FY2016 Annual Report

G0 Cell Unit
Professor Mitsuhiro Yanagida​​

Abstract

The G0 Cell Unit studies how cells in the proliferative (dividing) or quiescent (non-dividing) phase respond to nutritional shifts (e.g., nitrogen source starvation and glucose limitation). We identify gene products (mostly proteins) and chemical factors (small molecules, metabolites) that affect adaptation mechanisms in order to understand the basis for longevity of long-term quiescent cells. We employ fission yeast as a eukaryotic cell model as the great majority of this organism’s genes are conserved in human. In addition, we are studying chromosomal regulatory mechanisms involving condensin, cohesin complexes (which lead to proper chromosome segregation in proliferating cells), and other nutrient adaptation-related nuclear chromatin proteins. This line of studies aims to understand dynamics of nuclear chromatin in response to nutritional cues. Study on human blood metabolomics initiated from comparative study with fission yeast metabolomics now directly aims to identify and understand the roles of metabolites intimately related to human aging.

Our current principal research projects may be summarized as below:

(1a) Methodological development for metabolomic analysis.

(1b) Comprehensive and quantitative human blood metabolomics.

(2) Understanding cell regulation in response to nitrogen deprivation.

(3) Understanding cell regulation in response to glucose starvation.

(4) Understanding chromosomal regulatory mechanisms involving condensin, cohesin complexes, and other nutrient adaptation-related nuclear proteins.

In FY2016, we published original articles on a topoisomerase II inhibitor, ICRF-193, which induces arched telophase spindles and leads to a ploidy increase in fission yeast, and several metabolome protocols, as listed in 3. Activities and Findings and 4. Publications.

1. Staff

  • Dr. Yung-Ju Chen, Researcher (from May)
  • Dr. Takeshi Hayashi, Researcher
  • Dr. Norihiko Nakazawa, Researcher
  • Dr. Paul-Emile Poleni, Researcher 
  • Dr. Kenichi Sajiki, Researcher
  • Dr. Emily Tsang, Researcher (until September)
  • Dr. Xingya Xu, Researcher
  • Dr. Haifeng Zhang, Researcher 
  • Ms. Orie Arakawa, Technician
  • Ms. Wendy Gutierrez, Technician (until April)
  • Ms. Ayaka Mori, Technician
  • Ms. Michiko Suma, Technician (from February, 2017)
  • Ms. Yuria Tahara, Technician
  • Ms. Junko Takada, Technician
  • Dr. Takayuki Teruya, Technician
  • Ms. Risa Uehara, Technician
  • Ms. Li Wang, Technician
  • Ms. Caroline Starzynski, OIST Student
  • Mr. Shijin Zhang, OIST Student (from May to August)
  • Mr. Tsung-Yen Huang, OIST Student (from September to December)
  • Ms. Chikako Sugiyama, Research Unit administrator

2. Collaborations

  • Theme: Screening for low-glucose sensitive mutants in fission yeast
    • Type of collaboration: Joint research
    • Researchers:
      • Professor Shigeaki Saitoh, Institute of Life Science, Kurume University
  • Theme: Identification of the molecular mechanism, required for the maintenance of cell viability in low glucose condition
    • Type of collaboration: Joint research
    • Researchers:
      • Professor Kunihiro Ohta, Department of Life Science, Graduate School of Arts and Science, The University of Tokyo
  • Theme: Analysis of biomarkers, discovered by research using S.pombe, in human blood
    • Type of collaboration: Joint research
    • Researchers:
      • Dr. Hiroshi Kondoh, Department of Geriatric Medicine, Graduate School of Medicine, Kyoto University
      • Dr. Takumi Mikawa, Department of Geriatric Medicine, Graduate School of Medicine, Kyoto University
  • Theme: Proteome and phosphoproteome analysis of fission yeast using mass spectrometer
    • Type of collaboration: Joint research
    • Researchers:
      • Professor Takeshi Tomonaga, Project Leader, National Institutes of Biomedical Innovation, Health and Nutrition, a National Research and Development Agency
      • Dr. Jun Adachi, Project Researcher, National Institutes of Biomedical Innovation, Health and Nutrition, a National Research and Development Agency
      • Dr. Yuichi Abe, Specially Appointed Researcher, National Institutes of Biomedical Innovation, Health and Nutrition, a National Research and Development Agency
  • Theme: Structural understanding of the mechanisms of chromosomal cohesion by cohesin and chromosomal condensation/segregation by condensin.​
    • Type of collaboration: Joint research
    • Researchers:
      • Professor Chikashi Toyoshima,  Institute of Molecular and Cellular Biosciences, the University of Tokyo
      • Dr. Ryuta Kanai, Institute of Molecular and Cellular Biosciences, the University of Tokyo 
  • Theme: Comparative analysis of blood metabolome between healthy people and metabolic abnormality patients
    • Type of collaboration: Joint research
    • Researchers:
      • Professor Hiroaki Masuzaki, Division of Endocrinology, Diabetes and Metabolism, Hematology, Rheumatology (Second Department of Internal Medicine), Graduate School of Medicine, University of the Ryukyus
  • Theme: Blood metabolome analysis in abnormal cerebral function
    • Type of collaboration: Joint research
    • Researchers:
      • Dr. Yasuhide Fukuji, Director, National Hospital Organization Ryukyu Hospital
      • Dr. Taku Otsuru, Deputy Director, National Hospital Organization Ryukyu Hospital

