Annual Report 2019
Division of Translational Informatics
Katsuya Tsuchihara, Riu Yamashita, Hideki Makinoshima, Sachiyo Mimaki, Izumi Miki, Megumi Iwakura, Jun Enmi, Junyang Du, Yamato Hamaya, Yumi Hakozaki, Hiroyasu Esumi, Yutaka Suzuki, Ayako Suzuki, Atsushi Yagishita, Tatsunosuke Ikemura, Keita Masuzawa, Joji Nakayama, Ami Maruyama
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 are 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
Information on the frequency of genomic aberrations of approximately 10,000 cases collected in the first and second phases of SCRUM-Japan was registered in the public database MGeND. A revision of “Clinical practice guidance for next-generation sequencing in cancer diagnosis and treatment” was conducted. Rare EGFR mutations were extracted from the lung cancer genome data accumulated in SCRUM-Japan and their susceptibility to various EGFR inhibitors was compared with cell models and molecular simulation models using supercomputers in order to develop technologies for treatment optimization.
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, staff physicians and residents of Keio University. Bioinformatics education for multi-professional staff in the hospital has been started.
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 2019
Journal
1. Fujii S, Magliocco AM, Kim J, Okamoto W, Kim JE, Sawada K, Nakamura Y, Kopetz S, Park WY, Tsuchihara K, Kim TW, Raghav K, Yoshino T. International Harmonization of Provisional Diagnostic Criteria for ERBB2-Amplified Metastatic Colorectal Cancer Allowing for Screening by Next-Generation Sequencing Panel. JCO Precision Oncology, 4:6-19, 2020
2. Kageyama SI, Junyan D, Hojo H, Motegi A, Nakamura M, Tsuchihara K, Akimoto T. PARP inhibitor olaparib sensitizes esophageal carcinoma cells to fractionated proton irradiation. J Radiat Res, 61:177-186, 2020
3. Naito Y, Mishima S, Akagi K, Igarashi A, Ikeda M, Okano S, Kato S, Takano T, Tsuchihara K, Terashima K, Nishihara H, Nishiyama H, Hiyama E, Hirasawa A, Hosoi H, Maeda O, Yatabe Y, Okamoto W, Ono S, Kajiyama H, Nagashima F, Hatanaka Y, Miyachi M, Kodera Y, Yoshino T, Taniguchi H. Japan society of clinical oncology/Japanese society of medical oncology-led clinical recommendations on the diagnosis and use of tropomyosin receptor kinase inhibitors in adult and pediatric patients with neurotrophic receptor tyrosine kinase fusion-positive advanced solid tumors, cooperated by the Japanese society of pediatric hematology/oncology. Int J Clin Oncol, 25:403-417, 2020
4. Mishima S, Taniguchi H, Akagi K, Baba E, Fujiwara Y, Hirasawa A, Ikeda M, Maeda O, Muro K, Nishihara H, Nishiyama H, Takano T, Tsuchihara K, Yatabe Y, Kodera Y, Yoshino T. Japan Society of Clinical Oncology provisional clinical opinion for the diagnosis and use of immunotherapy in patients with deficient DNA mismatch repair tumors, cooperated by Japanese Society of Medical Oncology, First Edition. Int J Clin Oncol, 25:217-239, 2020
