Bulletin of the Medical Research Institute
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Bulletin of the Medical Research Institute
Advanced Molecular Medicine Molecular Medicine and Metabolism Prof. Yoshihiro OGAWA Molecular Pharmacology Prof. Masaki NODA Molecular Cell Biology Prof. Hiroshi SHIBUYA Molecular Neuroscience Prof. Kohichi TANAKA Cell Regulation Prof. Yuji YAMANASHI Bio-informational Pharmacology Prof. Tetsushi FURUKAWA Autonomic Physiology Prof. Yoshifumi KATAYAMA ● Molecular Medicine and Metabolism Professor Associate Professor Assistant Professor Yoshihiro OGAWA Yasutomi KAMEI Takayoshi SUGANAMI Our mission is to elucidate the molecular basis of and to develop the therapeutic strategies against the metabolic syndrome, the coexistence of several risk factors for atherosclerosis, including visceral obesity, hyperglycemia, atherogenic dyslipidemia, and hypertension. Accordingly, we have been focusing on the pathophysiologic and therapeutic implications of adipocytokines, nuclear hormone receptors, and transcriptional co-activators/co-repressors in the metabolic syndrome. ―Research projects― Preadipocytes Mature ● Pathophysiologic and therapeutic implications of adipocytokines (leptin, TNF-α, free fatty acids adipocytes etc.) ● Pathophysiologic and therapeutic implications of chronic, low-grade inflammation in the metabolic syndrome ● Molecular mechanisms of adipocyte proliferation and differentiation ● Pathophysiologic and therapeutic implications of nuclear hormone receptors, transcriptional co-activators/co-repressors Measurement of % body ● Molecular genetics of congenital metabolic disorders fat, muscle mass, and bone density ―Publications― A. Yasoda et al. Overexpression of CNP in chondrocytes rescues achondroplasia through a MAPK-dependent pathway. Nat. Med. 10: 80-86, 2004. E. Suganami et al. Leptin stimulates ischemia-induced retinal neovascularization: possible role of vascular endothelial growth factor expressed in retinal endothelial cells. Diabetes 53: 2443-2448, 2004. Y. Kamei et al. Skeletal muscle FOXO1 (FKHR)-transgenic mice have less skeletal muscle mass, down-regulated type I (slow twitch/red muscle) fiber genes. J. Biol. Chem. 279: 41114-41123, 2004. T. Suganami et al. Prevention and reversal of renal injury by leptin in a new mouse model of diabetic nephropathy. FASEB J. 19:127-129, 2005. Genetically obese ob/ob mice (left) and lean littermates (right) 1 MRI 2005 homepage:http://www.tmd.ac.jp/mri/prm/index.html contact:Yoshihiro Ogawa ([email protected]) locarion:Surugadai area, 5th floor ● Molecular Pharmacology Professor Lecturer Lecturer Masaki NODA Yoichi EZURA Kazuhisa NAKASHIMA To clarify the molecular mechanism for the pathogenesis of major diseases affecting skeletal system (ex, osteoporosis, osteoarthrosis and rheumatoid arthritis), we examine the abnormality in mineral homeostasis or calcium metabolism, cellular responses, and cytokine network affecting the etiological bases for those diseases. Bone Mass Analysis ―Research projects― ● Transcription factors regulating bone cell differentiation ● Cytokines and growth factors ● Mechanical stress and cell attachment ● Developmental biology on bone and cartilage ―Publications― Morinobu M, Noda M, et al.: The nucleocytoplasmic shuttling protein CIZ reduces adult bone mass by inhibiting bone morphogenetic protein induced bone formation. J. Exp. Med. 201(6):, 961-970 (2005) Elefteriou F, Noda M,et al.: Leptin regulation of bone resorption by the sympathetic nervous system and CART. Nature Osteocyte Net Work 434:514-520 (2005) Usui M, Noda M,et al.: Tob deficiency superenhances osteoblastic activity after ovariectomy to block estrogen deficiency-induced osteoporosis. Proc. Natl. Acad. Sci. USA 101( 17):6653-6658 (2004) Yumoto K, Noda M, et al.: Osteopontin deficiency protects joints against destruction in anti-type II collagen antibody-induced arthritis in mice. Proc. Natl. Acad. Sci. USA 99(7):4556-61 (2002) Bone Loss Signaling ● Molecular Cell Biology homepage:http://www.tmd.ac.jp/mri/mph/index.html contact:Masaki NODA ([email protected]) location : Surugadai area, 7・8th floor Professor Associate Professor Assistant Professor Lecturer Hiroshi SHIBUYA Junji OHNISHI Kiyotoshi SATOH Tetsuo MORIGUCHI Morphogenesis and organogenesis of the vertebrate are regulated by various signaling molecules inducing the cell-growth and differentiation. The failure of many these signal molecules has also been achieved with induction of the diseases. Therefore, the elucidation of signal transduction network regulating generation and differentiation becomes an important problem upon clarifying the mechanism of morphogenesis, organogenesis and diseases. We focus the signal transduction network regulating the mechanisms of morphogenesis and organogenesis in developmental process. ―Research projects― ● Signal transduction mechanism, which controls the cell proliferation and differentiation. ● Analysis of signaling molecules, which regulate the development and differentiation using the model animals. ―Publications― Ohkawara, B., et al.: Role of the TAK1-NLK-STAT3 pathway in TGF-β-mediated mesoderm induction. Genes Dev. 18,381-386 (2004). Hyodo-Miura, J. et al.: Involvement of NLK and Sox11 in neural induction in Xenopus development. Genes Cells 7, 487-496 (2002). Nishita, M. et al.: Interaction between Wnt and TGF-β signalling pathways during formation of Spemann's organizer. Nature 403, 781-785 (2000). homepage:http://www.tmd.ac.jp/mri/mri-mcb/index_j.html contact:Hiroshi SHIBUYA ([email protected]) location : Surugadai area, Bldg. 3, 3rd・4th floor 2 MRI 2005 ● Molecular Neuroscience Professor Associate Professor Assistant Professor Kohichi TANAKA Hiroko OHKI-HAMAZAKI Michihiro MIEDA The final goal of our research is to understand molecular, cellular, and neuronal ensemble mechanisms