3. Activities and Findings

ICRF-193, an anticancer topoisomerase II inhibitor, induces arched telophase spindles that snap, leading to a ploidy increase in fission yeast. (From OIST news center article "Paving the Road to Drug Discovery" by Sarah Wong)

Cancer is a notoriously difficult disease to treat. Not only do a wide variety of cancers exist, requiring specialized treatments for each type, but cancer cells within an individual can morph and render previously potent therapeutics ineffective. Thus, there is a continual need to discover new, effective drugs. Research from Dr. Norihiko Nakazawa in the G0 Cell Unit at the Okinawa Institute of Science and Technology Graduate University (OIST) led by Prof. Mitsuhiro Yanagida, may help make the discovery process easier. This research was published in Genes to Cells.

Cancer cells differ from normal cells in a variety of different ways. Most notably, malignant cells exhibit a much higher rate of replication and proliferation than normal ones. The rapid growth of these cells can result in tumor formation and metastasis, or the spreading of cancer to other parts of the body. Fortunately, scientists have been able to exploit these properties to create new treatments. Since the proteins involved in DNA replication are considerably more active in cancer cells than in normal ones, researchers have discovered that drugs which target these proteins will disproportionately affect the malignant cells. These drugs are designed to only affect active proteins, so that even though the same proteins exist in normal cells, the majority of the normal cells will contain inactive proteins at the time of treatment, and thus be unaffected. 

Dr. Nakazawa’s research centered on the use of a specific anti-cancer drug, ICRF-193, which targets a protein called DNA topoisomerase II. As part of his research, Dr. Nakazawa treated fission yeast with ICRF-193 and observed the effects. Typically, during cell reproduction, DNA is copied so that a cell temporarily contains twice the amount of DNA than it normally does. These two copies of chromosomal DNA are pulled to different ends of the cell by a protein structure called the mitotic spindle. Once the chromosomal DNA is separated, the cell begins to divide into two identical daughter cells.

When Dr. Nakazawa treated fission yeast with ICRF-193, he noticed that the cells appeared to have difficulty separating after DNA replication had occurred. Instead of separating normally, the mitotic spindle appeared to continue to lengthen despite failing to fully separate the two copies of DNA, producing an arched shape until eventually snapping in the middle. This “arched and snapped” appearance seemed to be unique to the ICRF-193 treated cells.

Researchers can utilize this “arched and snapped” appearance to look for other drugs that affect fission yeast proteins in the same manner. The replication machinery and DNA-bound proteins of fission yeast are highly conserved and thus remarkably similar to other organisms, including humans. Because of this similarity, drugs that affect these proteins in fission yeast are likely to affect the related highly active proteins in human cancers. This research makes it plausible to use fission yeast in the place of human cells in the discovery process of novel cancer drugs.

There are many disadvantages to using human cells in the initial stages of creating a new therapy. Scientists often have to test a large number of compounds in order to find one that is effective against a particular target. Human cells are costly to take care of and require a lot of time and specific conditions in order to grow. According to Dr. Nakazawa, “fission yeast is a relatively fast, easy to use model system that is low cost,” making it advantageous for use in drug screens.  Time and cost are often major hurdles in the process of drug development, so any discoveries that expedite the process can help get the next cancer cure in the hands of patients sooner. 

4. Publications

4.1 Journals

1. Kondoh H, Yanagida M (2016) Reply to Mäkinen and Ala-Korpela: Small-scale but accurate metabolomics with high reproducibility for identifying age-related blood metabolites. Proc Natl Acad Sci U S A. 113(25):E3471-2 [PubMed]

2. Nakazawa N, Mehrotra R, Arakawa O, Yanagida M (2016) ICRF-193, an anticancer topoisomerase II inhibitor, induces arched telophase spindles that snap, leading to a ploidy increase in fission yeast. Genes Cells. 21(9):978-93 [PubMed] 

3. Shah M, Su D, Scheliga JS, Pluskal T, Boronat S, Motamedchaboki K, Campos AR, Qi F, Hidalgo E, Yanagida M, Wolf DA (2016) A Transcript-Specific eIF3 Complex Mediates Global Translational Control of Energy Metabolism. Cell Rep. 16(7):1891-902 [PubMed]

4. Pluskal T, Yanagida M (2016) Metabolomic Analysis of Schizosaccharomyces pombe: Sample Preparation, Detection, and Data Interpretation. Cold Spring Harb Protoc.  2016(12) : pdb. top079921 [PubMed]

