Tomita, Masaru

写真a

Affiliation

Faculty of Environment and Information Studies (Shonan Fujisawa)

Position

Professor

External Links

Other Affiliation 【 Display / hide

  • School of Medicine, 慶應義塾大学医学部兼担教授

Career 【 Display / hide

  • 1987.07
    -
    1990.05

    カーネギーメロン大学 ,助教授

  • 1990.06
    -
    1997.03

    大学助教授(環境情報学部)

  • 1994.04
    -
    Present

    大学院政策・メディア研究科委員

  • 1997.04
    -
    Present

    大学教授(環境情報学部)

  • 1999.10
    -
    2001.09

    大学国際センター副所長

display all >>

Academic Background 【 Display / hide

  • 1976.04
    -
    1981.03

    Keio University, Faculty of Engineering, Department of Mathematics

    University, Graduated

  • 1981.09
    -
    1983.05

    Carnegie Mellon University, School of Computer Science

    USA, Graduate School, Completed, Master's course

  • 1983.05

    Other, コンピューター科学科

    -, Graduate School, Completed, Master's course

Academic Degrees 【 Display / hide

  • Ph.D in Computer Science, Carnegie Mellon University, Coursework, 1985.05

  • Ph.D in Electrical Engineering , Kyoto University, Dissertation, 1994.07

  • Ph.D in Molecular Biology, Keio University, Coursework, 1998.03

  • Ph.D in Media and Governance, Keio University, Dissertation, 2019.08

    The creation of Tsuruoka Science Park and regional development

 

Research Areas 【 Display / hide

  • System Biology

  • Biological simulation

  • computer science

  • Genome Informatics

  • Bioinformatics

 

Books 【 Display / hide

  • Advances in Systems Immunology and Cancer

    Tomita, M., Selvarajoo, K. and Tsuchiya, M., Frontiers Media SA, 2014

  • E-Cell System : Basic Concepts and Applications.

    TOMITA MASARUSatya Nanda Vel Arjunan; Pawan K Dhar, Springer, 2013

  • 最新医学 臨床遺伝子学’07-ゲノム科学の臨床へのインパクト―

    曽我朋義,大橋由明,冨田 勝, 最新医学社, 2007

    Scope: 56-63,

  • Metabolomics-A Powerful Tool in Systems Biology-(vol.18)

    Martin, R., Soga, T. and Tomita, M., Springer, 2007

    Scope: 189-234

  • バイオインフォマティクス事典

    櫻田剛史,冨田 勝, 共立出版, 2006

    Scope: 706-707

display all >>

Papers 【 Display / hide

  • Reliability of urinary charged metabolite concentrations in a large-scale cohort study using capillary electrophoresis-mass spectrometry

    Ishibashi Y., Harada S., Takeuchi A., Iida M., Kurihara A., Kato S., Kuwabara K., Hirata A., Shibuki T., Okamura T., Sugiyama D., Sato A., Amano K., Hirayama A., Sugimoto M., Soga T., Tomita M., Takebayashi T.

    Scientific Reports (Scientific Reports)  11 ( 1 )  2021.12

     View Summary

    Currently, large-scale cohort studies for metabolome analysis have been launched globally. However, only a few studies have evaluated the reliability of urinary metabolome analysis. This study aimed to establish the reliability of urinary metabolomic profiling in cohort studies. In the Tsuruoka Metabolomics Cohort Study, 123 charged metabolites were identified and routinely quantified using capillary electrophoresis-mass spectrometry (CE-MS). We evaluated approximately 750 quality control (QC) samples and 6,720 participants’ spot urine samples. We calculated inter- and intra-batch coefficients of variation in the QC and participant samples and technical intraclass correlation coefficients (ICC). A correlation of metabolite concentrations between spot and 24-h urine samples obtained from 32 sub-cohort participants was also evaluated. The coefficient of variation (CV) was less than 20% for 87 metabolites (70.7%) and 20–30% for 19 metabolites (15.4%) in the QC samples. There was less than 20% inter-batch CV for 106 metabolites (86.2%). Most urinary metabolites would have reliability for measurement. The 96 metabolites (78.0%) was above 0.75 for the estimated ICC, and those might be useful for epidemiological analysis. Among individuals, the Pearson correlation coefficient of 24-h and spot urine was more than 70% for 59 of the 99 metabolites. These results show that the profiling of charged metabolites using CE-MS in morning spot human urine is suitable for epidemiological metabolomics studies.

  • Reprogramming of glutamine metabolism via glutamine synthetase silencing induces cisplatin resistance in A2780 ovarian cancer cells

    Guo J., Satoh K., Tabata S., Mori M., Tomita M., Soga T.

