FY2022 Annual Report

Cell Signal Unit

Professor Tadashi Yamamoto

Abstract

The Cell Signal Unit studies molecular and cellular events that are relevant to and important for maintaining healthy life. The Unit studies gene regulation that is critical in responding to environmental cues. Particularly, we are interested in CCR4-NOT complex-mediated post-transcriptional regulation in which microRNAs, long non-coding RNAs and RNA binding proteins participates. Unit explores the link between the CCR4-NOT complex and various diseases that include cancer, neuronal disorder, immunological diseases, diabetes/obesity, and developmental failure. The Unit also characterizes protein kinase-mediated cell signaling especially in the control of the brain function such as emotions, learning and memory.

1. Staff

  • Dr. Akiko Yanagiya, Staff Scientist (-April, 2022)
  • Dr. Rieko Ajima, Staff Scientist (September, 2022-)
  • Dr. Shou Soeda, Postdoctoral Scholar (-June, 2022)
  • Dr. Hiroaki Sako, Postdoctoral Scholar
  • Dr. Lea Picard, Postdoctoral Scholar
  • Dr. Haytham Mohamed Aly Mohamed, Postdoctoral Scholar (August, 2022-)
  • Dr. Olga Elisseeva, Visiting Researcher
  • Dr. Guillaume Vares, Visiting Researcher
  • Dr. Emi Kawamoto, Visiting Researcher (-March, 2023)
  • Dr. Saori Nishijima, Technical Staff
  • Ms. Risa Ishida, Technical Staff
  • Ms. Nao Ohmine, Technical Staff
  • Ms. Atsuko Sato, Technical Staff
  • Mr. Mohieldin Magdy Mahmoud Youssef, Graduate Student (-September, 2022)
  • Ms. Aisulu Maipas, Graduate Student
  • Mr. Yuki Tara, Graduate Student
  • Ms. Ting-Hua Chen, Graduate Student (Wolf Unit)
  • Ms. Ena Hashimoto, Visiting Research Student (-March, 2023)
  • Ms. Eriko Okamatsu, Research Unit Administrator

2. Collaborations

TBD

2.1 Physiology and Molecular Cellular Biology of the CCR4-NOT complex
  • Description: Analyze the physiological and molecular biological roles of each component of the CCR4-NOT complex using gene-modified mice.
  • Type of collaboration: Joint research
  • Researchers:
    • Dr. Keiji Kuba, Department of Physiology, Graduate School of Medicine, Akita University
    • Dr. Toru Suzuki, (Division of RNA and Gene Regulation,) The Institute of Medical Science, The University of Tokyo
    • Dr. Toshinobu Fujiwara, Laboratory of Biochemistry, Faculty of Pharmacy, Kindai University
    • Dr. Taishin Akiyama, RIKEN
    • Dr. Masahiro Morita, Department of Molecular Medicine, University of Texas Health Science Center at San Antonio
    • Dr. Nahum Sonenberg, Department of Biochemistry, McGill University

2.2 Basic cancer research for prevention and treatment

  • Description: Search for substances that contribute to the prevention and treatment of cancer from biological resources, and elucidate its mechanism of action
  • Type of collaboration: Joint research I and II
  • Researchers:
    • I. Representative director Kuniaki Nerome, Nerome Institute of Biological Resources
    • II. Professor Shinya Ikematsu, National Institute of Technology, Okinawa College

2.3 Mechanisms and physiological roles of CCR4-NOT complex-regulated gene expression in the brain

  • Description: Electrophysiological studies of gene modified mice with abnormal social behavior
  • Type of collaboration: Joint research
  • Researchers:
    • Team leader Masaru Tamura, RIKEN

2.4 Analysis of CNOT9 function during mouse development

  • Type of collaboration: Joint research
  • Researchers:
    • Team leader Hiroshi Hamada, RIKEN
    • Technical staff Eriko Kajikawa, RIKEN

2.5 The neuromuscular junction as a new target for treatment of Hereditary Motor and Sensory Neuropathy, Okinawa-type, and related disorders

  • Description: Analyzing the pathogenic mechanism of HMSN-P using a mouse model; and analyzing the action mechanism(treatment mechanism) of enhancing NMJK formation on HMSN-P(HMSN with proximal dominancy)-like pathology, at the physiological, and molecular levels.
  • Type of collaboration: Joint research
  • Researchers:
    • Professor Yuji Yamanashi, The University of Tokyo.