underlying higher order brain functions including learning and memory. For that purpose, we combine molecular genetics, physiological and behavioral methods. The laboratory also studies the mechanism that underlies neuronal cell death and regeneration. Epilepsy in glutamate transporter knockout mice ―Research projects― ● Role of astrocyte-neuron interactions in higher brain function ● Role of glutamate transporters in the brain ● Role of neuropeptides in higher brain function (bombesin receptors and orexin) ● Neural basis of learning and memory in avian model ―Publications― Apparatus for the imprinting behavior Sleep/wake cycles of transgenic and wild-type mice ● Cell Maekawa F. et al.: Leptin resistance and enhancement of feeding facilityation by melanin-concentrating hormone in mice lacking bombesin receptor subtaype-3. Diabetes 53, 570-576 (2004). Mieda M, et al.: Orexin peptides prevent cataplexy and improve wakefulness in orexin neuron-ablated model of narcolepsy in mice. Proc. Natl. Acad. Sci. USA. 101, 4649-4654 (2004). Voutsinos-Porche B. et al.: Glial glutamate transporters mediate a functional metabolic crosstalk between neurons and astrocytes in the mouse developing cortex. Neuron 37, 275-2846 (2003) homepage : http://www.tmd.ac.jp/mri/aud/index.html contact : Kohochi TANAKA ([email protected]) location : Yushima area, Bldg. 3, 3rd floor Regulation Professor Associate Professor Assistant Professor Yuji YAMANASHI Osamu HIGUCHI Ryuichi MASHIMA The major interest is in molecular signals regulating a variety of cellular activities, aiming to address how deregulated cellular signals cause neoplastic, immune, neural, infectious, and developmental diseases. We currently study the molecular mechanisms of such signaling events through experiments with cultured cells, model animals, and clinical samples. Role of the Dok proteins. ―Research projects― ● Roles of Dok-family adaptors in cellular signaling ● Identification of novel signaling molecules downstream of protein-tyrosine kinases ● Roles of signaling molecules in embryogenesis and muscle differentiation. ● Mechanisms of protein-tyrosine kinase-mediated tumorigenesis. ―Publications― Novel signaling molecules Mouse model system 3 MRI 2005 Shinohara H, Inoue A, ---, & Yamanashi Y.: Dok-1 and Dok-2 are negative regulators of lipoplysaccharide-indcued signaling. J. Exp. Med. 201, 333-339 (2005) Yasuda T, Shirakata M, ---, & Yamanashi Y.: Role of Dok-1 and Dok-2 in myeloid homeostasis and suppression of leukemia. J. Exp. Med. 200, 1681-1687 (2004) Imadome K, Shirakata M, ---, & Yamanashi Y.: CD40 ligand is a critical effector of Epstein-Barr virus in host cell survival and transformation. Proc. Natl. Acad. Sci. USA. 100, 7836-7840 (2003) dok Yamanashi Y, Tamura T, ---, & Baltimore D.: Role of the rasGAP-associated docking protein p62 in negative regulation of B cell receptor-mediated signaling. Genes Dev. 14, 11-16 (2000) homepage : http://www.tmd.ac.jp/mri.creg/index.html contact : Yuji YAMANASHI ([email protected]) location : Yushima area, Bldg. 3, 3rd floor ● Bio-informational Pharmacology Professor Assistant Professor Tetsushi FURUKAWA Junko KUROKAWA We study function and structure of ion channels and transporters from both physiological and molecular approaches, with collaboration with bio-informatics, structural biology, and organic chemistry. Our aims are to establish a novel strategy for prevention and treatment of common cardiovascular diseases, such as arrhythmias and heart failure. ―Research projects― ● Gender-specific medicine for sudden death and lethal arrhythmias (Single-channel recording by ● Personalized medicine for sudden death and lethal arrhythmias patch-clamp technique) ● Cardiac channelopathy (LQT, Brugada syndrome, etc.) ● Discovery of leads/seeds and drugs for lifestyle-related diseases in tranditional medicines (kannpo・herbs etc.) and natural foods (isoflavone・saponin etc.) ● Establishment of novel cardiac regeneration system and autograft system Functional study ―Publications― Bio-informatics (ion channel structure) Cardiomyocyte regeneration (Cell transplantation in animal models) ● Autonomic Bai CX, Kurokawa J, Furukawa T, et al.: Non-genomic regulation of cardiac repolarization currents by testosterone. Circulation in press (2005). Bai CX, Kurokawa J, Furukawa T, et al.: Role of nitric oxide in Ca2+-sensitivity of the delayed rectifier K+ current in cardiac myocytes. Circ. Res. 96, 64-72 (2005). Kurokawa J, Kass RS, et al.:Regulatory action of the A-kinase anchoring protein Yotiao on a heart potassium channel downstream of PKA phosphorylation. Proc. Natl. Acad. Sci. USA 101, 16374-16378 (2004). Marx SO, Kurokawa J, et al.: Requirement of a macromolecular signaling complex for β-adrenergic receptor modulation of the KCNQ1-KCNE1 potassium channel. Science 295, 496-499 (2002). homepage:http://www.tmd.ac.jp/mri/cph/index.html contact:Tetsushi FURUKAWA ([email protected]) location: Surugadai area, 6・8th floor Professor Associate Professor Research Associate Physiology Yoshifumi KATAYAMA Keiji HIRAI Eiichiro KANDA Autonomic functions are essentially involved in maintaining the “homeostasis”. Mechanisms underlying the regulation of the autonomic functions are investigated at intracellular, cellular, tissue and organ levels by using the electrophysiological method together with optical, immunocytochemical and molecular biological techniques. Glutamate release from the growth cones ―Research projects― ● Cellular culture of autonomic sensory neurons and analysis of electrophysiological properties and chemosensitivities of their growth cones. ● Electrophysiological and immunocytochemical studies on functional organization of the enteric nervous system. ● Comparative studies on actions of endogenous and food-related bioactive substances on gut functions. ● Electrophysiolgical and