Proteome Research

Members

Theme Leader :
Yuri Miura, Ph.D.
Researcher :
Hiroki Tsumoto, Ph.D., Keitaro Umezawa, Ph.D., Kyojiro Kawakami, Ph.D.

Keywords

Proteome, Proteomics, Glycomics, Supersulfide, Extracellular vesicles (Exosomes), Oxidative stress, Post-translational modification, Healthy longevity, Biomarker protein

Major Research Titles

  1. Proteome research on the post-translational modifications involved in age-related diseases.
  2. Proteome research on healthy aging.
  3. Proteome research on disease-related biomarker proteins.

Profile

"Proteome" is a compound of "protein" and "-ome", which means constitutive whole proteins including post-translational modifications. Proteomics is a strategy for analyzing proteome comprehensively. We perform proteomics using LC-MS/MS, and investigate proteins responsible for the mechanisms of aging and age-related diseases. Furthermore, we focus post-translational modifications such as N-glycosylation, O-glycosylation, and supersulfide. We performed N-glycoproteomics of plasma proteins in Japanese centenarians (≥100 years), and expect that this approach will lead to the discovery of glycans and glycoproteins related to healthy longevity.

References

  1. Uchiyama, J., Shimizu, Y., Unoki, T., Kasamatsu, S., Ida, T., Ihara, H., Kim, Y. G., Hase, K., Miura, Y., Maehama, T., Kusano, M., Umezawa, K., Akiyama, M.: Formation of a reducing microenvironment and regulation of protein supersulfidation by gut microbial supersulfides. Redox Biol., 2026, 92, 104123.
  2. Shichi, Y., Tsumoto, H., Fujiwara, M., Nonaka, K., Hasegawa, Y., Shinji, S., Rokutan, H., Takahashi, K., Arai, T., Miura, Y., Ishiwata, T.: Proteomic and immunocytochemical analyses of squamous components in two- and three-dimensional-cultured pancreatic ductal adenocarcinoma cell lines, Oncology Letters, 2026, accepted
  3. Shiiba, I., Ishikawa, Y., Oshio, H., Ito, N., Yamaguchi, F., Nagashima, S., Ando, H., Umezawa, K., Miura, Y., Araiso, Y., Nakamura, K., Hirabayashi, Y., Inatome, R., Yanagi, S.: MFN2-STIM1-mediated mitochondria-melanosome contact: A key to melanosome maturation, Nat. Commun., 2026, https://doi.org/10.1038/s41467-026-70282-w
  4. Ikeda-Imafuku, M., Sakai, M., Umezawa, K., Nakagawa, H., Maruyama, T., Otagiri, M., AkaikeT., Sawa, T., Xian, M., Miura, Y., Ishida, T., Ishima, Y.: Unique response of polysulfide in serum albumin against oxidative stress, Sci. Rep.,2025, 15, 42689.
  5. Akimoto, Y., Miura, Y., Kudo, A., Fukutomi, T., Arai, T., Chiba, Y., Kaname, S., Yan, K., Endo, T., Hart, G.W.: The O-GlcNAcylation of β-actin Ser199 controls nuclear speckle localization and is dysregulated in diabetes, Histochem.Cell Biol.,2025, 163, 106.
  6. Mukherjee, A., Yamashita, Y., Maeda, R., Akiyama, T., Endo, K., Takada, Y., Tsumoto, H., Moriyama, Y., Ito, A., Shirai, F., Tachibana, M., Itoh, Y., Suzuki, T.: A novel PROTAC G9a/GLP degrader that inhibits, similar to G9a siRNA, the migration of MCF-7 breast-cancer cells without affecting proliferation. J. Med. Chem.,2025, 68, 18258-18271.
  7. Takikawa, K., Namiki, S., Umezawa, K., Asanuma, D., Hirose, K., Nishimune H.: Development of a hybrid-type fluorescent GABA sensor through structure-guided efficient screening. ACS Sensors,2025, 10, 7302-7312.
  8. Sasaki,N., Kawakami, K., Itakura, Y., Fujita, T., Miyagawa, S., Ishigami, T., Kubo, H., Miura, Y., Chiba, Y.: Characterization of extracellular vesicles derived from cortical bone stem cells compared with Mesenchymal stem cells, Mol. Cell. Biochem., 2025, 480, 5861-5876.
  9. Kawakami, K., Edo, N., Morita, K., Ishikawa, T., Onose, H., Fukumori, T., Tsumoto, H., Umezawa, K., Ito, M., Miura, Y.: Proteomic analysis reveals elevated RAB21 in serum-derived extracellular vesicles from follicular thyroid carcinoma patients, Oncology Letters, 2025, 30, 444.
  10. Mori, S., Zhou, H., Omura, T., Tsumoto, H., Miura, Y., Shigemoto, K.: Muscle-specific kinase levels in blood are an early diagnostic biomarker for SOD1-93A mouse model of ALS, Front. Neurol., 2025, 16, 1556120.
  11. Yoshida, Y, Ishizaki, T, Hirata,T, Masui, Y, Inagaki, H, Miura, Y, Ogawa, M, Ito, K, Arai, Y, Kamide, K, Ikebe, K, Gondo, Y.: Impact of polypharmacy on self-rated health in community-dwelling older adults: A 3-year SONIC study, J. Am. Med. Dir. Assoc.2025, 26, 105621.