5. Pluskal T, Nakamura T, Yanagida M (2016) Preparation of Intracellular Metabolite Extracts from Liquid Schizosaccharomyces pombe Cultures. Cold Spring Harb Protoc. 2016(12) : pdb. prot091553 [PubMed]

6. Pluskal T, Yanagida M (2016) Measurement of Metabolome Samples Using Liquid Chromatography-Mass Spectrometry, Data Acquisition, and Processing. Cold Spring Harb Protoc. 2016(12): pdb. prot091561 [PubMed]

4.2 Books and other one-time publications

Nothing to report

4.3 Oral and Poster Presentations

1. Sajiki, K. Scientific analysis of Okinawan traditional pottery, Science Cafe at Goblin Park, Aoyama, Tokyo, 13 May (2016).       

2. Yanagida, M. Can Blood Test tell Aging degree?, Okinawa Prefectural South Medical Treatment Center, Okinawa, 20 May (2016).

3. Yanagida, M. Longevity and Food,  Food Symposium & Festival 'The Science on Your Plate', OIST auditorium, Okinawa, 28 May (2016).

4. Yanagida, M. Progress of chromosome mechanism research in near future, Osaka University, Osaka, 4 June (2016).

5. Yanagida, M. Seeking for functional diversity and quantitativeness of human blood metabolite, Kurume University, Fukuoka, 24 June (2016).

6. Sajiki, K. Scientific analysis of Okinawan traditional pottery, Sacience Cafe at Sakurazaka Theater, Okinawa, 28 June (2016).

7. Nakazawa, N. Unique spindle phenotype induced by ICRF-193, an anticancer topoisomerase II inhibitor, in fission yeast, The 49th Yeast Genetics and Molecular Biology Forum, Kobe, 10 September (2016).

8. Sajiki, K. Essential Genes for G0 phase, The 49th Yeast Genetics and Molecular Biology Forum, Kobe, 10 September (2016).

9. Yanagida, M. Blood metabolomics for human health and longevity: toward understanding roles of age-related metabolites, The 23rd East Asia Joint Symposium, National Taiwan Normal University, Taipei, Taiwan, 18 October (2016).

10. Chen, Y. Impact of Dietary Broccoli on Non-Alcoholic Fatty Liver Disease and Liver Cancer in Mice Fed a Wester Diet, The 23rd East Asia Joint Symposium, National Taiwan Normal University, Taipei, Taiwan, 17-21 October (2016).

11. Sajiki, K. Essential Genes for Healthy Quiescence: yeast study to understand cellular longevity, The 23rd East Asia Joint Symposium, National Taiwan Normal University, Taipei, Taiwan, 17-21 October (2016).

12. Yanagida, M. Individual variability in human blood metabolites: Identification of age-related differences, The Institute of Molecular and Cellular Biosciences , The University of Tokyo, Tokyo, 15 November (2016).

13. Nakazawa, N. Unique spindle phenotype induced by ICRF-193, an anticancer topoisomerase II inhibitor, in fission yeast, The 39th Annual Meeting of the Molecular Biology Society of Japan, Pacifico Yokohama, Yokohama, 1 December (2016).

14. Yanagida, M. Toward Elucidation of Cohesin and Condensin Function, The 4th Histone Variant Meeting, Tohoku University, Sendai, 11 February (2017).

5. Intellectual Property Rights and Other Specific Achievements

Nothing to report

6. Meetings and Events

Seminars 

1. Title: Glycolysis in senescence and metabolites in ageing

  • Date: Febraury 2, 2017
  • Venue: C016, OIST Campus Lab1
  • Speaker: Dr. Hiroshi Kondoh (Associate professor, Geriatric Unit, Department of community network and collaborative medicine, Graduate School of Medicine, Kyoto University)

2. Title:Regulation of Ribosomal RNA gene stability and Its Role in cellular senescence and Evolutionary Adaptability in Yeast

  • Date: Febrary 23, 2017
  • Venue: D014, OIST Campus Lab1
  • Speaker: Prof. Takehiko Kobayashi (Institute of Molecular and Cellular Biosciences, The University of Tokyo)

3. Title: NIPBL and Aff4, Yin and Yang of global regulator of transcription 

  • Date: March 7, 2017
  • Venue: C016, OIST Campus Lab1
  • Speaker: Prof. Katsuhiko Shirahige (Institute of Molecular and Cellular Biosciences, The University of Tokyo)

4. Title: alpha-Klotho in health and diseases

  • Date: March 16, 2017
  • Venue: D014, OIST Campus Lab1
  • Speaker: Prof. Yo-ichi Nabeshima (Principal Investigator, Laboratory of Molecular Life Science Director, Institute of Biomedical Research and Innovation Foundation for Biomedical Research and Innovation)

7. Other

Nothing to report.