    BMC Cancer (BMC Cancer)  21 ( 1 )  2021.12

     View Summary

    Background: Cisplatin (CDDP) significantly prolongs survival in various cancers, but many patients also develop resistance that results in treatment failure. Thus, this study aimed to elucidate the underlying mechanisms by which ovarian cancer cells acquire CDDP resistance. Methods: We evaluated the metabolic profiles in CDDP-sensitive ovarian cancer A2780 cells and CDDP-resistant A2780cis cells using capillary electrophoresis-time-of-flight mass spectrometry (CE-TOFMS). We further examined the expression of glutamine metabolism enzymes using real-time PCR and Western blot analyses. Cell viability was accessed using 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) assay. Results: The results showed that levels of glutamine, glutamate, and glutathione (GSH), a key drug resistance mediator synthesized from glutamate, were significantly elevated in A2780cis cells than those in A2780 cells. Furthermore, glutamine starvation decreased the GSH levels and CDDP resistance in A2780cis cells. Interestingly, the expression of glutamine synthetase (GS/GLUL), which synthesizes glutamine from glutamate and thereby negatively regulates GSH production, was almost completely suppressed in resistant A2780cis cells. In addition, treatment of A2780cis cells with 5-aza-2′-deoxycytidine, a DNA-demethylating agent, restored GS expression and reduced CDDP resistance. In contrast, GS knockdown in CDDP-sensitive A2780 cells induced CDDP resistance. Conclusions: The results indicate that upregulation of GSH synthesis from glutamine via DNA methylation-mediated silencing of GS causes CDDP resistance in A2780cis cells. Therefore, glutamine metabolism could be a novel therapeutic target against CDDP resistance.

  • Metabolomic analysis of small extracellular vesicles derived from pancreatic cancer cells cultured under normoxia and hypoxia

    Hayasaka R., Tabata S., Hasebe M., Ikeda S., Ohnuma S., Mori M., Soga T., Tomita M., Hirayama A.

    Metabolites (Metabolites)  11 ( 4 )  2021.04

     View Summary

    Extracellular vesicles (EVs) released from cancer cells contribute to various malignant phenotypes of cancer, including metastasis, cachexia, and angiogenesis. Although DNA, mRNAs, miRNAs, and proteins contained in EVs have been extensively studied, the function of metabolites in EVs remains unclear. In this study, we performed a comprehensive metabolomic analysis of pancreatic cancer cells, PANC-1, cultured under different oxygen concentrations, and small EVs (sEVs) released from them, considering the fact that hypoxia contributes to the malignant behavior of cells in pancreatic cancer, which is a poorly diagnosed cancer. sEVs were collected by ultracen-trifugation, and hydrophilic metabolites were analyzed using capillary ion chromatography-mass spectrometry and liquid chromatography-mass spectrometry, and lipids were analyzed by supercrit-ical fluid chromatography-tandem mass spectrometry. A total of 140 hydrophilic metabolites and 494 lipids were detected in sEVs, and their profiles were different from those in cells. In addition, the metabolomic profile of sEVs was observed to change under hypoxic stress, and an increase in metabolites involved in angiogenesis was also detected. We reveal the hallmark of the metabolites contained in sEVs and the effect of tumor hypoxia on their profiles, which may help in understanding EV-mediated cancer malignancy.

  • Xanthurenic acid is the main pigment of trichonephila clavata gold dragline silk

    Fujiwara M., Kono N., Hirayama A., Malay A.D., Nakamura H., Ohtoshi R., Numata K., Tomita M., Arakawa K.

    Biomolecules (Biomolecules)  11 ( 4 )  2021.04

     View Summary

    Spider silk is a natural fiber with remarkable strength, toughness, and elasticity that is attracting attention as a biomaterial of the future. Golden orb-weaving spiders (Trichonephila clavata) construct large, strong webs using golden threads. To characterize the pigment of golden T. clavata dragline silk, we used liquid chromatography and mass spectrometric analysis. We found that the major pigment in the golden dragline silk of T. clavata was xanthurenic acid. To investigate the possible function of the pigment, we tested the effect of xanthurenic acid on bacterial growth using gram-negative Escherichia coli and gram-positive Bacillus subtilis. We found that xanthurenic acid had a slight antibacterial effect. Furthermore, to investigate the UV tolerance of the T. clavata threads bleached of their golden color, we conducted tensile deformation tests and scanning electron microscope observations. However, in these experiments, no significant effect was observed. We therefore speculate that golden orb-weaving spiders use the pigment for other purposes, such as to attract their prey in the sunlight.

  • Charged metabolite biomarkers of food intake assessed via plasma metabolomics in a population-based observational study in Japan

    Shibutami E., Ishii R., Harada S., Kurihara A., Kuwabara K., Kato S., Iida M., Akiyama M., Sugiyama D., Hirayama A., Sato A., Amano K., Sugimoto M., Soga T., Tomita M., Takebayashi T.

