RIKEN Center for Advanced Intelligence Project Cancer Translational Research Team

Team Director: 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

Medicine, Dentistry & Pharmacy

Related Research Fields

Informatics
Complex Systems
Biological Sciences

Selected Publications

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

1. Asada, K., Kaneko, S., Takasawa, K., Shiraishi, K., Shinkai, N., Shimada, Y., Takahashi, S., Machino, H., Kobayashi, K., Bolatkan, A., Komatsu, M., Yamada, M., Miyake, M., Watanabe, H., Tateishi, A., Mizuno, T., Okubo, Y., Mukai, M., Yoshida, T., Yoshida, Y., Horinouchi, H., Watanabe, S.I., Ohe, Y., Yatabe, Y., Kohno, T., Hamamoto, R.:
"Multi-omics and clustering analyses reveal the mechanisms underlying unmet needs for patients with lung adenocarcinoma and identify potential therapeutic targets"
Molecular Cancer 23, 182 (2024)
2. Kaneko, S., Takasawa, K., Asada, K., Shiraishi, K., Ikawa, N., Machino, H., Shinkai, N., Matsuda, M., Masuda, M., Adachi, S., Takahashi, S., Kobayashi, K., Kouno, N., Bolatkan, A., Komatsu, M., Yamada, M., Miyake, M., Watanabe, H., Tateishi, A., Mizuno, T., Okubo, Y., Mukai, M., Yoshida, T., Yoshida, Y., Horinouchi, H., Watanabe, S.I., Ohe, Y., Yatabe, Y., Saloura, V., Kohno, T., Hamamoto, R.:
"Mechanism of ERBB2 gene overexpression by the formation of super-enhancer with genomic structural abnormalities in lung adenocarcinoma without clinically actionable genetic alterations"
Molecular Cancer 23, 126 (2024)
3. Mochizuki, A., Shiraishi, K., Honda, T., Higashiyama, R.I., Sunami, K., Matsuda, M., Shimada, Y., Miyazaki, Y., Yoshida, Y., Watanabe, S.I., Yatabe, Y., Hamamoto, R., Kohno, T.:
"Passive smoking-induced mutagenesis as a promoter of lung carcinogenesis"
Journal of Thoracic Oncology 19, 984-994 (2024)
4. Kobayashi, K., Gu, L., Hataya, R., Mizuno, T., Miyake, M., Watanabe, H., Takahashi, M., Takamizawa, Y., Yoshida, Y., Nakamura, S., Kouno, N., Bolatkan, A., Kurose, Y., Harada, T., Hamamoto, R.:
"Sketch-based semantic retrieval of medical images"
Medical Image Analysis 92, 103060 (2024)
5. Igarashi, T., Mazevet, M., Yasuhara, T., Yano, K., Mochizuki, A., Nishino, M., Yoshida, T., Yoshida, Y., Takamatsu, N., Yoshimi, A., Shiraishi, K., Horinouchi, H., Kohno, T., Hamamoto, R., Adachi, J., Zou, L., Shiotani, B.:
"An ATR-PrimPol pathway confers tolerance to oncogenic KRAS-induced and heterochromatin-associated replication stress"
Nature Communications 14, 4991 (2023)
6. Kobayashi, K., Hataya, R., Kurose, Y., Miyake, M., Takahashi, M., Nakagawa, A., Harada, T., Hamamoto, R.:
"Decomposing normal and abnormal features of medical images for content-based image retrieval of glioma imaging"
Medical Image Analysis 74, 102227 (2021)
7. Matsuno, Y., Atsumi, Y., Shimizu, A., Katayama, K., Fujimori, H., Hyodo, M., Minakawa, Y., Nakatsu, Y., Kaneko, S., Hamamoto, R., Shimamura, T., Miyano, S., Tsuzuki, T., Hanaoka, F., Yoshioka, K.I.:
"Replication stress triggers microsatellite destabilization and hypermutation leading to clonal expansion in vitro"
Nature Communications 10, 3925 (2019)
8. *Hamamoto, R., Saloura, V., Nakamura, Y.:
"Critical roles of non-histone protein lysine methylation in human tumorigenesis"
Nature Reviews Cancer 15, 110-124 (2015)
9. *Sone, K., Piao, L., Nakakido, M., Ueda, K., Jenuwein, T., Nakamura, Y., Hamamoto, R.:
"Critical role of lysine 134 methylation on histone H2AX for γ-H2AX production and DNA repair"
Nature Communications 10, 3925 (2019)
10. *Cho, H.S., Shimazu, T., Toyokawa, G., Daigo, Y., Maehara, Y., Hayami, S., Ito, A., Masuda, K., Ikawa, N., Field, H.I., Tsuchiya, E., Ohnuma, S., Ponder, B.A.J., Yoshida M., Nakamura, Y., Hamamoto, R.:
"Enhanced HSP70 lysine methylation promotes proliferation of cancer cells through activation of aurora kinase B"
Nature Communications 3, 1072 (2012)