2.6 Development of siRNA molecules that dramatically enhance the effect of anticancer drugs

  • Description: Examining the effects of tob-siRNA in other cultured human cancer cells, and to further investigate whether the efficacy of anticancer drugs is enhanced by introducing tob-siRNA into cancer-bearing mice implanted with breast, pancreatic, osteosarcoma, and bladder cancers. in vivo experiments.
  • Type of collaboration: Joint research
  • Researchers:
    • Dr. Kensuke Osada, National Institute for Quantum Sciend and Technology
    • Dr. Kiyoshi Yoshida, Nano Career Co. Ltd.
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3. Activities and Findings

TBD

3.1. Neuronal XRN1 is required for maintenance of whole-body metabolic homeostasis
(iScience Volume 24, Issue 10, 22 October 2021, 103151)

Control of mRNA stability and degradation is essential for appropriate gene expression, and its dysregulation causes various disorders, including cancer, neurodegenerative diseases, diabetes, and obesity.

The 5’–3’ exoribonuclease XRN1 executes the last step of RNA decay, but its physiological impact is not well understood. To address this, forebrain-specific Xrn1 conditional knockout mice (Xrn1-cKO) were generated, as Xrn1 null mice were embryonic lethal. Xrn1-cKO mice exhibited obesity with leptin resistance, hyperglycemia, hyper- phagia, and decreased energy expenditure. Obesity resulted from dysregulated communication between the central nervous system and peripheral tissues. Moreover, expression of mRNAs encoding proteins that regulate appetite and energy expenditure was dysregulated in the hypothalamus of Xrn1-cKO mice. Therefore, we propose that XRN1 function in the hypothalamus is critical for maintenance of metabolic homeostasis.

An Image of This Study

Figure 1: Forebrain specific Xrn1-cKO mice exhibit obesity (left) with hyperphagia (right) at 12 weeks old.

Figure 2: AgRP expression is upregulated in the Xrn1-cKO hypothalamus: Quantitative PCR analysis of the indicated mRNA levels in the hypothalamus of 10 to 14 week-old mice

3.2 Regulation of Early Lymphocyte Development via mRNA Decay Catalyzed by the CCR4-NOT Complex-a review
(Front. Immunol., 19 July 2021)

Development of lymphocytes is precisely regulated by various mechanisms. In addition to transcriptional rates, post-transcriptional regulation of mRNA abundance contributes to differentiation of lymphocytes. mRNA decay is a post-transcriptional mechanism controlling mRNA abundance. The carbon catabolite repression 4 (CCR4)-negative on TATA-less (NOT) complex controls mRNA longevity by catalyzing mRNA deadenylation, which is the rate-limiting step in the mRNA decay pathway. mRNA decay, regulated by the CCR4-NOT complex, is required for differentiation of pro-B to pre-B cells and V(D)J recombination in pro-B cells. In this process, it is likely that the RNA-binding proteins, ZFP36 ring finger protein like 1 and 2, recruit the CCR4-NOT complex to specific target mRNAs, thereby inducing cell quiescence of pro-B cells. A recent study showed that the CCR4-NOT complex participates in positive selection of thymocytes. Mechanistically, the CCR4-NOT deadenylase complex inhibits abnormal apoptosis by reducing the expression level of mRNAs encoding pro-apoptotic proteins, which are otherwise up-regulated during positive selection. We discuss mechanisms regulating CCR4-NOT complex-dependent mRNA decay in lymphocyte development and selection.

Figure 1: Active RNA decay pathways mediated by the CCR4-NOT complex. The CCR4-NOT complex can be recruited by RNA binding proteins (RBP), miRNA- Ago2 complex, and YTHDF2 bound to N6-methyladeonsine, which is generated by the METTL3 and METTL14 methyltransferase complexes. The CCR4-NOT complex deadenylates polyA tails of recruited mRNAs. After deadenylation, 5’-decapping enzymes are recruited and eliminate the cap structure. Finally, 5’- exonucleases (Xrn1 and 2) causes degradation of target mRNAs.

