Annual Report 2020
Division of Translational Informatics
Katsuya Tsuchihara, Riu Yamashita, Hideki Makinoshima, Sachiyo Mimaki, Izumi Miki, Megumi Iwakura, Junyang Du, Yamato Hamaya, Yumi Hakozaki, Masato Aoshima, Hiroyasu Esumi, Yutaka Suzuki, Ayako Suzuki, Atsushi Yagishita, Junko Zenko
Introduction
It is necessary to obtain high-quality clinical information for cancer research. In addition, multi-omics data from patient specimens and model systems are indispensable to investigate the carcinogenic mechanism and the effects of therapeutic drugs. Several new multi-omics technologies such as single-cell analysis and microbiome analysis have been developed in recent years, and clinical sequence platforms enable us to obtain a large amount of omics data with clinical information. Not only clinical and biological knowledge but also bioinformatics which extract meaningful information effectively is essential to integrate and analyze those data.
The Team and What We Do
The Division of Translational Informatics is designing an efficient pipeline for data processing and constructing web database servers for user convenience.
Research activities
Our division joined the operation of a database that integrates clinical and genomic data from SCRUM-Japan and shared it with participating companies and medical institution networks. The results of MONSTAR-SCREEN for gastrointestinal cancer showed the clinical usefulness of liquid biopsy. A revised version of "Clinical practice guidance for next-generation sequencing in cancer diagnosis and treatment" was published. The usefulness of single-cell transcriptome analysis and long-read genome sequencing analysis using lung cancer cell lines was demonstrated.
Clinical trials
Screening project for individualized medicine in Japan (SCRUM-Japan): Data center.
Education
Our division accepted and trained the following trainees: Graduate students from the University of Tokyo and Tokyo University of Science. Bioinformatics education for multi-professional staff in the EPOC and the Hospital East has been conducted.
Future Prospects
Development of new technologies that integrate clinical and multi-omics data will be more important and necessary to move forward cancer research and drug development. Supplying well trained translational informaticians with various backgrounds is also needed.
List of papers published in 2020
Journal
1. Naito Y, Aburatani H, Amano T, Baba E, Furukawa T, Hayashida T, Hiyama E, Ikeda S, Kanai M, Kato M, Kinoshita I, Kiyota N, Kohno T, Kohsaka S, Komine K, Matsumura I, Miura Y, Nakamura Y, Natsume A, Nishio K, Oda K, Oda N, Okita N, Oseto K, Sunami K, Takahashi H, Takeda M, Tashiro S, Toyooka S, Ueno H, Yachida S, Yoshino T, Tsuchihara K. Clinical practice guidance for next-generation sequencing in cancer diagnosis and treatment (edition 2.1). Int J Clin Oncol, 26:233-283, 2021
2. Kashima Y, Togashi Y, Fukuoka S, Kamada T, Irie T, Suzuki A, Nakamura Y, Shitara K, Minamide T, Yoshida T, Taoka N, Kawase T, Wada T, Inaki K, Chihara M, Ebisuno Y, Tsukamoto S, Fujii R, Ohashi A, Suzuki Y, Tsuchihara K, Nishikawa H, Doi T. Potentiality of multiple modalities for single-cell analyses to evaluate the tumor microenvironment in clinical specimens. Sci Rep, 11:341, 2021
3. Kageyama SI, Du J, Kaneko S, Hamamoto R, Yamaguchi S, Yamashita R, Okumura M, Motegi A, Hojo H, Nakamura M, Tsuchihara K, Akimoto T. Identification of the mutation signature of the cancer genome caused by irradiation. Radiother Oncol, 155:10-16, 2021
