwata, Ryuji Hamamoto, Hidehito Tochio, Mamoru Sato, Mariko Ariyoshi, Masahiro Shirakawa.:
"Recognition of modification status on a histone H3 tail by linked histone reader modules of UHRF1."
Proc Natl Acad Sci USA, 109, 12950-12955 (2012)
8. *Gouji Toyokawa, Ken Masuda, Yataro Daigo, Hyun-Soo Cho, Masanori Yoshimatsu, Masashi Takawa, Shinya Hayami, Kazuhiro Maejima, Makoto Chino, Helen I. Field, David E. Neal, Eijyu Tsuchiya, Bruce A.J. Ponder, Yoshihiko Maehara, Yusuke Nakamura, Ryuji Hamamoto.:
"Minichromosome Maintenance Protein 7 is a potential therapeutic target in human cancer and a novel prognostic marker of non-small cell lung cancer."
Molecular Cancer, 10, 65 (2011)
9. *Shinya Hayami, Masanori Yoshimatsu, Abhimanyu Veerakumarasivam, Motoko Unoki, Yukiko Iwai, Tatsuhiko Tsunoda, Helen I. Field, John D. Kelly, David E. Neal, Hiroki Yamaue, Bruce A.J. Ponder, Yusuke Nakamura, Ryuji Hamamoto.:
"Over-expression of the JmjC histone demethylase KDM5B in human carcinogenesis: involvement in the proliferation of cancer cells through the E2F/RB pathway."
Molecular Cancer, 9, 59 (2010)
10. *Ryuji Hamamoto, Yoichi Furukawa, Masashi Morita, Yumiko Iimura, Fabio Pittella Silva, Meihua Li, Ryuichiro Yagyu, Yusuke Nakamura.:
"SMYD3 encodes a histone methyltransferase involved in the proliferation of cancer cells."
Nature Cell Biology, 6, 731-740 (2004)