Figure 2: Early lymphocyte development regulated by the CCR4-NOT complex. The CCR4-NOT complex is required for differentiation of pro-B cells to pre-B cells and positive selection of DP thymocytes. ZFP36L1 and ZFP36L2 (ZFP36L1/2) regulate the pro-B cell to pre-B cell transition and b-selection of the DN3 thymocyte stage. Involvement of the CCR4-NOT complex in b selection has not been verified yet. Some differentiation stages were omitted for simplicity. CLP, common lymphoid progenitor; DN, CD4 CD8 double negative thymocyte; DP, CD4 CD8 double positive thymocyte; SP, CD4 or CD8 single positive thymocytes.

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4. Publications

4.1 Journals

  1. Youssef M, Hamada H T, Lai E S, Kiyama Y, Eltabbal M, Kiyonari H, Nakano K, Kuhn B and Yamamoto T, TOB is an effector of the hippocampus-mediated acute stress response, Translational Psychiatry, volume 12, Article number: 302, 2022 (Published: 29 July 2022)
  2. Matsuura K, Aly Mohamed H M, Youssef M, Yoshida Y, and Yamamoto T, Synaptotagmin 2 is ectopically overexpressed in excitatory presynapses of a widely used CaMKⅡα-Cre mouse line, iScience, Vol. 25 Issue 8, 2022 (Published online: June 30, 2022)
  3. Aly Mohamed H M, Takahashi A, Nishijima S, Adachi S, Murai I, Okamura H and Yamamoto T.CNOT1 regulates circadian behavior through Per2 mRNA decay in a deadenylation-dependent manner, RNA Biology, Volume19, Issue1, 2022 (Published online: 05 May 2022)

4.2 Books and other one-time publications

Nothing to report

4.3 Oral and Poster Presentations

  1. Tara Y, Yanagiya A, Yamamoto T, "Regulation of mRNA decay mediated by YTHDF2 to maintain pancreatic β cell homeostasis", The Molecular Biology Society of Japan, Makuhari, Japan, December 2, 2022, onsite
  2. Sako H, Youssef M, Elisseeva O, Akimoto T, Suzuki K, Ushida T, Yamamoto T, "miRNA slows translating ribosomes to prevent protein misfolding", The Molecular Biology Society of Japan, Makuhari, Japan, December 1, 2022, onsite
  3. Ajima R, "ATXN10 was Identified as a Wnt5a downstream target, which regulates planar cell polarity establishment during early development in mouse", EMBO Workshop Wnt 2022, Awaji, Hyogo, Japan, November 16, 2022, onsite
  4. Ajima R, Saga Y, "E3 Ubiquitin Ligase HUWE1 Regulates Planar Cell Polarity Through Controlling Pk Localization", 68TH NIBB conference "Principles of Cell Communication in Tissue", Okazaki, Aichi, Japan, November 14, 2022, onsite
  5. Tara Y, Yamamoto T, "mRNA turnover mediated by YTHDF2 to maintain pancreatic β cell homeostasis, Nature Conferences", Metabolic Communication Across Biological Scales, Online, November 2, 2022, online
  6. Ajima R, "E3 ubiquitin ligase HUWE1 regulates planar cell polarity through controlling Pk localization", OIST-Kyoto University Joint Workshop, OIST, Okinawa, Japan, November 2, 2022, onsite
  7. Ajima R, "マウス初期発生においてE3ユビキチンライゲースHUWE1は平面内極性制御により左右軸形成を制御する", 第12回シグナルネットワーク研究会, Online, October 28, 2022, online
  8. Tara Y, Yamamoto T, "Regulation of mRNA turnover mediated by YTHDF2 and CCR4-NOT complex to maintain pancreatic β cell homeostasis", The 9th CCR4-NOT meeting, Shiga, Japan, October 25, 2022, onsite
  9. Maipas A, Yamamoto T, "The role of the CCR4-NOT complex in post-transcriptional regulation of cellular senescence", The 9th CCR4-NOT meeting, Shiga, Japan, October 25, 2022, onsite
  10. Mohieldin M Youssef, Hiro Hamada, Esther Lai, Yuji Kiyama, Mohamed Eltabbal, Bernd Kuhn, Tadashi Yamamoto, "Deciphering the role of Tob in the brain: An insight into stress coping machinery", Japanese Neuroscience society meeting (Neuro2022), Okinawa, Japan, , July 1, 2022, onsite *Selected Best presentation award for young researchers "Wakate Dojo"