    PLoS ONE (PLoS ONE)  16 ( 2 February )  2021.02

     View Summary

    Food intake biomarkers can be critical tools that can be used to objectively assess dietary exposure for both epidemiological and clinical nutrition studies. While an accurate estimation of food intake is essential to unravel associations between the intake and specific health conditions, random and systematic errors affect self-reported assessments. This study aimed to clarify how habitual food intake influences the circulating plasma metabolome in a free-living Japanese regional population and to identify potential food intake biomarkers. To achieve this aim, we conducted a cross-sectional analysis as part of a large cohort study. From a baseline survey of the Tsuruoka Metabolome Cohort Study, 7, 012 eligible male and female participants aged 40-69 years were chosen for this study. All data on patients' health status and dietary intake were assessed via a food frequency questionnaire, and plasma samples were obtained during an annual physical examination. Ninety-four charged plasma metabolites were measured using capillary electrophoresis mass spectrometry, by a non-targeted approach. Statistical analysis was performed using partial-least-square regression. A total of 21 plasma metabolites were likely to be associated with long-term food intake of nine food groups. In particular, the influential compounds in each food group were hydroxyproline for meat, trimethylamine- N-oxide for fish, choline for eggs, galactarate for dairy, cystine and betaine for soy products, threonate and galactarate for carotenoid-rich vegetables, proline betaine for fruits, quinate and trigonelline for coffee, and pipecolate for alcohol, and these were considered as prominent food intake markers in Japanese eating habits. A set of circulating plasma metabolites was identified as potential food intake biomarkers in the Japanese community-dwelling population. These results will open the way for the application of new reliable dietary assessment tools not by self-reported measurements but through objective quantification of biofluids.

display all >>

Papers, etc., Registered in KOARA 【 Display / hide

display all >>

Reviews, Commentaries, etc. 【 Display / hide

  • Publisher Correction: Base editors for simultaneous introduction of C-to-T and A-to-G mutations (Nature Biotechnology, (2020), 38, 7, (865-869), 10.1038/s41587-020-0509-0)

    Sakata R.C., Ishiguro S., Mori H., Tanaka M., Tatsuno K., Ueda H., Yamamoto S., Seki M., Masuyama N., Nishida K., Nishimasu H., Arakawa K., Kondo A., Nureki O., Tomita M., Aburatani H., Yachie N.

    Nature Biotechnology (Nature Biotechnology)  38 ( 7 )  2020.07

    ISSN  10870156

     View Summary

    An amendment to this paper has been published and can be accessed via a link at the top of the paper.

  • Does the gut microbiota modulate host physiology through polymicrobial biofilms?

    Yang J., Yang Y., Ishii M., Nagata M., Aw W., Obana N., Tomita M., Nomura N., Fukuda S.

    Microbes and Environments (Microbes and Environments)  35 ( 3 ) 1 - 13 2020

    ISSN  13426311

     View Summary

    Microbes inhabit various environments, such as soil, water environments, plants, and animals. Humans harbor a complex commensal microbial community in the gastrointestinal tract, which is known as the gut microbiota. The gut microbiota participates not only in various metabolic processes in the human body, it also plays a critical role in host immune responses. Gut microbes that inhabit the intestinal epithelial surface form polymicrobial biofilms. In the last decade, it has been widely reported that gut microbial biofilms and gut microbiota-derived products, such as metabolites and bacterial membrane vesicles, not only directly affect the host intestinal environment, but also indirectly influence the health of the host. In this review, we discuss the most recent findings from human and animal studies on the interactions between the gut microbiota and hosts, and their associations with various disorders, including inflammatory diseases, atopic dermatitis, metabolic disorders, and psychiatric and neurological diseases. The integrated approach of metabologenomics together with biofilm imaging may provide valuable insights into the gut microbiota and suggest remedies that may lead to a healthier society.

  • Detecting A-to-I RNA editing in RNA-Seq data

    Galipon Josephine(ガリポン・ジョセフィーヌ), 石黒宗, 富田勝, 程久美子

    NGS Professional シリーズRNA-Seqマスターブック (株式会社 羊土社)   2016.04

    Introduction and explanation (scientific journal), Joint Work

  • Detecting A-to-I RNA editing in RNA-Seq data

    TOMITA MASARU

    NGS Professional シリーズRNA-Seqマスターブック ((羊土社))   2016

    Introduction and explanation (scientific journal)

  • The application of omics technologies in the functional evaluation of inulin and inulin-containing prebiotics dietary supplementation

    Tsurumaki, M., Kotake, M., Iwasaki, M., Saito, M., Tanaka, K., Aw, W., and *Fukuda, S. and Tomita, M.

