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Sasaki S, Oba K, Kodera Y, Itakura M, Shichiri M. ANGT_HUMAN[448–462], an Anorexigenic Peptide Identified using Plasma Peptidomics. J Endocr Soc 2022; 6:bvac082. [PMID: 35702602 PMCID: PMC9184509 DOI: 10.1210/jendso/bvac082] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Indexed: 11/19/2022] Open
Abstract
Abstract
The discovery of bioactive peptides is an important research target that enables the elucidation of the pathophysiology of human diseases and provides seeds for drug discovery. Using a large number of native peptides previously identified using plasma peptidomics technology, we sequentially synthesized selected sequences and subjected them to functional screening using human cultured cells. A 15-amino-acid residue proangiotensinogen-derived peptide, designated ANGT_HUMAN[448–462], elicited cellular responses and bound to cultured human cells. Synthetic fluorescent-labeled and biotinylated ANGT_HUMAN[448–462] peptides were rendered to bind to cell- and tissue-derived proteins and peptide-cell protein complexes were retrieved and analyzed using liquid chromatography-tandem mass spectrometry, revealing the β-subunit of ATP synthase as its cell-surface binding protein. Because ATP synthase mediates the effects of anorexigenic peptides, the ability of ANGT_HUMAN[448–462] to modulate eating behavior in mice was investigated. Both intraperitoneal and intracerebroventricular injections of low doses of ANGT_HUMAN[448–462] suppressed spontaneous food and water intake throughout the dark phase of the diurnal cycle without affecting locomotor activity. Immunoreactive ANGT_HUMAN[448–462], distributed throughout human tissues and in human-derived cells, is mostly co-localized with angiotensin II and is occasionally present separately from angiotensin II. In this study, an anorexigenic peptide, ANGT_HUMAN[448–462], was identified by exploring cell surface target proteins of the human native peptides identified using plasma peptidomics.
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Affiliation(s)
- Sayaka Sasaki
- Department of Endocrinology, Diabetes and Metabolism, Kitasato University School of Medicine Kanagawa 252-0374, Japan
| | - Kazuhito Oba
- Department of Endocrinology, Diabetes and Metabolism, Kitasato University School of Medicine Kanagawa 252-0374, Japan
| | - Yoshio Kodera
- Department of Physics, Kitasato University School of Science, Kanagawa 252-0373, Japan
- Center for Disease Proteomics, Kitasato University School of Science, Kanagawa 252-0373, Japan
| | - Makoto Itakura
- Department of Biochemistry, Kitasato University School of Medicine, Kanagawa 252-0374, Japan
| | - Masayoshi Shichiri
- Department of Endocrinology, Diabetes and Metabolism, Kitasato University School of Medicine Kanagawa 252-0374, Japan
- Department of Diabetes, Endocrinology and Metabolism, Tokyo Kyosai Hospital, Tokyo 153-8934, Japan
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Hoshiyama A, Fujimoto K, Konno R, Sasaki S, Momozono A, Kodera Y, Shichiri M. Identification of plasma binding proteins for glucose-dependent insulinotropic polypeptide. Endocr J 2019; 66:621-628. [PMID: 31061246 DOI: 10.1507/endocrj.ej18-0472] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Glucose-dependent insulinotropic polypeptide (GIP), secreted from enteroendocrine K cells, has potent insulin-releasing and extrapancreatic glucoregulatory activities. However, exogenous GIP has less potent biological effects compared with another incretin hormone, GLP-1, which limits its use for the treatment of type 2 diabetes. The fate and secretion of administered native GIP remain unclear. The aim of this study was to identify plasma binding proteins for human GIP. Fluorescent-labelled GIP was added to fresh human plasma and subjected to clear native polyacrylamide gel electrophoresis (CN-PAGE). Then fluorescent protein bands were in-gel trypsin-digested and subjected to liquid chromatography tandem-mass spectrometry (LC-MS/MS) analysis, revealing the presence of albumin, immunoglobulin G (IgG) and transferrin. In contrast to GIP, the binding of fluorescent GLP-1 and glucagon to plasma protein fractions were minimal. CN-PAGE analysis of synthetic GIP incubated with human serum albumin, purified IgG or transferrin, and subsequent western blot analysis revealed that GIP binds to each of these proteins. Taken together, these results indicate that GIP readily binds to albumin, IgG and transferrin, three plasma proteins highly abundant in the human peripheral circulation. Separation of protein complexes using CN-PAGE and the identification of in-gel digested proteins by LC-MS/MS analysis provide a promising strategy to identify plasma binding proteins for bioactive peptides.