immunocytochemical studies of actions of sleeping-feeding neuropeptides on the autonomic functions ―Publications― Electrophysiological effects of orexin-A and B on an enteric neuron. Katayama Y, Homma T, Hara Y & Hirai K: Tea catechin, (-)-epigallocatechin gallate, facilitates cholinergic ganglion transmission in the myenteric plexus of the guinea-pig small intestine. Neurosci Lett 319, 63-66 (2002). Soeda H, Tatsumi,H., Katayama,Y et al.: Functional characterization of calcium channels localized on the growth cones of cultured rat dorsal root ganglion cells. Neurosci Lett 325, 5-8 (2002). Katayama Y, Homma T, Honda K & Hirai K: Actions of orexin-A in the myenteric plexus of the guinea-pig small intestine. NeuroReport 14, 1515-1518 (2003). Katayama Y, Hirai K et al.: Actions of orexins on individual myenteric neurons of the guinea-pig ileum: orexin-A or-B? NeuroReport, 16, 745-749 (2005). homepage:http://www.tmd.ac.jp/mri/auto/index_j.html contact:Yoshifumi KATAYAMA ([email protected]) location : Surugadai area, 2nd floor 4 MRI 2005 Pathophysiology Neuropathology Prof. Hitoshi OKAZAWA Pathological Biochemistry Prof. Hirobumi TERAOKA Developmental and Regenerative Biology Prof. Hiroshi NISHINA Criminal Psychiatry Prof. Akira YAMAGAMI Immunology Prof. Takeshi TSUBATA Molecular Pathogenesis Prof. Akinori KIMURA Virus Research Unit Associate Prof. Norio SHIMIZU ● Neuropathology Transcriptome analysis of polyQ diseases Professor Associate Professor Assistant Professor COE Research Associate Hitoshi OKAZAWA Yasushi ENOKIDO Kazuhiko TAGAWA Mei-lingQI Our goals in research are elucidation of molecular mechanisms of neurodegenerative disorders (especially, polyglutamine diseases, Alzheimer’s diseases and motor neuron diseases) and development of novel therapeutics of those intractable disorders. ―Research projects― ● Transcriptome and proteome analyses of neurodegeneration ● Development and analysis of animal models of neurodegnerative disorders ● Analysis of nuclear dysfunction in neurodegeneration and molecular definition of neurodegeneration ● Understanding of molecular basis of intelligence ● Analysis of molecular mechanism of neural stem cell differentiation ―Publications― PQBP1disease Drosophila model Oct-3/4 in neural stem cells 5 MRI 2005 Okazawa H., Rich T., Chang A., Lin X., Waragai M., Kajikawa M., Enokido Y., Komuro A., Kato S. Shibata M., Hatanaka H., Mouradian M.M., Sudol M., Kanazawa I. (2002) Interaction between mutant ataxin-1 and PQBP-1 affects transcription and cell death. Neuron 34, 701-713. Okuda T., Hattori H., Takeuchi S., Shimizu J., Ueda H., Palvimo J.J., Kanazawa I., Kawano H.., Nakagawa M., Okazawa H. (2003) PQBP-1 transgenic mice show a late-onset motor neuron disease phenotype. Human Mol. Genet. 12, 711-725. Okazawa H, Okamoto K, Ishino, F, Ishino-Kaneko T, Takeda S, Toyoda Y, Muramatsu M and Hamada H (1991) The oct-3 gene, a gene for an embryonic transcription factor, is controlled by a retinoic acid repressible enhancer. EMBO J. 10, 2997-3005. Okamoto K, Okazawa H, Okuda A, Sakai M, Muramatsu M and Hamada H (1990) A novel octamer binding transcription factor is differentially expressed in mouse embryonic cells. Cell 60, 461-472. homepage:http://www.tmd.ac.jp/mri/npat/index.html contact: Hitoshi OKAZAWA ([email protected]) location : Yushima area, Bldg. 3, 7th floor ● Pathological IR/drugs, S-phase DSB Ku (p70/p86) DNA-PK (p470) DNA ligase IV XRCC4 ? Molecular mechanism of NHEJ Biochemistry Professor Assistant Professor Hirobumi TERAOKA Kinji ASAHINA In relationship between cell fate and DNA metabolism, we examine molecular mechanism of NHEJ in DNA double-strand break repair and hepatocyte differentiation from extrahepatic origins including ES cells and cord blood cells for clinical application. ―Research projects― ● Repair of DNA double-strand breaks by nonhomologous end-joining ● Regulation of cellular function by PI3K-related protein kinases (DNA-PK, ATM, ATR) ● Epigenetic expression of hepatocyte-related and hepatocyte-specific genes ● Hepatocyte differentiation from embryonic stem (ES) cells, and isolation/expansion ● Hepatic differentiation from umbilical cord blood cells, and for clinical application ―Publications― Shibata A, et al.: Parp-1 deficiency causes an increase of deletion mutations and insertions /rearrangements in vivo after treatment with an alkylating agent. Oncogene 24,1328-1337 (2005) Asahina K, et al.: Expression of the liver-specific gene Cyp7a1 reveals hepatic differentiation in embryoid bodies derived from mouse embryonic stem cells. Genes Cells 9, 1297-1308 (2004) Kakinuma S, et al.: Human umbilical cord blood as a source of transplantable hepatic progenitor cells. Stem Cells 21, 217-227 (2003) Chinzei R, et al.: Embryoid-body cells derived from an mouse embryonic stem cell line show differentiation capacity into functional hepatocytes. Hepatology 36, 22-29 (2002) homepage:http://www.tmd.ac.jp/mri/pbc/hyousi.html contact:Hirobumi TERAOKA ([email protected]) location : Surugadai area, 3rd・4th floor Hepatocyte differentiation from extrahepatic origins ● Developmental and Regenerative Biology Professor Assistant Professor Hiroshi NISHINA Teiji WADA We are studying physiological roles of stress signaling pathways in organ formation and regeneration using knockout mice, and are identifying signaling pathways regulating liver formation and function using Medaka mutants. Furthermore, we are trying to establish a cell therapy for intractable diseases such as liver failures using self-bone marrow cells. Fig. 1 Defective liver formation Fig. 2 Signaling pathways ―Research projects― ● Physiological roles of the SAPK/JNK signaling pathway in organ development and regeneration in mice ● Signaling pathways that regulate liver formation and function in Medaka ● Establishment of model organisms for human diseases ● Establishment