4. Sunami K, Naito Y, Aimono E, Amano T, Ennishi D, Kage H, Kanai M, Komine K, Koyama T, Maeda T, Morita S, Sakai D, Kohsaka S, Tsuchihara K, Yoshino T. The initial assessment of expert panel performance in core hospitals for cancer genomic medicine in Japan. Int J Clin Oncol, 26:443-449, 2021
5. Mukohara T, Hosono A, Mimaki S, Nakayama A, Kusuhara S, Funasaka C, Nakao T, Fukasawa Y, Kondoh C, Harano K, Naito Y, Matsubara N, Tsuchihara K, Kuwata T. Effects of Ado-Trastuzumab Emtansine and Fam-Trastuzumab Deruxtecan on Metastatic Breast Cancer Harboring HER2 Amplification and the L755S Mutation. Oncologist, 2021
6. Yagishita A, Ueno T, Tsuchihara K, Urano Y. Amino BODIPY-Based Blue Fluorescent Probes for Aldehyde Dehydrogenase 1-Expressing Cells. Bioconjug Chem, 32:234-238, 2021
7. Suzuki Y, Sato M, Awazuhara T, Nukui Y, Yoshida A, Terashima T, Watanabe K, Fujioka R, Tsuchihara K, Kishino S, Ohno K. Simultaneous quantification of arctigenin and its glucuronide conjugate in mouse plasma using ultra-high performance liquid chromatography coupled to tandem mass spectrometry. J Sep Sci, 44:1299-1306, 2021
8. Nakamura Y, Taniguchi H, Ikeda M, Bando H, Kato K, Morizane C, Esaki T, Komatsu Y, Kawamoto Y, Takahashi N, Ueno M, Kagawa Y, Nishina T, Kato T, Yamamoto Y, Furuse J, Denda T, Kawakami H, Oki E, Nakajima T, Nishida N, Yamaguchi K, Yasui H, Goto M, Matsuhashi N, Ohtsubo K, Yamazaki K, Tsuji A, Okamoto W, Tsuchihara K, Yamanaka T, Miki I, Sakamoto Y, Ichiki H, Hata M, Yamashita R, Ohtsu A, Odegaard JI, Yoshino T. Clinical utility of circulating tumor DNA sequencing in advanced gastrointestinal cancer: SCRUM-Japan GI-SCREEN and GOZILA studies. Nat Med, 26:1859-1864, 2020
9. Sakamoto Y, Xu L, Seki M, Yokoyama TT, Kasahara M, Kashima Y, Ohashi A, Shimada Y, Motoi N, Tsuchihara K, Kobayashi SS, Kohno T, Shiraishi Y, Suzuki A, Suzuki Y. Long-read sequencing for non-small-cell lung cancer genomes. Genome Res, 30:1243-1257, 2020
10. Nakamura Y, Sasaki A, Yukami H, Jogo T, Kawazoe A, Kuboki Y, Taniguchi H, Yamashita R, Kuwata T, Ozawa M, Nakamura M, Yoshino T, Shitara K. Emergence of Concurrent Multiple EGFR Mutations and MET Amplification in a Patient With EGFR-Amplified Advanced Gastric Cancer Treated With Cetuximab. JCO Precis Oncol, 4:2020
11. Takei H, Fukuda H, Pan G, Yamazaki H, Matsumoto T, Kazuma Y, Fujii M, Nakayama S, Kobayashi IS, Shindo K, Yamashita R, Shirakawa K, Takaori-Kondo A, Kobayashi SS. Alternative splicing of APOBEC3D generates functional diversity and its role as a DNA mutator. Int J Hematol, 112:395-408, 2020
12. Sato K, Mimaki S, Yamashita R, Togashi Y, Naito T, Udagawa H, Katsumata S, Nakasone S, Miyoshi T, Tane K, Aokage K, Sugano M, Kojima M, Fujii S, Kuwata T, Ochiai A, Goto K, Tsuboi M, Tsuchihara K, Ishii G. Association between the mutational smoking signature and the immune microenvironment in lung adenocarcinoma. Lung Cancer, 147:12-20, 2020
13. Saito S, Aoki Y, Tamahara T, Goto M, Matsui H, Kawashima J, Danjoh I, Hozawa A, Kuriyama S, Suzuki Y, Fuse N, Kure S, Yamashita R, Tanabe O, Minegishi N, Kinoshita K, Tsuboi A, Shimizu R, Yamamoto M. Oral Microbiome Analysis in Prospective Genome Cohort Studies of the Tohoku Medical Megabank Project. Front Cell Infect Microbiol, 10:604596, 2020
14. Ishida N, Aoki Y, Katsuoka F, Nishijima I, Nobukuni T, Anzawa H, Bin L, Tsuda M, Kumada K, Kudo H, Terakawa T, Otsuki A, Kinoshita K, Yamashita R, Minegishi N, Yamamoto M. Landscape of electrophilic and inflammatory stress-mediated gene regulation in human lymphoblastoid cell lines. Free Radic Biol Med, 161:71-83, 2020