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Affiliation(s)
- Ayako Hoshiyama
- Department of Endocrinology, Diabetes and Metabolism, Kitasato University School of Medicine, Kanagawa, Japan
| | - Kazumi Fujimoto
- Department of Endocrinology, Diabetes and Metabolism, Kitasato University School of Medicine, Kanagawa, Japan
- Laboratory of Biomolecular Physics, Kitasato University School of Science, Kanagawa, Japan
| | - Ryo Konno
- Laboratory of Biomolecular Physics, Kitasato University School of Science, Kanagawa, Japan
- Center for Disease Proteomics, Kitasato University School of Science, Kanagawa, Japan
| | - Sayaka Sasaki
- Department of Endocrinology, Diabetes and Metabolism, Kitasato University School of Medicine, Kanagawa, Japan
| | - Akari Momozono
- Department of Endocrinology, Diabetes and Metabolism, Kitasato University School of Medicine, Kanagawa, Japan
| | - Yoshio Kodera
- Laboratory of Biomolecular Physics, Kitasato University School of Science, Kanagawa, Japan
- Center for Disease Proteomics, Kitasato University School of Science, Kanagawa, Japan
| | - Masayoshi Shichiri
- Department of Endocrinology, Diabetes and Metabolism, Kitasato University School of Medicine, Kanagawa, Japan
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Satoh M, Takano S, Sogawa K, Noda K, Yoshitomi H, Ishibashi M, Mogushi K, Takizawa H, Otsuka M, Shimizu H, Miyazaki M, Nomura F. Immune-complex level of cofilin-1 in sera is associated with cancer progression and poor prognosis in pancreatic cancer. Cancer Sci 2017; 108:795-803. [PMID: 28161904 PMCID: PMC5406537 DOI: 10.1111/cas.13181] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2016] [Revised: 01/16/2017] [Accepted: 01/25/2017] [Indexed: 12/13/2022] Open
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is one of the most lethal malignancies. To improve its outcome, reliable biomarkers are urgently needed. In this study, we aimed to elucidate the key molecules involved in PDAC progression using proteomics approaches. First, we undertook 2‐D electrophoresis to identify the proteins overexpressed in PDAC tissues. Following the analysis of agarose gel spots, cofilin‐1 was identified and verified as a candidate protein commonly upregulated in PDAC tissues. In immunohistochemistry, cofilin‐1 was strongly expressed in the cytoplasm of PDAC cells. Samples were divided into two groups based on the level of cofilin‐1 expression. The high expression group showed significantly higher incidence of hematogenous dissemination in relapsed patients than the low expression group (P = 0.0083). In in vitro experiments, knockdown of cofilin‐1 significantly decreased chemotaxis in PDAC cell lines. After we confirmed that cofilin‐1 was secreted from PDAC cells, we established a detection system for the immune‐complex of cofilin‐1 in sera. Using this system, we measured the IC levels of cofilin‐1 in sera and observed that the IC levels of cofilin‐1 in PDAC patients were higher than those in healthy volunteers and patients with pancreatitis (PDAC vs. healthy volunteers, P < 0.0001; PDAC vs. patients with pancreatitis, P < 0.026). Notably, the IC levels of cofilin‐1 showed a stepwise increase during PDAC progression (P = 0.0034), and high IC levels of cofilin‐1 indicated poor prognosis of patients after surgery (P = 0.039). These results suggest that the IC of cofilin‐1 in sera is a potentially attractive serum biomarker for the prognosis of PDAC.