of a cell therapy for liver failures using self bone marrow cells ―Publications― Wada T, et al.: The molecular scaffold Gab2 is a critical component of RANK signaling and osteoclastogenesis. Nat. Med.11, 394-399 (2005). Wada T, et al.: MKK7 couples stress signaling to G2/M cell cycle progression and cellular senescence. Nat Cell Biol. 6, 215-226 (2004). Watanabe T, et al.: Mutations affecting liver development and function in Medaka, Oryzias latipes, screened by multiple criteria. Mech. Dev. 121, 791-802 (2004). Nishitai G, et al.: Stress induces mitochondria-mediated apoptosis independent of SAPK/JNK activation in ES cells. J. Biol. Chem. 279, 1621-1626 (2004). Fig. 3 Medaka as a model organism for human diseases homepage:http://www.tmd.ac.jp/dbio/index.html contact:Hiroshi NISHINA ([email protected]) location : Yushima area, Bldg. 3, 3rd・4th floor 6 MRI 2005 ● Criminal Psychiatry Unravel Crime, Behavior disorder, Victimization and find out Strategy of Treatment and Prevention Improve Mental Health of the Society Minimize Crime and Victimization Establish standard assessment tool for Risk Accumulate and Analyze Data of Mentally Disordered Offenders Evidencebased new treatment strategy for PTSD Effective treatment program for sex offenders Accumulate and Analyze Data of Sex Offenders Treatment of serious PTSD cases and evaluation of the effect Establish Research Center for Forensic Mental Health Professor Associate Professor Akira YAMAGAMI Shugo OBATA We unravel crime, juvenile delinquency, behavior disorder and trauma of victims psychiatrically, and try to find out methods of treat and prevent them. This department is expected to be a leading center of forensic psychiatry in Japan, and was given special fund for the research projects written below from Ministry of Education, Science. ―Research projects― ● Analysis of risk factors concerning to the violence of mentally disordered offenders, and establishing the assessment standard to evaluate the risk. ● Evaluation and classification of sex offenders, and development of new treatment program for them. ● Establishment of evidence-based new treatment strategy for PTSD of crime victims. ―Publications― Akira Yamagami: How to treat mentally disordered offenders? Gendaikeijihou. No.44:24-29, 2002, Akira Yamagami, Fumiko Anada: Psychology of victims of crime and Support for them. Horei Publication, 2001, Dussich J.P.J., Friday P.C., Okada T., Yamagami A.& Knudten D.:Different Response to Violence in Japan and America. pp201, Criminal Justice Press, USA, 2001, homepage:http://www.tmd.ac.jp/mri/mri-crps/index_j.html contact:Taeko Hagiwara ([email protected]) location:Surugadai area, 6th floor ● Immunology Professor Associate Professor Assistant Professor Takeshi TSUBATA Takahiro ADACHI Kozo WATANABE We investigate basic mechanisms of immune responses by focusing on lymphocyte apoptosis and carbohydrate signals and we attempt to establish novel strategies for controlling autoimmunity, allergy and infection based on the new paradigm. A normal cell and an apoptotic cell Cell signaling analysis (Intracellular Ca2+ mobilization) Immunohistological analysis (Lymphoid architecture of spleens) 7 MRI 2005 ―Research projects― ● Investigation of the mechanisms that maintain the normal humoral immune system which is not induced by self antigens or environmental antigens respond to pathogenic microorganisms ● Investigation of the mechanisms of vaccination and immunological memory of host defense by vaccination induced immune memory ● Elucidation of the function of carbohydrate signals in immune responses ● Establishment of novel strategies for controlling autoimmunity and allergy ● Establishment of novel strategies for host defense against microorganisms ―Publications― Nitschke, L. and Tsubata, T. (2004): Molecular interactions regulate BCR signal inhibition by CD22 and CD72. Trends Immunol. 25: 543-550. Wakabayashi, C., Adachi, T., Wienands, J. and Tsubata, T. (2002): A distinct signaling pathway used by the IgG-containing B cell antigen receptor. Science 298: 2392-2395. Higuchi, T., Aiba, Y., Nomura, T., Matsuda, J., Mochida, K., Suzuki, M., Kikutani, H., Honjo, T., Nishioka, K. and Tsubata T. (2002): Cutting Edge: Ectopic expression of CD40 ligand on B cells induces lupus-like autoimmune disease. J. Immunol. 168: 9-12. homepage:http://www.tmd.ac.jp/mri/imm/HP/index.html contact:Takeshi TSUBATA ([email protected]) location:Yushima area, Bldg. 2, 5th floor ● Molecular I 1 II - 1 - +3 - - 2+ - 2 - +3- Pathogenesis +4- - 5+ 4 SCD III +1 - +2- -3 - - 4+ Genetic analysis of multiplex family GFPGFP-WT 488nm YFPYFP-Mut 514nm GFPGFP-WT 488nm 488nm 10mm 10mm merge YFPYFP-Mut 514nm 10mm merge F 10mm Functional analysis of disease-related genes SL MI SL CAD SL 0.0 logP (2xn) -1.0 -2.0 -3.0 ∼0.7 Mb -4.0 -6.0 ∼3.2 Mb within 0.9Mb -5.0 ∼4.9 Mb MS334 ∼1.1 Mb within 0.4Mb 128Ser 128Arg leukocyte Genome-wide approach and functional analysis of CAD Akinori KIMURA Michio YASUNAMI Takuro ARIMURA To develop new strategies for curative treatments of various cardiovascular diseases (cardiomyopathy, arrhythmia and coronary atherosclerosis) and immune-related diseases (insulin-dependent diabetes mellitus, autoimmune thyroiditis, rheumatoid arthritis and Takayasu disease), we identify and analyze the human genome diversities involved in the etiology and pathogenesis of the diseases. In addition, genome diversities of immune-related genes are investigated to obtain a new strategy for developing vaccines. ―Research projects― ● Identification and functional analysis of novel disease genes for idiopathic cardiomyopathy and idiopathic ventricular arrhythmia ● Functional modification of disease-related molecules ● Genome-wide approach to identify the disease gene for coronary disease ● Genome diversity of immune-related genes in immune response ―Publications― Hayashi T, et al: TCAP mutations in hypertrophic cardiomyopathy and dilated cardiomyopathy. J Am Col Cardiol 44; 2192-2201 (2004) Ueda K, et al: Functional characterization of a trafficking-defective HCN4 mutation, D553N, associated with cardiac arrhythmia. J Biol Chem 279; 27194-27198 (2004) Arimura T, et al: A Cypher/ZASP mutation associated with dilated cardiomyopathy alters the binding affinity to protein kinase C. J Biol Chem 279: 6746-6752 (2004) Matano T, et al: Cytotoxic T lymphocyte-based control of simian immunodeficiency virus replication in a preclinical AIDS vaccine trial, J Exp Med 199: 1709-1718(2004) homepage:http://www.tmd.ac.jp/mri/m-path/index.html contact:Akinori KIMURA ([email protected]) location:Surugadai area, 3rd・4th floor Frontier Research Unit - Virus Research Unit ● Professor Associate Professor Assistant Professor Associate Professor Assistant Professor Norio SHIMIZU Masaki SHIRAKATA As refractory virus infections are serious problems for congenital or acquired immunocompromised hosts, development of new treatment techniques and new anti-viral drugs are urgent problems to solved. The goals of our research unit are the elucidation of development mechanisms of EB virus infections, the employment of immunodeficiency animals for the creation of virus research models and investigating the practicality of utilizing adoptive immunotherapy for the treatment of virus infections and malignant carcinomas. ―Research projects― T cell therapy (Center for cell therapy) ● Treatment of refractory virus infections and malignant carcinomas through the use of adoptive immunotherapy using activated T lymphocytes. ● Development of new exhaustive laboratory tests for viruses which can be used in quality checks of cellular preparations used in cell therapy and regenerative medicine as well as clinical inspections. ● Employment of immunodeficiency mice for AIDS model research in the development of new AIDS drugs. Development of new AIDS drugs ● Analysis of the development mechanisms of EB virus infections. ―Publications― 30 25 F DC L C p2 4 ( n g / m l) 20 15 10 Fib r o bla s t( HF L 1) 5 0 FD C L C + マ ン ナ ン M O L T4 の み -5 Oyoshi M.K., Nagata H., Kimura N., et al. Preferential expansion of Vgamma9-JgammaP/Vdelta2 -Jdelta3 gamma delta T-cells in nasal T-cell lymphoma and chronic active Epstein-Barr virus (EBV) infection. Am.. J. Patol.162, 1629-1638 (2003) Nagata H., Konno A., Kimura N., et al.: Characterization of novel natural killer (NK) and gamma/delta T-cell lines established from primary lesions of nasal T/NK cell lymphomas associated with Epstein-Barr virus. Blood 97, 708-713 (2001). Shimizu N., Sekine T., K.Ito et al.: Large-scale ex vivo expansion of primary T-lymphocyte in late-stage AIDS patients. AIDS. Res. Hum. Retroviruses 16, 611-612(2000). Analysis of EBV homepage: http://www.tmd.ac.jp/mri/mri-vir/index.html, http://www.tmd.ac.jp/grad/cct1/ contact:Norio SHIMIZU ([email protected]) location : Yushima area, Bldg. 2, 4th floor 8 MRI 2005 Medical Genomics Molecular Cytogenetics Prof. Johji INAZAWA Molecular Genetics Prof. Yoshio MIKI Molecular Epidemiology Prof. Masaaki MURAMATSU Biochemical Genetics Prof. Shigetaka KITAJIMA Functional Genomics Prof. Masatoshi HAGIWARA Epigenetics Prof. Fumitoshi ISHINO Bioinformatics Prof. Hiroshi TANAKA Redox Response Cell Biology Assoc. Prof. Shun-ichi KURATA ● Molecular Cytogenetics Professor Associate Professor Assistant Professor HTDFRP Associate Professor Johji INAZAWA Issei IMOTO Sana YOKOI- ISHIHARA Ken-ici OZAKI Our goal is to establish personalized medicine in human diseases including cancer and genetic diseases by the integrated genome approach in the post-sequence era. For this purpose, we examine genomic copy-number aberrations using custom-made tools, analyze gene expression systematically, and explore epigenetically dysregulated genes and functional DNA elements. Genomic analysis of cancer using CGH-array Diagnosis of genetic disease using CGH-array Genome-wide screening of methylated sequence by BAMCA 9 MRI 2005 ―Research projects― ● Identification and characterization of genes involved in carcinogenesis ● Identification and functional analyses of genes related to genetic diseases ● Development of genomic micro-arrays and their application for analyses of cancer and genetic diseases ● Development of novel methods for diagnosis and therapy of cancer and genetic diseases ―Publications― Izumi H, et al: Frequent silencing of DBC1 is by genetic or epigenetic mechanisms in non-small cell lung cancers. Hum. Mol. Genet. 14, 997-1007 (2005) Yokoi S, et al: Amplification and overexpression of SKP2 are associated with metastasis of non-small- cell lung cancers to lymph nodes. Am. J. Pathol. 165, 175-80 (2004) Imoto I, et al: Identification of ZASC1 encoding a Kruppel-like zinc finger protein as a novel target for 3q26 amplification in esophageal squamous cell carcinomas. Cancer Res. 63, 5691-6 (2003) homepage:http://www.tmd.ac.jp/mri/cgen/framepage.html contact:Johji INAZAWA ([email protected]) location:Yushima area, Bldg. 3, 6th floor ● Molecular Genetics Professor Assistant Professor COE Program Lecturer Yoshio MIKI Kiyotsugu YOSHIDA Yuki HAMANO Our purpose is Basic biological research which clarifies the biological nature of cancer and establishing new diagnosis and medical treatment of the cancer based on the information acquired by the research. Concretely, we analyze the roles of DNA damage repair and apoptosis in carcinogenesis, focusing on some kinases which bear this signal transduction, or BRCA1 and BRCA2. Subcellular localization of BRCA2 ―Research projects― ● The investigation of a mechanism in breast carcinogenesis • Functional analysis of the gene responsible for hereditary breast cancer, BRCA2 • Development of the personalized medicine for breast cancer applying genome