Department of Peptidomics


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Chief (Principal Investigator) Kazuki Sasaki, M.D., Ph.D. e-mail: k-sasaki
Research Scientist Masao Nakamura, Ph.D. e-mail: m-nakamura

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Peptidomics is a comprehensive study of naturally occurring peptides smaller than 10,000 Da. Apart from peptide hormones and anti-microbial peptides, they are in a relatively uncharted territory of the proteome. We have developed a platform for profiling endogenous peptides using mass spectrometry. Our profiling study helps to elucidate proteolytic processing sites of secretory proteins and transmembrane proteins, marking the locations where peptide hormones are cleaved off, or soluble receptors are created to be a ligand sink, to name a few. Given that the processing is not just regulated by particular sequences but by post-translational modifications, like glycosylation, neighboring the cleavage sites, the whole picture is so complicated that in silico prediction falls well short of our expectation. This situation makes peptidomics the method of choice for delineating processing sites in an unbiased manner. Our earlier study to define procesussing sites of secretory proteins led to the identification of biologically active peptides functioning in the nervous and endocrine systems. We are currently looking at transmembrane proteins that undergo extracellular processing with the aim of identifying potential targets applicable to the therapeutics and diagnostics of pancreatic ductal adenocarcinoma. Unlike other omics, peptidomics has lagged behind and remained underrepresented, but this study is part of a larger pattern we are going to see over the years to come.


Our efforts are directed towards the identification of transmembrane proteins that could serve as a potential target for treating pancreatic ductal adenocarcinoma. Some transmembrane proteins undergo ectodomain shedding, leaving behind membrane stubs on the cell surface. These membrane-associated segments can be a potential target of antigen-dependent cellular cytotoxicity. We have demonstrated that peptidomics-based endogenous peptide profiling helps to identify proteolytic processing sites of secretory or transmembrane proteins. This is accomplished by mass spectrometric sequencing of peptides larger than 3,000 Da, which are beyond the reach of current bottom-up proteomics.

Publications (last 5 years)

  1. Sasaki K, Tsuchiya T, and Osaki T: Isolation of Endogenous Peptides from Cultured Cell Conditioned Media for Mass Spectrometry. Methods MolBiol. 1719: 51-58 (2018)
  2. Tsuchiya T, Iwakura H, Minamino N, Kangawa K, and Sasaki K: Endogenous peptide profile for elucidating biosynthetic processing of the ghrelin precursor. Biochem. Biophys. Res. Commun. 490: 1142-1146 (2017)
  3. Namkoong C, Toshinai K, Waise Z, Sakoda H, Sasaki K, Ueta Y, Kim MS, Minamino N, and Nakazato M: NERP-2 regulates gastric acid secretion and gastric emptying via the orexin pathway. Biochem. Biophys. Res. Commun. 485: 409-413 (2017)
  4. Choi SG, Wang Q, Jia J, Chikina M, Pincas H, Dolios G, Sasaki K, Wang R, Minamino N, Salton SRJ, and Sealfon SC: Characterization of gonadotrope secretoproteome identifies neurosecretory protein VGF-derived peptide suppression of follicle-stimulating hormone gene expression. J. Biol. Chem. 291: 21322-21334 (2016)
  5. Tsuchiya T, Osaki T, Minamino N, and Sasaki K: Peptidomics for studying limited proteolysis. J. Proteome Res. 14: 4921-4931 (2015)
  6. Marie Rhee JW, Park JH, Yamaguchi H, Sasaki K, Minamino N, Nakazato M, Song DK, and Yoon KH: Chronic effects of neuroendocrine regulatory peptide (NERP-1 and -2) on insulin secretion and gene expression in pancreatic β-cells. Biochem. Biophys. Res. Commun. 457: 148-53 (2015)
  7. Toshinai K, Saito T, Yamaguchi H, Sasaki K, Tsuchimochi W, Minamino N, Ueta Y, and Nakazato M: Neuroendocrine regulatory peptide-1 and -2 (NERPs) inhibit the excitability of magnocellular neurosecretory cells in the hypothalamus. Brain Res. 1563: 52-60 (2014)
  8. Nonaka M, Kim R, Fukushima H, Sasaki K, Suzuki K, Okamura M, Ishii Y, Kawashima T, Kamijo S, Takemoto-Kimura S, Okuno H, Kida S, and Bito H: Region-Specific Activation of CRTC1-CREB signaling mediates long-term fear memory. Neuron 84: 92-106 (2014)
  9. Tomiyama A, Uekita T, Kamata R, Sasaki K, Takita J, Ohira M, Nakagawara A, Kitanaka C, Mori K, Yamaguchi H, and Sakai R: Flotillin-1 regulates oncogenic signaling in neuroblastoma cells by regulating ALK membrane association. Cancer Res. 74: 3790-3801 (2014)