Nippon Medical School

Graduate School

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Department of Biochemistry and Molecular Biology

Publications

  1. Liu L, Koike H, Ono T, Hayashi S, Kudo F, Kaneda A, Kagechika H, Manabe I, Nakashima T, Oishi, Y. Identification of a KLF5-dependent program and drug development for skeletal muscle atrophy. Proc Natl Acad Sci U S A. 118, 35. doi: 10.1073/pnas.2102895118

  2. Kuwabara Y, Ono S, Katayama A, Kurihara S, Oishi Y, Takeshita T. Plasma and follicular fluid osteopontin levels during ovarian cycle and their correlation with follicular fluid vascular endothelial growth factor levels. Sci Rep volume 11, Article number: 286, 2021. doi: 10.1038/s41598-020-79453-1.

  3. Kitazawa M, Hayashi S, Imamura M, Oishi Y, Takeda S, Kaneko-Ishino T, and Ishino F. Lack and overexpression of Rtl1 in the mouse cause distinct muscle abnormalities related to the Temple and Kagami-Ogata syndromes, respectively. Development 2020, 147, dev185918. doi:10.1242/dev.185918

  4. Nakayama Y, Fujiu K, Yuki R, Oishi Y, Morioka M, Isagawa T, Matsuda J, Oshima T, Matsubara T, Sugita J, Kudo F, Kaneda A, Endo Y, Nakayama T, Nagai R, Komuro I, Manabe I. A long noncoding RNA regulates inflammation resolution by mouse macrophages through fatty acid oxidation activation. Proc Natl Acad Sci USA 11:14365-75, 2020

  5. Oishi Y. and Manabe I. “Organ system crosstalk in cardiometabolic disease in the age of multimoribidity. Front Cardiovasc Med 7:64, 2020

  6. Orekhov A*, Sukhorukov V, Nikiforov N, Kubekina M, Sobenin I, Foxx K, Pintus S, Stegmaier S, Stelmashenko D, Kel A, Poznyak A*,Manabe I, Oishi Y. Signaling Pathways Potentially Responsible for Foam Cell Formation: Cholesterol Accumulation or Inflammatory Response - What is First? Int J Mol Sci, 21, 2716，2020

  7. Orekhov A, Nikiforov N, Sukhorukov V, Kubekina M, Sobenin I, Wu W, Foxx K, Pintus S, Stegmaier P, Stelmashenko D, Kel A, Gratchev A, Melnichenko A, Wetzker R, Summerhill V, Manabe I, Oishi Y. Role of phagocytosis in the pro-inflammatory response in LDL-induced foam cell formation; a transcriptome analysis.　Int J Mol Sci 21(3) 817, 2020

  8. Orekhov AN, Oishi Y, Nikiforov NG, Zhelankin AV, Dubrovsky L, Sobenin IA, Kel A, Stelmashenko D, Makeev VJ, Foxx K, Jin X, Kruth HS, Bukrinsky M. (2018) Modified Ldl Particles Activate Inflammatory Pathways In Monocyte-Derived Macrophages: Transcriptome Analysis. Curr Pharm Des. 25:28.

  9. Orekhov A, Pushkarsky, T, Oishi Y, Nikiforov N, Zhelankin A, Duborovsky L, Makeev V, Foxx K, Jin X, Kruth H, Sobenin I, Sukhorukov V, Burkinsky M.(2018) HDL activates expression of genes stimulating cholesterol efflux in human monocyte-derived macrophages. Exp Mol Pathol. 105: 202-207.

  10. Oishi Y. and Manabe I.(2018) Macrophages in inflammation, repair and regeneration. International Immunology. 30:511-528.

  11. Oishi Y. and Manabe I.(2018) Kruppel –like factors in metabolic homeostasis and cardiometabolic diseases. Frontiers in cardiovascular medicine. doi: 10:3389/fcvm.2018.00069

  12. Saeki K, Hayakawa S, Nakano S, Ito S, Oishi Y, Suzuki Y, Isemura M. (2018) In vitro and in silico studies of molecular interaction of epigallocatechin-3-O-gallate (EGCG) with proteins that explain the health benefits of green tea. Molecules 23: E1295.

  13. Oishi Y, Spann, NJ, Link VM, Muse ED, Strid T, Edillor C, Kolar MJ, Matsuzaka T, Hayakawa S, Tao J, Kaikkonen M, Lam MT, Manabe I, Shimano H, Saghatelian A and Glass CK. (2017) SREBP1 contributes to resolution of pro-inflammatory TLR4 signaling by reprogramming fatty acid metabolism. Cell Metab. 25: 412-427.

  14. Oishi Y, Hayashi S, Isagawa T, Oshima M, Iwama A, Shimba S, Okamura H and Manabe I. (2017) Bmal1 regulates inflammatory responses in macrophages by modulating enhancer RNA transcription. Sci Rep. 7:7086.