science ● The intracellular signaling transduction and cell death in DNA damage • Analysis of the cell cycle control mechanism by protein kinase C delta • The investigation of the mechanism of apoptosis induction by c-Abl ―Publications― Clustering analysis Yoshida K, Yamaguchi T, Natsume T, Kufe D, Miki Y: JNK phosphorylation of 14-3-3- regulates nuclear targeting of c-Abl in the apoptotic response to DNA damage. Nat. Cell Biol. 7, 278-285 (2005) Yoshida K, Miki Y: Role of BRCA1 and BRCA2 as regulators of DNA repair, transcription, and cell cycle in response to DNA damage. Cancer Sci. 95, 866-871 (2004) Morotomi-Yano K, Yano K, Saito H, Sun Z, Iwama A, Miki Y: Human relatory factor X4 (RFX4) is a testis-specific dimeric DNA-binding protein that cooperates with other human RFX memberes. J. Biol. Chem. 277, 836-842 (2002) homepage:http://www.tmd.ac.jp/mri/mgen/index.html contact:Yoshio MIKI ([email protected]) location:Yushima area, Bldg. 3, 6th floor c-Abl 核内移行モデル A model of c-Abl transfer to nucleous ● Molecular Epidemiology Professor Assistant Professor Masaaki MURAMATSU Tomomi KIMURA We are interested in the study of discovering the genetic cause of the diseases, which leads the primary prevention, molecular diagnosis, and development of new medicine in the near future. In addition to the environmental and lifesyle factors, we focus on the inherited personal differencies, such as SNPs (single nucleotude polymorphisms). SNP typing ―Research projects― ● Individual difference of the susceptibilities of diseases dependent on the polymorphisms ● Genetic difference between the responders and non-responders for the drug therapies ● Bioinformatics using polymorphisms and haplotypes ―Publications― Araki J, Ohashi J, Muramatsu M: Application of discordant sib-pair linkage analysis for mapping minor histocompatibility antigen loci in a novel graft-vs-host-disease model. Tissue Antigens 64, 243-50 (2004) Kitano H, Oda K, Kimura T, Matsuoka K, Csete M, Doyle J, Muramatsu M: Metabolic syndrome and robustness tradeoffs. Diabetes 53 (Suppl 3), S6-S15 (2004) Kimura T, Yokoyama T, Matsumura Y, Yoshiike N, Date C, Muramatsu M, Tanaka H: NOS3 genotype dependent correlation between blood pressure and physical activity. Hypertension 41, 355-360 (2003) Haplotype and promoter activity homepage:http://www.tmd.ac.jp/mri/epi/index.html contact:Masaaki MURAMATSU (muramatsu/[email protected]) location:Surugadai area, 9th floor 10 MRI 2005 ● Biochemical Genetics Promoter clearance IIo IIa IIB TBP TATA IIF IIE IIH Ini P-TEFb Holoenzyme IIo IIa Stall Ini IIa Shigetaka KITAJIMA Yujiro TANAKA Mimi TAMAMORI-ADACHI Our group studies on basic mechanism of Pol II transcription, structure and biological function of specific transcription factors, and re-activation of cell cycle of terminally-differentiated cardiac cells, thus aiming to develop novel therapy of disease. Preinitiation complex (PIC) IIB IIF TBP TATA Professor Associate Professor Assistant Professor FCP1 IIF Termination polyA & RecyclingIIo ―Research projects― ● Basic mechanism of Pol II transcription cycle from elongation, termination and recycling ● Histone methylation and chromatin regulation ● Cell fate-determining activity of bZip-type transcription factor ATF3 ● Cell cycle reactivation of terminally differentiated cardiac cells Elongation ElonginA IIF Transcription cycle by RNA polymerase c-myc+/+ c-myc-/- BrdU DAPI A2 merge ―Publications― c-myc+/+ Tamura K, et al: Stress response gene ATF3 is a target of c-myc in serum-induced cell proliferation. EMBO J. revised Kip1 promotes cell proliferation of rat neonatal cardiomyocytes Tamamori-Adachi M, et al: Down-regulation of p27 induced by nuclear expression of cyclin D1 and CDK4. J. Biol. Chem. 279, 50429-50436 (2004) Yamazaki K, et al: Mammalian Elongin A Is not essentual for cell viability but required for proper cell-cycle progression with limited alteration of gene expression. J. Biol. Chem. 278, 13585-13589 (2003) Yamazaki Y, et al: Identification and characterization of a novel transcription elongation factor elongin A3. J. Biol. Chem. 277, 26444-26451 (2002) Hashimoto Y, et al: An alternatively spliced isoform of transcriptional repressor ATF3 and its induction by stress stimuli. Nucleic Acids Res. 30, 2398-2406 (2002) Cai Y, et al: Homocysteine-responsive ATF3 gene expression in human vascular endothelial cells: activation of c-Jun NH2-terminal kinase and promoter response element. Blood 96, 2140-2148 (2000) c-myc-/- A2 Cross-talk regulation of ATF3 and c−Myc in cell 第一の障害サイクリンD1の核内発現障害 増殖刺激 G1 S G0 第二の障害 p27の分解障害 M G2 homepage : http://www.tmd.ac.jp/mri/bgen/open.html contact : Shigetaka KITAJIMA ([email protected]) location: Yushima area, Bldg. 3, 6th floor Reactivation cell cycle of cardiomyocytes ● Functional SR proteins Genomics DNA Transcription Pre-mRNA Phosphorylation Dephosphorylation m7G RNA splicing Other processing EJC Mature (A) n mRNA Nuclear pore Export Translation m7G (A) n mRNA Processing Professor Associate Professor Lecturer Assistant Professor Masatoshi HAGIWARA Tetsuro HIROSE Hidehito KUROYANAGI Takeshi FUKUHARA We are studying mechanisms by which genome-encoded information become functional; how the fate of primary transcripts are determined, how the RNAs are processed exported out of the nucleus and how their quality is controlled. We are also developing drugs that can modulate the function of such regulation systems and applying them to the clinical aspect. ―Research projects― ● Development and application of SR protein kinase inhibitors. ● Processing and quality control mechanisms of cellular RNAs. ● Mechanisms of tissue-specific alternative splicing in vivo. ● in vitro transcription-splicing coupling system. ● CREB (cAMP response element binding protein) signals in C. elegans dauer formation. ―Publications― RFP GFP DIC In vivo monitoring system of tissue-specific alternative splicing 11 MRI 2005 Muraki M, et al: Manipulation of alternative splicing by a newly developed inhibitor of Clks. J. Biol. Chem. 279, 24246-24254 (2004) Katsu R, et al: Novel SR-related protein Clasp specifically interacts with inactivated Clk4 and induces the exon EB inclusion of Clk. J. Biol. Chem. 277, 44220-44228 (2002) Nagai Y, et al: A fluorescent indicator for visualizing cAMP-induced phosphorylation in vivo. Nat. Biotechnol. 