  12. Akimoto, Y., Miura, Y., Kudo, A., Tsumoto, H., Fukutomi, T., Sugahara, D., Arai, T., Chiba, Y., Kaname, S., Yan, K., Kawakami, H., Endo, T., and Hart, G.W.: Immunohistochemical study on O-GlcNAcylation in diabetic pathologies: Molecular mechanisms and implications, Acta Histochem. Cytochem., 2025, 58, 115-121.
  13. Shiiba, I., Ito, N., Oshio, H., Ishikawa, Y., Nagao, T., Shimura, H., Oh, K. W., Takasaki, E., Yamaguchi, F., Konagaya, R., Kadowaki, H., Nishitoh, H., Tanzawa, T., Nagashima, S., Sugiura, A., Fujikawa, Y., Umezawa, K., Tamura, Y., Lee, B., Hirabayashi, Y., Okazaki, Y., Sawa, T., Inatome, R., Yanagi, S.: ER-mitochondria contacts mediate lipid radical transfer via RMDN3/PTPIP51 phosphorylation to reduce mitochondrial oxidative stress. Nat. Commun., 2025, 16, 1508.
  14. Nishimura, A., Ogata, S., Tang, X., Hengphasatporn, K., Umezawa, K., Sanbo, M., Hirabayashi, M., Kato, Y., Ibuki, Y., Kumagai, Y., Kobayashi, K., Kanda, Y., Urano, Y., Shigeta, Y., Akaike, T., Nishida, M.: Polysulfur-based bulking of dynamin-related protein 1 prevents ischemic sulfide catabolism and heart failure in mice. Nat. Commun., 2025, 16, 276.
  15. Nishimura, A., Tanaka, T., Shimoda, K., Ida, T., Sasaki, S., Umezawa, K., Imamura, H., Urano, Y., Ichinose, F., Kaneko, T., Akaike, T., Nishida, M.: Non-thermal atmospheric pressure plasma-irradiated cysteine protects cardiac ischemia/reperfusion injury by preserving supersulfides, Redox Biol., 2024, 79, 103445.
  16. Ebina, M., Miura, Y., Sakane, F.: Ubiquitin-specific peptidase 11 selectively interacts with and deubiquitination-dependently stabilizes diacylglycerol kinase d to maintain cellular glucose uptake, Biochim. Biophys. Acta, Mol. Cell Res., 2024, 1872, 119883.
  17. Wu, T., Sun, Y., Wang, D., Isaji, T., Fukuda, T., Suzuki, C., Hanamatsu, H., Nishikaze, T., Tsumoto, H., Miura, Y., Furukawa, J., Gu, J.: The acetylglucosaminyltransferase GnT-Ⅲ regulates erythroid differentiation through ERK/MAPK signaling, J. Biol. Chem., 2024, 300, 108010.
  18. Yoshida, Y., Ishizaki, T. Masui, M., Miura, Y., Matsumoto, K., Nakagawa, T., Inagaki, H., Ito, K., Arai, Y., Kabayama, M., Kamide, K., Rakugi, H., Ikebe, K., Gondo, Y.: Effects of multimorbidity and polypharmacy on physical function in community-dwelling older adults: a 3-year follow-up analysis of the SONIC study, Arch. Gerontol. Geriatr.2024, 126, 105521.
  19. Imae, R., Manya, H., Tsumoto, H., Umezawa, K., Miura, Y., and Endo, T.: Changes in the amount of nucleotide sugars in aged mouse tissues, Glycobiology, 2024, 34, cwae032.
  20. Zhang, Z., Aoki, H., Umezawa, K., Kranrod, J., Miyazaki, N., Oshima,T., Hirao, T., Miura, Y., Ito, K., Aoki, S: Potential role of lipophagy impairment for anticancer effects of glycolysis-suppressed pancreatic ductal adenocarcinoma cells, Cell Death Discov., 2024, 10, 166.
  21. Kato, Y., Byeon, J., Noto, A. Kashiwaya, S., Aoki, Y., Watanabe, N., Tsumoto, H., Miura, Y., Fukui, K.: Tocotrienols prevent the decline of learning ability in high-fat high-sucrose diet-fed C57BL/6 mice, Int. J. Mol. Sci., 2024, 25, 3561.
  22. Kondo, M., Nakamura, Y., Kato, Y., Nishimura, A., Fukata, M., Moriyama, S., Ito, T., Umezawa, K., Urano, Y., Akaike, T., Akashi, K., Kanda, Y., Nishida, M.: Inorganic sulfides prevent osimertinib-induced mitochondrial dysfunction in human iPS cell-derived cardiomyocytes, J. Pharmacol. Sci.2024, 156, 69-76.
  23. Zhou, L., Nishimura, A., Umezawa, K., Kato, Y., Mi, X., Ito, T., Urano, Y., Akaike, T., Nishida, M.: Supersulfide catabolism participates in maladaptive remodeling of cardiac cells. J. Pharmacol. Sci.2024, 155, 121-130.
  24. Miura, Y., Tsumoto, H., Masui, Y., Inagaki, H., Ogawa, M., Ideno, Y., Kawakami, K., Umezawa, K., Kabayama, M., Akagi, Y., Akasaka, H., Yamamoto, K., Rakugi, H., Ishizaki, T., Arai, Y., Ikebe, K., Kamide, K., Gondo, Y., Endo, T.: A characteristic N-glycopeptide signature associated with diabetic cognitive impairment identified in a longitudinal cohort study, Biochim. Biophys. Acta, Gen. Sub., 2023, 1867, 130318.
  25. Fujita, Y., Shinkai, S., Taniguchi. Y., Miura, Y., Tanaka, M., Ohsawa, I., Kitamura, A., Ito, M.: Association between serum GDF15 concentration and total mortality in community-dwelling Japanese older populations: The involvement of renal dysfunction, J. Gerontol. A Biol. Sci. Med. Sci.2023, 78, 1701-1707.