5. Kuriyama S, Metoki H, Kikuya M, Obara T, Ishikuro M, Yamanaka C, Nagai M, Matsubara H, Kobayashi T, Sugawara J, Tamiya G, Hozawa A, Nakaya N, Tsuchiya N, Nakamura T, Narita A, Kogure M, Hirata T, Tsuji I, Nagami F, Fuse N, Arai T, Kawaguchi Y, Higuchi S, Sakaida M, Suzuki Y, Osumi N, Nakayama K, Ito K, Egawa S, Chida K, Kodama E, Kiyomoto H, Ishii T, Tsuboi A, Tomita H, Taki Y, Kawame H, Suzuki K, Ishii N, Ogishima S, Mizuno S, Takai-Igarashi T, Minegishi N, Yasuda J, Igarashi K, Shimizu R, Nagasaki M, Tanabe O, Koshiba S, Hashizume H, Motohashi H, Tominaga T, Ito S, Tanno K, Sakata K, Shimizu A, Hitomi J, Sasaki M, Kinoshita K, Tanaka H, Kobayashi T; Tohoku Medical Megabank Project Study Group, Kure S, Yaegashi N, Yamamoto M. Cohort Profile: Tohoku Medical Megabank Project Birth and Three-Generation Cohort . Int J Epidemiol, 49:18-19m. doi: 10.1093/ije/dyz169, 2020
6. Ikemura S, Yasuda H, Matsumoto S, Kamada M, Hamamoto J, Masuzawa K, Kobayashi K, Manabe T, Arai D, Nakachi I, Kawada I, Ishioka K, Nakamura M, Namkoong H, Naoki K, Ono F, Araki M, Kanada R, Ma B, Hayashi Y, Mimaki S, Yoh K, Kobayashi SS, Kohno T, Okuno Y, Goto K, Tsuchihara K, Soejima K. Molecular dynamics simulation-guided drug sensitivity prediction for lung cancer with rare EGFR mutations. Proc Natl Acad Sci U S A, 116:10025-10030, 2019
7. Suzuki A, Onodera K, Matsui K, Seki M, Esumi H, Soga T, Sugano S, Kohno T, Suzuki Y, Tsuchihara K. Characterization of cancer omics and drug perturbations in panels of lung cancer cells. Sci Rep, 9:19529, 2019
8. Fujii S, Yoshino T, Yamazaki K, Muro K, Yamaguchi K, Nishina T, Yuki S, Shinozaki E, Shitara K, Bando H, Mimaki S, Nakai C, Matsushima K, Suzuki Y, Akagi K, Yamanaka T, Nomura S, Esumi H, Sugiyama M, Nishida N, Mizokami M, Koh Y, Abe Y, Ohtsu A, Tsuchihara K. Histopathological factors affecting the extraction of high quality genomic DNA from tissue sections for next-generation sequencing. Biomed Rep, 11:171-180, 2019
9. Maruyama A, Kami K, Sasaki K, Sato H, Sato Y, Tsuchihara K, Makinoshima H. Extraction of Aqueous Metabolites from Cultured Adherent Cells for Metabolomic Analysis by Capillary Electrophoresis-Mass Spectrometry. J Vis Exp, doi: 10.3791/59551, 2019
10. Ishizawa K, Yamanaka M, Saiki Y, Miyauchi E, Fukushige S, Akaishi T, Asao A, Mimori T, Saito R, Tojo Y, Yamashita R, Abe M, Sakurada A, Pham NA, Li M, Okada Y, Ishii T, Ishii N, Kobayashi S, Nagasaki M, Ichinose M, Tsao MS, Horii A. CD45+CD326+ Cells are Predictive of Poor Prognosis in Non-Small Cell Lung Cancer Patients. Clin Cancer Res, 25:6756-6763, 2019
11. Minegishi N, Nishijima I, Nobukuni T, Kudo H, Ishida N, Terakawa T, Kumada K, Yamashita R, Katsuoka F, Ogishima S, Suzuki K, Sasaki M, Satoh M, Tohoku Medical Megabank Project Study Group, Yamamoto M. Study (TMM BirThree Cohort Study): rationale, progress and perspective. Tohoku J Exp Med, 248:45-55, 2019
12. Tadaka S, Katsuoka F, Ueki M, Kojima K, Makino S, Saito S, Otsuki A, Gocho C, Sakurai-Yageta M, Danjoh I, Motoike IN, Yamaguchi-Kabata Y, Shirota M, Koshiba S, Nagasaki M, Minegishi N, Hozawa A, Kuriyama S, Shimizu A, Yasuda J, Fuse N, Tamiya G, Yamamoto M, Kinoshita K. 3.5KJPNv2: an allele frequency panel of 3552 Japanese individuals including the X chromosome. Hum Genome Var, 6:28, 2019
13. Yamaguchi-Kabata Y, Yasuda J, Uruno A, Shimokawa K, Koshiba S, Suzuki Y, Fuse N, Kawame H, Tadaka S, Nagasaki M, Kojima K, Katsuoka F, Kumada K, Tanabe O, Tamiya G, Yaegashi N, Kinoshita K, Yamamoto M, Kure S. Estimating carrier frequencies of newborn screening disorders using a whole-genome reference panel of 3552 Japanese individuals. Hum Genet, 138:389-409, 2019