18, 313-316 (2000) homepage:http://www.tmd.ac.jp/mri/mri-end/index.html contact:Masatoshi HAGIWARA ([email protected]) location:Yushima area, Bldg. 3, 5th floor ● Epigenetics Professor Lecturer Fumitoshi ISHINO Takashi KOHDA From the viewpoint of genomic function, we study inheritance, development and evolution by genetical and epigenetical approaches. By understanding genomic function Peg of mammals including human, we would like to contribute to establish “new human biology and medicine” in the 21th century. ―Research projects― ● Genomic imprinting in mammals (There is a very good biological reason for having Meg both father and mother for everyone.) ● Somatic cloned animals (Genetic identity does not necessarily mean that cloned Genomic imprinting animals are the same as donor animals.) ● Evolution of mammalian genomic function (Genetic evidence indicates relationship between changes of genomic function and evolution of living organism.) ―Publications― Mouse embryo at 12.5dpc Shiura H et al: Meg1/Grb10 overexpression causes postnatal growth retardation and insulin resistance via negative modulation of the IGF1R and IR cascades. Biochem. Biophys. Res. Commun. 329, 909-916 (2005) Suzuki S et al: Genomic imprinting of IGF2, P57KIP2 and PEG1/MEST in a marsupial, thetammar wallaby. Mechanisms of Develop. 122, 213-222 (2005) Ono R et al: Identification of a large novel imprinted gene cluster on mouse proximal chromosome 6. Genome Res. 13, 1696-1705 (2003) Kaneko-Ishino T et al: The regulation and biological significance of genomic imprinting in mammals. J. Biochem. (Review) 133, 699-711 (2003) homepage:http://www.tmd.ac.jp/mri/epgn/index.html contact:Fumitoshi ISHINO ([email protected]) location:Surugadai area, 5th floor Professor Associate Professor Adjunct Professor Adjunct Associate Professor ● Bioinformatics Hiroshi TANAKA Yoshito MIIMURA Hiroshi MIZUSHIMA Fengrong Ren We study the challenges in life science and medicine from the points of view to understand life and disease as an unified system. In life science, we are trying to build a new field which might be called “systems evolutionary biology”. In medical field, we are engaged in developing systems pathology based on the comprehensive clinical omics. olfactory receptor evolution C11 C02 A04 A17 A11 A08 A14 A12 B11 B01 B02 B07 B16 B09 B15 B18 C08 C05 C16 C01*1 C09*1 C06*2 C04*2 HIV within-host evolution ―Research projects― ● Molecular evolution of olfactory receptor multigene family. ● Analysis of the evolutionary process of within-host HIV and prediction of anti-HIV drug resistance by bioinformatics approaches. ● Systems evolutionary biology: evolutionary analysis of Hox developmental systems. ● Ubiquitous medicine, systems pathology of cancer. ―Publications― Niimura, Y. Nei, M: From The Cover: Evolutionary dynamics of olfactory receptor genes in fishes and tetrapods.、 Proc. Natl. Acad. Sci. USA 102, 6039-6044 (2005) Ogishima S, Gojobori T, Tanaka H: Missing-link in the evolution of Hox clusters (submitting) F. Ren, S. Ogishima, H. Tanaka: Longitudinal phylogenetic tree of within-host viral evolution from noncontemporaneous samples: a distance-based sequential-linking method. Gene, 317, 89-95 (2003) Hox cluster evolution homepage:http://bioinfo.tmd.ac.jp contact:Hiroshi TANAKA ([email protected]) location:Yushima area, Bldg. 2, 5th floor 12 MRI 2005 ● Frontier Research Unit -Redox Response Cell Biology Associate Professor Shun-ichi KURATA Our research aims to understand molecular mechanisms mediating diverse cellular responses to oxidative stress, as well as to approach redox system failure causing various diseases by chemical biology. ―Research Projects― ● The newly identified apoptosis-inducing mechanism inside the mitochondria by physiological redox stress. (See the pathway indicated by bold arrows in the Figure.) ● Cellular signal transduction pathways and transcriptional regulation in response to oxidative stress: the NF-κB and MAPK cascades. ● Functions of p63, a p53 family protein, in epithelial tissue development and carcinogenesis: trans-activation of genes for cell adhesion and migration. Apoptosis-inducing pathways in mitochondria Cytochrome c ∆ψm ATP ADP Outer membrane Inner membrane Inner membrane damage Matrix Physiological oxidative stress Pro-apoptotic Bcl-2 family proteins Outer membrane permeability transition ∆ψm-low Bcl-2 ―Publications― ∆ψm-hypo ∆ψm Cytochrome c released Procaspase-9 Apaf-1 Caspase-9 Bcl-2 Activated caspase-9 released Procaspase-3 Dimerization S S Katoh I, Tomimori Y, Ikawa Y, Kurata S: Dimerization and processing of procaspase-9 by redox stress in mitochondria. J. Biol. Chem., 279, 15515-15523, (2004) Kurata S et al: p51/p63 controls subunit α3 of the major epidermis integrin anchoring the stem cells to the niche. J. Biol. Chem. 279, 50069-50077 (2004) Kurata S: Selective activation of p38 MAPK cascade and mitotic arrest caused by low level oxidative stress. J. Biol. Chem. 275, 23413-23416 (2000) Outer membrane traffic contact: Shun-ichi KURATA contact:Shun-ichi KURATA([email protected]) ([email protected]) location:Yushima area, Bldg. 3, 5th floor location:Yushima area, Bldg. 3, 5th floor Caspase-3 Caspase cascade Apoptosis Project Research Unit ● access(e-mail or homepage) Assoc. Prof. Tatsuro IKEUCHI Assoc. Prof. Seiko KAWANO http://www.tmd.ac.jp/TMDU/mri/mri-card Assoc. Prof. Michinori