Annual Report 2022
Division of Translational Informatics
Katsuya Tsuchihara, Riu Yamashita, Hideki Makinoshima, Sung-Gi Chi, Sachiyo Mimaki, Izumi Miki, Megumi Iwakura, Shiho Maeda, Junyang Du, Yamato Hamaya, Shunsuke Sakai, Yuichi Sakamoto, Yutaka Suzuki, Ayako Suzuki, Atsushi Yagishita, Junko Zenko
Introduction
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, spatial omics analysis and microbiome analysis have been developed in recent years, and these data as well as clinical sequencing 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
This division constructed a database to store and analyze data mainly from large-scale clinical-omics projects led by the Hospital East such as MONSTAR-SCREEN. In dealing with diversifying omics data, a system was operated to integrate and analyze ctDNA analysis data, transcriptome data including single-cell analysis, and microbiome data with clinical information and information from external databases. A web application for computing microbiome diversity based on gene function called QINDAO (Quantitative Index Alpha diversity Overview) was introduced.
Under a comprehensive collaboration agreement with Fujitsu Limited, patient journey analyses using electronic medical record were conducted in collaboration with pharmaceutical companies.
Clinical Trials
MONSTAR-SCREEN Data center.
Education
Lectures and research guidance were provided for graduate students of cooperating graduate schools (Graduate School of Frontier Sciences, The University of Tokyo and Tokyo University of Science). A bioinformatics education course for multiple professions was conducted for EPOC, the Research Institute, and the Hospital East.
Future Prospects
The division will promote data-driven translational research in which clinical researchers and data scientist collaborate. The division will also carry out the analysis and visualization of patient journeys based on the platform for secure utilization of clinical information and personal health records for the prediction of holistic prognosis individual patients.
List of papers published in 2022
Journal
1. Nakai C, Mimaki S, Matsushima K, Shinozaki E, Yamazaki K, Muro K, Yamaguchi K, Nishina T, Yuki S, Shitara K, Bando H, Suzuki Y, Akagi K, Nomura S, Fujii S, Sugiyama M, Nishida N, Mizokami M, Koh Y, Koshizaka T, Okada H, Abe Y, Ohtsu A, Yoshino T, Tsuchihara K. Regulation of MEK inhibitor selumetinib sensitivity by AKT phosphorylation in the novel BRAF L525R mutant. International journal of clinical oncology, 28:654-663, 2023
2. Nakamura Y, Yamashita R, Okamoto W, Komatsu Y, Yuki S, Ueno M, Kato K, Taniguchi H, Kagawa Y, Denda T, Hara H, Esaki T, Moriwaki T, Sunakawa Y, Oki E, Nagashima F, Nishina T, Satoh T, Kawakami H, Yamaguchi K, Ohtsubo K, Kato T, Horita Y, Tsuji A, Yasui H, Goto M, Hamamoto Y, Wakabayashi M, Ikeno T, Shitara K, Bando H, Tsuchihara K, Miki I, Ichiki H, Ohtsu A, Yoshino T. Efficacy of Targeted Trials and Signaling Pathway Landscape in Advanced Gastrointestinal Cancers From SCRUM-Japan GI-SCREEN: A Nationwide Genomic Profiling Program. JCO precision oncology, 7:e2200653, 2023
3. Hamaya Y, Suzuki A, Suzuki Y, Tsuchihara K, Yamashita R. Classification and characterization of alternative promoters in 26 lung adenocarcinoma cell lines. Japanese journal of clinical oncology, 53:97-104, 2023
4. Tanaka Y, Yamashita R, Kawashima J, Mori H, Kurokawa K, Fukuda S, Gotoh Y, Nakamura K, Hayashi T, Kasahara Y, Sato Y, Fukudo S. Further notice of omics profiles of fecal and oral microbiota change in irritable bowel syndrome patients with diarrhea and symptom exacerbation. Journal of gastroenterology, 58:427-428, 2023
5. Nakamura M, Kageyama SI, Hirata H, Tochinai T, Hojo H, Motegi A, Kanai A, Suzuki Y, Tsuchihara K, Akimoto T. Detection of Pretreatment Circulating Tumor DNA Predicts Recurrence after High-Dose Proton Beam Therapy for Early-Stage Non-Small Cell Lung Cancer. International journal of radiation oncology, biology, physics, S0360-3016(23)00166-9, 2023