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Affiliation(s)
- Mamoru Satoh
- Division of Clinical Mass Spectrometry, Chiba University Hospital, Chiba, Japan.,Department of Molecular Diagnosis, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Shigetsugu Takano
- Department of General Surgery, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Kazuyuki Sogawa
- Department of Molecular Diagnosis, Graduate School of Medicine, Chiba University, Chiba, Japan.,Department of Biochemistry, School of Life and Environmental Science, Azabu University, Kanagawa, Japan
| | - Kenta Noda
- R&D Department, Nittobo Medical Co., Ltd., Koriyama, Japan
| | - Hideyuki Yoshitomi
- Department of General Surgery, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Masumi Ishibashi
- Department of Molecular Diagnosis, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Kaoru Mogushi
- Center for Genomic and Regenerative Medicine, Juntendo University, Tokyo, Japan
| | - Hirotaka Takizawa
- Kashiwado Clinic in Port-Square, Kashiwado Memorial Foundation, Chiba, Japan
| | - Masayuki Otsuka
- Department of General Surgery, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Hiroaki Shimizu
- Department of General Surgery, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Masaru Miyazaki
- Department of General Surgery, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Fumio Nomura
- Division of Clinical Mass Spectrometry, Chiba University Hospital, Chiba, Japan.,Department of Molecular Diagnosis, Graduate School of Medicine, Chiba University, Chiba, Japan
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Proteome analysis of hemofilter adsorbates to identify novel substances of sepsis: a pilot study. J Artif Organs 2016; 20:132-137. [PMID: 27858178 DOI: 10.1007/s10047-016-0936-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2016] [Accepted: 11/09/2016] [Indexed: 12/18/2022]
Abstract
Blood purification therapy using hemofilters with high adsorbing capabilities has been reported to remove excessive humoral mediators from the blood of patients with sepsis. However, there are insufficient studies of the adsorbates bound to hemofilter membranes. We hypothesized that these adsorbates in acute kidney injury (AKI) patients with sepsis were different from those in patients without sepsis and that proteome analysis of the adsorbates would identify novel substances of sepsis. This study included 20 patients who had AKI upon admission to intensive care units (ICUs) and who received continuous renal replacement therapy using polymethyl methacrylate hemofilters. We isolated adsorbates from the hemofilters after use and performed comprehensive proteome analysis. A total of 429 proteins were identified in these adsorbates. Adsorbates from the hemofilters of patients with sepsis had significantly increased frequency of proteins associated with "immune system process" and "biological adhesion" functions compared to those of non-sepsis patients (P < 0.05). Of 429 proteins, 197 were identified only in sepsis adsorbates. Of these, 3 proteins including carbonic anhydrase 1 (CA1) and leucine-rich alpha-2-glycoprotein (LRG1) were identified in all samples from sepsis patients and have not been previously reported in sepsis patients. Validation analysis of patient serum revealed that patients with sepsis had increased serum levels of CA1 and LRG1 compared to patients without sepsis (P < 0.05). To conclude, there were significant differences in the characteristics of the adsorbates from sepsis and non-sepsis patients. CA1 and LRG1 appear to be novel substances associated with sepsis.
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Beppu M, Sawai S, Satoh M, Mori M, Kazami T, Misawa S, Shibuya K, Ishibashi M, Sogawa K, Kado S, Kodera Y, Nomura F, Kuwabara S. Autoantibodies against vinculin in patients with chronic inflammatory demyelinating polyneuropathy. J Neuroimmunol 2015; 287:9-15. [PMID: 26439954 DOI: 10.1016/j.jneuroim.2015.07.012] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2015] [Revised: 07/19/2015] [Accepted: 07/24/2015] [Indexed: 11/30/2022]
Abstract
To identify the target molecules of chronic inflammatory demyelinating polyneuropathy (CIDP), we used proteomic-based approach in the extracted proteins from porcine cauda equina. Two of 31 CIDP patients had markedly elevated serum autoantibodies against vinculin, a cell adhesion protein. Both of the patients with anti-vinculin antibodies had similar clinical manifestation, which are compatible with those of "typical" CIDP. Immunocytochemistry showed that vinculin was stained at the myelin sheath of the sciatic nerves by serum samples. Our results suggest that vinculin is a possible immunological target molecule in a subpopulation of typical CIDP patients.
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Affiliation(s)
- Minako Beppu
- Department of Neurology, Graduate School of Medicine, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba 260-8670, Japan; Department of Molecular Diagnosis, Graduate School of Medicine, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba 260-8670, Japan.
| | - Setsu Sawai
- Department of Molecular Diagnosis, Graduate School of Medicine, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba 260-8670, Japan
| | - Mamoru Satoh
- Department of Molecular Diagnosis, Graduate School of Medicine, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba 260-8670, Japan
| | - Masahiro Mori
- Department of Neurology, Graduate School of Medicine, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba 260-8670, Japan
| | - Takahiro Kazami
- Department of Molecular Diagnosis, Graduate School of Medicine, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba 260-8670, Japan