    Nutr Diabetes. 5   e185 2015

    Introduction and explanation (scientific journal), Joint Work

Presentations 【 Display / hide

  • 越冬時における赤カブ‘温海かぶ’の胚軸の成分プロファイルの変化

    TOMITA MASARU

    第11回メタボロームシンポジウム (大阪府、吹田市) , 2017.11, Poster (general)

  • 修復関連タンパクを用いたハイスループット変異検出手法の開発

    TOMITA MASARU

    生命情報科学 若手の会 第9回研究会 (愛知県蒲郡市) , 2017.10, Poster (general)

  • Differential gene expression analysis of Euglena gracilis chloroplast deleted mutant

    TOMITA MASARU

    生命情報科学 若手の会 第9回研究会 (愛知県蒲郡市) , 2017.10, Poster (general)

  • 配列類似性ネットワークに基づくHIV-1 Pol上のサブタイプ分化と対応する 領域の解析

    TOMITA MASARU

    生命情報科学 若手の会 第9回研究会 (愛知県蒲郡市) , 2017.10, Poster (general)

  • Microbial communities of university campuses in Japan.

    TOMITA MASARU

    IIBMP2017 (北海道大学情報科学研究科) , 2017.09, Poster (general)

display all >>

Research Projects of Competitive Funds, etc. 【 Display / hide

  • 「In vivoヒト代謝システム生物学拠点」

    2007
    -
    2009

    グローバルCOEプログラム, Other

  • 「先端生命科学」

    2006
    -
    2010

    山形県研究教育補助金 第2期, Commissioned research

  • 「メタボローム解析のための計測技術開発とそれを用いた代謝経路推定」

    2006
    -
    2009

    科研費・特定領域研究「生命システム情報」公募研究A02, Commissioned research

  • 「システム生物学による生命機能の理解と制御」

    2005
    -
    2007

    21世紀COEプログラム(生命科学分野), Other

  • 「システムバイオロジーのためのモデリング・シミュレーション環境の構築」

    2004
    -
    2009

    戦略的創造研究推進事業(CREST)「シミュレ-ション技術の革新と実用化基盤の構築」研究領域, Commissioned research

display all >>

Awards 【 Display / hide

  • Honorary Fellow of the Metabolomics Society

    2017.06, Metabolomics Society

    Type of Award: International Academic Awards

  • WIRED Audi INNOVATION AWARD 2016

    2016

    Type of Award: Other Awards

  • Award for Academic Startups

    2014

  • Award for Academic Startups

    2014

  • 福澤賞

    TOMITA MASARU, 2009.11

    Type of Award: Keio commendation etc.

display all >>

Other 【 Display / hide

  • 2015年05月

     View Details

    KAUST Computational Bioscience Research Center Scientific Advisory Board Meeting (Jeddah, Saudi Arabia)
    にて座長を務める

 

Courses Taught 【 Display / hide

  • SYSTEMS OF LIFE

    2021

  • SPECIAL RESEARCH PROJECT B

    2021

  • SEMINAR B

    2021

  • MASTER SEMINAR

    2021

  • INDEPENDENT RESEARCH

    2021

display all >>

Courses Previously Taught 【 Display / hide

  • 生命と知能の進化

    Keio University, 2015, Autumn Semester, General education subject, Within own faculty

  • 生命システム

    Keio University, 2015, Spring Semester, General education subject, Lecture, Within own faculty, 512people

 

Social Activities 【 Display / hide

  • 経産省・産業構造審議会商務流通情報分科会バイオ小委員会

    2016.03
    -
    Present
  • 山形ブランド特命大使

    2016.03
    -
    Present
  • 特定非営利活動法人全脳アーキテクチャ・イニシアティブ顧問

    2015.09
    -
    2017.06
  • 横浜市立横浜サイエンスフロンティア高等学校科学技術顧問

    2013.04
    -
    Present
  • 鶴岡ふるさと観光大使

    2010.04
    -
    Present

display all >>

Memberships in Academic Societies 【 Display / hide

  • 情報計算化学生物学会(CBI学会), 

    2007.05
    -
    Present
  • International Society for Computational Biology(ISCB), 

    2001
    -
    Present
  • 日本バイオインフォマティクス学会, 

    2000
    -
    Present
  • 日本分子生物学会

     
  • 日本オミックス医療学会

     

display all >>

Committee Experiences 【 Display / hide

  • 2015
    -
    2018.03

    技術顧問, ㈱ヒューマン・メタボローム・テクノロジーズ

  • 2012.11
    -
    Present

    評議員, 全塾 評議員会

  • 2012.04
    -
    Present

    客員教授, 京都大学化学研究所

  • 2011.04
    -
    Present

    委員, 信濃町 慶應医学賞

  • 2011
    -
    Present

    所長, 先端生命科学研究所

display all >>