6. Okumura M, Du J, Kageyama SI, Yamashita R, Hakozaki Y, Motegi A, Hojo H, Nakamura M, Hirano Y, Okuma Y, Okuma HS, Tsuchihara K, Akimoto T. Comprehensive screening for drugs that modify radiation-induced immune responses. British journal of cancer, 126:1815-1823, 2022
7. Kajiwara T, Nishina T, Nakasya A, Yamashita N, Yamashita R, Nakamura Y, Shiozawa M, Yuki S, Taniguchi H, Hara H, Ohta T, Esaki T, Shinozaki E, Takashima A, Moriwaki T, Denda T, Ohtsubo K, Sunakawa Y, Horita Y, Kawakami H, Kato T, Satoh T, Ando K, Mizutani T, Yasui H, Goto M, Okuyama H, Yamazaki K, Yoshino T, Hyodo I. NOTCH gene alterations in metastatic colorectal cancer in the Nationwide Cancer Genome Screening Project in Japan (SCRUM-Japan GI-SCREEN). Journal of cancer research and clinical oncology, 148:2841-2854, 2022
8. Imai M, Nakamura Y, Sunami K, Kage H, Komine K, Koyama T, Amano T, Ennishi D, Kanai M, Kenmotsu H, Maeda T, Morita S, Sakai D, Bando H, Makiyama A, Suzuki T, Hirata M, Kohsaka S, Tsuchihara K, Naito Y, Yoshino T. Expert panel consensus recommendations on the use of circulating tumor DNA assays for patients with advanced solid tumors. Cancer science, 113:3646-3656, 2022
9. Sunami K, Naito Y, Komine K, Amano T, Ennishi D, Imai M, Kage H, Kanai M, Kenmotsu H, Koyama T, Maeda T, Morita S, Sakai D, Kohsaka S, Tsuchihara K, Saigusa Y, Yoshino T. Chronological improvement in precision oncology implementation in Japan. Cancer science, 113:3995-4000, 2022
10. Naito Y, Sunami K, Kage H, Komine K, Amano T, Imai M, Koyama T, Ennishi D, Kanai M, Kenmotsu H, Maeda T, Morita S, Sakai D, Watanabe K, Shirota H, Kinoshita I, Yoshioka M, Mamesaya N, Ito M, Kohsaka S, Saigusa Y, Yamamoto K, Hirata M, Tsuchihara K, Yoshino T. Concordance Between Recommendations From Multidisciplinary Molecular Tumor Boards and Central Consensus for Cancer Treatment in Japan. JAMA network open, 5:e2245081, 2022
11. Sakai SA, Aoshima M, Sawada K, Horasawa S, Yoshikawa A, Fujisawa T, Kadowaki S, Denda T, Matsuhashi N, Yasui H, Goto M, Yamazaki K, Komatsu Y, Nakanishi R, Nakamura Y, Bando H, Hamaya Y, Kageyama SI, Yoshino T, Tsuchihara K, Yamashita R. Fecal microbiota in patients with a stoma decreases anaerobic bacteria and alters taxonomic and functional diversities. Frontiers in cellular and infection microbiology, 12:925444, 2022
12. Tamiya Y, Nakai T, Suzuki A, Mimaki S, Tsuchihara K, Sato K, Yoh K, Matsumoto S, Zenke Y, Nosaki K, Izumi H, Shibata Y, Sakai T, Taki T, Miyazaki S, Watanabe R, Sakamoto N, Sakashita S, Kojima M, Hashimoto N, Tsuboi M, Goto K, Ishii G. The impact of tertiary lymphoid structures on clinicopathological, genetic and gene expression characteristics in lung adenocarcinoma. Lung cancer (Amsterdam, Netherlands), 174:125-132, 2022
13. Du J, Kageyama SI, Yamashita R, Hirata H, Hakozaki Y, Okumura M, Motegi A, Hojo H, Nakamura M, Hirano Y, Sunakawa H, Minamide T, Kotani D, Tanaka K, Yano T, Kojima T, Ohashi A, Tsuchihara K, Akimoto T. Impacts of the STING-IFNAR1-STAT1-IRF1 pathway on the cellular immune reaction induced by fractionated irradiation. Cancer science, 113:1352-1361, 2022
14. Tanaka S, Umemoto K, Kubo S, Sato Y, Mimaki S, Tsuchihara K, Takemura S, Shinkawa H, Mori A, Ikeda M. Nivolumab for treating patients with occupational cholangiocarcinoma. Journal of hepato-biliary-pancreatic sciences, 29:1153-1155, 2022
15. Nagai S, Nishihara H, Suzuki T, Nishio K, Taniguchi H, Tsuchihara K, Nakamura K, Takamatsu R, Ueno T, Aburatani H, Kohno T, Kohsaka S. Recommendations related to the analytical equivalence assessment of gene panel testing. Cancer science, 113:3282-3290, 2022
16. Tanaka Y, Yamashita R, Kawashima J, Mori H, Kurokawa K, Fukuda S, Gotoh Y, Nakamura K, Hayashi T, Kasahara Y, Sato Y, Fukudo S. Omics profiles of fecal and oral microbiota change in irritable bowel syndrome patients with diarrhea and symptom exacerbation. Journal of gastroenterology, 57:748-760, 2022
17. Terui H, Yamasaki K, Wada-Irimada M, Onodera-Amagai M, Hatchome N, Mizuashi M, Yamashita R, Kawabe T, Ishii N, Abe T, Asano Y, Aiba S. Staphylococcus aureus skin colonization promotes SLE-like autoimmune inflammation via neutrophil activation and the IL-23/IL-17 axis. Science immunology, 7:eabm9811, 2022