KUBOTA Assoc. Prof. Toshihiko KUROIWA http://www.tmd.ac.jp/mri/npat/kuroiwa/index.html Assoc. Prof. Shinobu SAKAMOTO Assoc. Prof. Yuji HIRANO [email protected] Assoc. Prof. Saburo HORIKAWA [email protected] Assoc. Prof. Tokio YAMAGUCHI [email protected] Assist. Prof. Toshiko OGATA Assist. Prof. Shuji SASA Assist. Prof. Hisae HORI [email protected] Assist. Prof. Noriko YAMAGUCHI [email protected] 13 MRI 2005 Division of Integrative Science ● Pathogenetic regulation:under construction ● Biosystem Generation :under construction Professor Assistant Professor Assistant Professor ● Neurotraumatology Superficial recording of γ oscillation during POCR session (super‐imposed) Toshinori NAKAMURA Keiji HASHIMOTO Kazuma ISHIMATSU The aim of our research is to elucidate the mental health status and the needs of victims including traffic accident survivors and their family members. We also intend to develop the psycho-medical and psycho-social approach to support the victims, especially the psychological technique in psychiatry and/or rehabilitational medicine for the people with higher brain dysfunction from traumatic brain injury. The department was funded by the General Insurance Association of Japan and was established in 2003. ―Research projects― ● Psycho-medical aspects of rehabilitations for the victims of traumatic brain injury, and the proper intervention for its issues. ● Psycho-social aspects of family members of the victims of traumatic brain injury, and the proper intervention for its issues ―Publications― rt. hemisphere lt. hemisphere The γ oscillation was represented predominantly on right frontal lobes. lobes. Nakamura T, et al.: Prefrontal cortex will be responsible for the cognitive integration of visual features, - as to a case of frontal dementia reversible during nootropic treatment. The Int J of Neuropsychopharmacology, 3(Suppl.1): S355, 2000 Nakamura T,, et al.: Prefrontal γ oscillation mediated a new cognitive rehabilitation intervention ( POCR ) for TBI and brain-damaged patients psychosocial human growth. SfN abstract2004. 11 Nakamura T, et al.: ADEQUATE PAIN RELIEF AND IMMEDIATE MENTAL CARE FOR PATIENTS WITH TRAUMATIC BRAIN INJURY IMPROVE PATIENT’S WELL-BEING AND QUALITY OF LIFE. J Trauma, 2005 in submission. homepage:http://www.tmd.ac.jp/mri/crps/neuro_trauma/index.html contact:Toshinori NAKAMURA ([email protected]) location:Surugadai area, 6th floor ● School of Biomedical Science ― Structural Biology Professor Associate Professor Nobutoshi ITO Teikichi IKURA We study structural and physicochemical features of biopolymers (especially proteins) by X-ray crystallography and other techniques to elucidate their function at atomic resolution. Such information is hoped to help understanding diseases and designing small molecules, potentially leading to new drugs. We also contribute to maintenance and development of the database for the protein structures as a member of the PDBj (Protein Data Bank Japan). ―Research projects― ● Structural analysis of SR protein kinases and their interactions with small ligands ● Physicochemical analysis of the functions of peptidyl-prolyl cis/trans isomerases ● Study of in vivo protein folding on the basis of structural analysis of trigger factor ―Publications― X-ray crystallography (upper: the barnase- barstar complex, lower: the active site of a catalytic antibody) Westbrook J, Ito N, Nakamura H, Herick K, Berman HM: PDBML: the representation of archival macromolecular structure data in XML. Bioinformatics 21, 988-992 (2005) Ikura T, Urakubo Y, Ito N: Water-mediated interaction at a protein-protein interface. Chem. Phys. 307, 111-119 (2004) Ito N, Sakamoto H, Kobayashi K, Kaneta Y, Kawaguchi Y, Ohkawa T, Nakamura H: New features of PDBj-ML, an XML format for protein data bank. Genome Informatics 13, 488-489 (2002) Higo J, Ito N, Kuroda M, Ono S, Nakajima N, Nakamura H: Energy landscape of a peptide consisting of α-helix, 31-helix, β-turn, β-hairpin, and other disordered conformations. Protein Sci. 10, 1160-1171 (2001) contact:Nobutoshi ITO ([email protected]) location:Yushima area common research bldg. 2nd floor 14 MRI 2005 Organization Medical Research Institute Devision of Advanced Molecular Medicine Department of Molecular Medicine and Metabolism Department of Molecular Pharmacology Department of Molecular Cell Biology Department of Molecular Neuroscience Department of Cell Regulation Department of Bio-informational Pharmacology Department of Autonomic Physiology Project Unit Devision of Pathophysiology Department of Neuropathology Department of Pathological Biochemistry Department of Virology Department of Developmental and Regenerative Biology Department of Criminal Psychiatry Department of Immunology Department of Molecular Pathogenesis Frontier Research Unit Virus Research Unit Project Research Unit Devision of Medical Genomics Department of Molecular Cytogenetics Department of Molecular Genetics Department of Molecular Epidemiology Department of Biochemical Genetics Department of Functional Genomics Department of Epigenetics Department of Bioinformatics Frontier Research Unit Redox Response Cell Biology Project Research Unit Division of Integrative Research Pathogenetic Regulation Biosystem Generation Neurotraumatology Advanced Technology Laboratory Genome Laboratory Cellular and Proteome Research Laboratory Laboratory of Recombinant Animals Animal Research Laboratory Laboratory of Anatomy and Cell Function Bioresource Labotatory Bioinformation Laboratory School of Biomedical Science 15 MRI 2005 Department of Medical Bioinformatics Genome Diversity Computational Biology Genome Structure and Regulation Department of Applied Structural Biology Structural Biology Organic and Medical Chemistry Medical Chemistry Department of Functional Biology Gene Expression Molecular Neuroscience Immunology Biosystem Modeling