  15. Hayashi S, Manabe I, Suzuki Y, and Oishi Y. (2016) Klf5 regulates muscle differentiation by directly targeting muscle specific genes in cooperation with MyoD in mice. eLife. DOI: http://dx.doi.org/10.7554/eLife.17462.
  16. Lam M, Cho H, Lesch H, Gosselin D, Heinz S, Oishi-Tanaka Y, Benner C, Kaikkonen M, Salim A, Rosenfeld M, Evans R, and Glass CK. (2013) Rev-Erbs negatively regulate macrophage gene expression by repressing enhancer-directed transcription. Nature. 498, 511-515.

  17. Eguchi K, Manabe I, Oishi-Tanaka Y, Osugi M, Kono N, Ogata F, Yagi N, Ohto U, Kimoto M, Miyake K, Tobe K, Arai H, Kadowaki T, and Nagai R. (2012) Saturated fatty acid and TLR signaling link ß cell dysfunction and islet inflammation. Cell Metab. 15: 518-533.

  18. Oishi Y, Manabe I, Tobe K, Osugi, M, Kubota T, Fujiu K, Maemura K, Kubota N, Kadowaki T, Nagai R. (2008) SUMOylation of KLF5 is a molecular switch regulating PPAR--containing transcriptional programs of lipid metabolism. Nat Med. 14: 656-666.

  19. Oishi Y, Manabe I, Tobe K, Tsushima K, Shindo T, Fujiu K, Nishimura G, Maemura K, Yamauchi T, Kubota N, Suzuki R, Kitamura T, Akira S, Kadowaki T, Nagai R. (2005) Krüppel-like transcription factor KLF5 is a key regulator of adipocyte differentiation. Cell Metab. 1:27-39.



Selected publications (Toshio Iwasaki, Ph.D)

  1. Iwasaki T, Miyajima-Nakano Y, Fukazawa R, Lin MT, Matsushita S, Hagiuda E, Taguchi AT, Dikanov SA, Oishi Y, Gennis RB. (2021) Escherichia coli amino acid auxotrophic expression host strains for investigating protein structure-function relationships. J Biochem. (Review), in press.

  2. Geldenhuys WJ, Long TE, Saralkar P, Iwasaki T, Nuñez RAA, Nair RR, Konkle ME, Menze MA, Pinti MV, Hollander JM, Hazlehurst LA, Robart AR. (2019) Crystal structure of the mitochondrial protein mitoNEET bound to a benze-sulfonide ligand. Communications Chemistry. 2, Article number: 77 (open access).

  3. Taguchi AT, Ohmori D, Dikanov SA, Iwasaki T. (2018) g-Tensor directions in the protein structural frame of hyperthermophilic archaeal reduced Rieske-type ferredoxin explored by 13C pulsed electron paramagnetic resonance. Biochemistry. 47, 4074-4082.

  4. Taguchi AT, Miyajima-Nakano Y, Fukazawa R, Lin MT, Baldansuren A, Gennis RB, Hasegawa K, Kumasaka T, Dikanov SA, Iwasaki T. (2018) Unpaired electron spin density distribution across reduced [2Fe-2S] cluster ligands by 13Cβ-cysteine labeling. Inorg Chem. 57, 741-746.

  5. Lin MT, Fukazawa R, Miyajima-Nakano Y, Matsushita S, Choi SK, Iwasaki T, Gennis RB. (2015) Escherichia coli auxotroph host strains for amino acid-selective isotope labeling of recombinant proteins. Methods Enzymol (Isotope Labeling of Biomolecules - Labeling Methods). 565, 45-66 (Review/Methods).

  6. Iwasaki T, Fukazawa R, Miyajima-Nakano Y, Baldansuren A, Matsushita S, Lin MT, Gennis RB, Hasegawa K, Kumasaka T, Dikanov SA. (2012) Dissection of hydrogen bond interaction network around an iron-sulfur cluster by site-specific isotope labeling of hyperthermophilic archaeal Rieske-type ferredoxin. J Am Chem Soc. 134, 19731-19738.

  7. Iwasaki T, Samoilova RI, Kounosu A, Ohmori D, Dikanov SA. (2009) Continuous-wave and pulsed EPR characterization of the [2Fe-2S](Cys)3(His)1 cluster in rat mitoNEET. J Am Chem Soc. 131, 13659-13667.

  8. Iwasaki T, Kounosu A, Tao Y, Li Z, Shokes JE, Cosper NJ, Imai T, Urushiyama A, Scott RA. (2005) Rational design of a mononuclear metal site into the archaeal Rieske-type protein scaffold. J Biol Chem. 280, 9129-9134.

  9. Iwasaki T, Kounosu A, Kolling DRJ, Crofts AR, Dikanov SA, Jin A, Imai T, Urushiyama A. (2004) Characterization of the pH-dependent resonance Raman transitions of archaeal and bacterial Rieske [2Fe-2S] proteins. J Am Chem Soc. 126, 4788-4789.

  10. Kounosu A, Li Z, Cosper NJ, Scott RA, Imai T, Urushiyama A, Iwasaki T. (2004) Engineering a three-cysteine, one-histidine ligand environment into a new hyperthermophilic archaeal Rieske-type [2Fe-2S] ferredoxin from Sulfolobus solfataricus. J Biol Chem. 279, 12519-12528.