5. Intellectual Property Rights and Other Specific Achievements

Nothing to report

6. Meetings and Events

6.1 Seminars

1. Elucidation of the role of the p53 pathway in cancers that retain wild-type p53

  • Date: April 6, 2022
  • Venue: OIST Campus Lab1
  • Speaker: Dr. Rieko Ohiki, National Cancer Center Research Institute

2. Identification and characterization of Wnt5a downstream targets during early development in mouse

  • Date: June 10, 2022
  • Venue: OIST Campus Conference Center
  • Speaker: Dr. Rieko Ajima, National Institute of Genetics

3. Cancer stem cells and their niches in tumorigenesis and treatment resistance

  • Date: July 25, 2022
  • Venue: OIST Campus Center Builiding
  • Speaker: Professor Naoki Oshimori, Oregon Health & Science University

4. SKP1A links Polycomb-repressed genes with proteasome

  • Date: November 14, 2022
  • Venue: OIST Campus Center Builiding
  • Speaker: Dr. Haruhiko Koseki, Center for Integrative Medical Sciences, RIKEN

5. EHE – Epithelial Hemangio-Endothelioma, cancer driven by fusions of YAP or TAZ oncogenes with genes that encode transcription factors

  • Date: January 25, 2023
  • Venue: zoom
  • Speaker: Associate Professor, Marius Sudol, Icahn School of Medicine at Mount Sinai

6. Peroxisome biogenesis and human disorders

  • Date: February 8, 2023
  • Venue: OIST Campus Lab3
  • Speaker: Professor Yukio Fujiki, Kyushu University

7. VIPR2 copy number variants as a risk factor for schizophrenia

  • Date: February 15, 2023
  • Venue: OIST Campus Lab3
  • Speaker: Professor Yukio Ago, Hiroshima University

8. Modeling autism spectrum disorders with iPS cell technology and disease model mice

  • Date: February 15, 2023
  • Venue: OIST Campus Lab3
  • Speaker: Professor Takanobu Nakazawa, Tokyo University of Agriculture

9. Cancer hijacks regulation of oxygen-sensing mechanisms by Mint3

  • Date: February 22, 2023
  • Venue: OIST Campus Lab1
  • Speaker: Distinguished Professor Takeharu Sakamoto, Kansai Medical University

10. New developments in antiviral drug: Further preparation for the next pandemic

  • Date: March 1, 2023
  • Venue: OIST Campus Lab3
  • Speaker: Project Professor Jun-ichiro Inoue, The University of Tokyo

11. Transcriptional regulation of immediate-early genes by a novel ERK substrate protein and its failure in cancer

  • Date: March 8, 2023
  • Venue: OIST Campus Lab3
  • Speaker: Professor Mutsuhiro Takekawa, The University of Tokyo

12. Current Trends in Anticancer Drugs

  • Date: March 15, 2023
  • Venue: OIST Campus Lab1
  • Speaker: Dr. Mina Delawary, Daiichi Sankyo Co., Ltd.

13. Role of c-Myc on the antimycin A sensitivity in cancer cells

  • Date: March 22, 2023
  • Venue: OIST Campus Lab3
  • Speaker: Dr. Nobumoto Watanabe, Center for Sustainable Resource Science, RIKEN

14. Artificial viruses to target cancers by polymer nanoassembly technology

  • Date: March 29, 2023
  • Venue: OIST Campus Lab3
  • Speaker: Dr. Kensuke Osada, National Institutes for Quantum Science and Technology

6.2 Meetings

Nothing to report

7. Other

Nothing to report.