| | - Sonoko Misawa
- Department of Neurology, Graduate School of Medicine, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba 260-8670, Japan
| | - Kazumoto Shibuya
- Department of Neurology, Graduate School of Medicine, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba 260-8670, Japan
| | - Masumi Ishibashi
- Department of Molecular Diagnosis, Graduate School of Medicine, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba 260-8670, Japan
| | - Kazuyuki Sogawa
- Department of Molecular Diagnosis, Graduate School of Medicine, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba 260-8670, Japan
| | - Sayaka Kado
- Chemical Analysis Center, Chiba University, 1-33 Yayoicho, Inage-ku, Chiba 263-8522, Japan
| | - Yoshio Kodera
- Department of Physics, School of Science, Kitasato University, 1-15-1, Kitasato, Minami-ku, Sagamihara, Kanagawa 252-0373, Japan
| | - Fumio Nomura
- Department of Molecular Diagnosis, Graduate School of Medicine, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba 260-8670, Japan
| | - Satoshi Kuwabara
- Department of Neurology, Graduate School of Medicine, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba 260-8670, Japan
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Tewari RK, Satoh M, Kado S, Mishina K, Anma M, Enami K, Hanaoka M, Watanabe M. Overproduction of stromal ferredoxin:NADPH oxidoreductase in H2O 2-accumulating Brassica napus leaf protoplasts. PLANT MOLECULAR BIOLOGY 2014; 86:627-639. [PMID: 25255860 DOI: 10.1007/s11103-014-0252-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2014] [Accepted: 09/11/2014] [Indexed: 06/03/2023]
Abstract
The isolation of Brassica napus leaf protoplasts induces reactive oxygen species generation and accumulation in the chloroplasts. An activated isoform of NADPH oxidase-like protein was detected in the protoplasts and the protoplast chloroplasts. The purpose of this study is to define the NADH oxidase-like activities in the H2O2-accumulating protoplast chloroplasts. Proteomic analysis of this protein revealed an isoform of ferredoxin:NADPH oxidoreductase (FNR1). While leaves highly expressed the LFNR1 transcript, protoplasts decreased the expression significantly. The protoplast chloroplasts predominantly expressed soluble FNR1 proteins. While the albino leaves of white kale (Brassica oleracea var. acephala f. tricolor cv. white pigeon) expressed FNR1 protein at the same level as B. napus leaves, the protoplasts of albino leaves displayed reduced FNR1 expression. The albino leaf protoplasts of white kale generated and accumulated H2O2 in the cytoplasm and on the plasma membrane. Intracellular pH showed that the chloroplasts were acidic, which suggest that excess H(+) was generated in chloroplast stroma. NADPH content of the protoplast chloroplasts increased by over sixfold during the isolation of protoplasts. This study reports a possibility of mediating electrons to oxygen by an overproduced soluble FNR, and suggests that the FNR has a function in utilizing any excess reducing power of NADPH.
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Affiliation(s)
- Rajesh Kumar Tewari
- Laboratory of Plant Nutrition, Faculty of Horticulture, Chiba University, 648 Matsudo, Chiba, 271-8510, Japan
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Toyotome T, Satoh M, Yahiro M, Watanabe A, Nomura F, Kamei K. Glucoamylase is a major allergen ofSchizophyllum commune. Clin Exp Allergy 2014; 44:450-7. [DOI: 10.1111/cea.12260] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2013] [Revised: 10/31/2013] [Accepted: 12/08/2013] [Indexed: 11/29/2022]
Affiliation(s)
- T. Toyotome
- Division of Clinical Research; Medical Mycology Research Center; Chiba University; Chiba Japan
- Research Center for Animal Hygiene and Food Safety; Obihiro University of Agriculture and Veterinary Medicine; Hokkaido Japan
| | - M. Satoh
- Clinical Proteomics Research Center; Chiba University Hospital; Chiba Japan
| | - M. Yahiro
- Division of Clinical Research; Medical Mycology Research Center; Chiba University; Chiba Japan
| | - A. Watanabe
- Division of Clinical Research; Medical Mycology Research Center; Chiba University; Chiba Japan
- Division of Control and Treatment of Infectious Diseases; Chiba University Hospital; Chiba Japan
| | - F. Nomura
- Clinical Proteomics Research Center; Chiba University Hospital; Chiba Japan
- Department of Molecular Diagnosis; Graduate School of Medicine; Chiba University; Chiba Japan
| | - K. Kamei
- Division of Clinical Research; Medical Mycology Research Center; Chiba University; Chiba Japan
- Division of Control and Treatment of Infectious Diseases; Chiba University Hospital; Chiba Japan
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Nishimura M, Satoh M, Nishimura S, Kakinuma S, Sato K, Sawai S, Tsuchida S, Kazama T, Matsushita K, Kado S, Kodera Y, Nomura F. Human apolipoprotein e resequencing by proteomic analysis and its application to serotyping. PLoS One 2014; 9:e85356. [PMID: 24454848 PMCID: PMC3891820 DOI: 10.1371/journal.pone.0085356] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2013] [Accepted: 11/26/2013] [Indexed: 01/02/2023] Open
Abstract
Background Apolipoprotein E (ApoE) typing is considered important because of the association between ApoE and Alzheimer’s disease and familial dyslipidemia and is currently performed by genetic testing (APOE genotyping). ApoE levels in plasma and serum are clinically determined by immunoassay. Methods Combining an ApoE immunoassay reagent with proteomic analysis using an Orbitrap mass spectrometer, we attempted to resequence ApoE from trace amounts of serum for typing (serotyping). Most (24 of 33) ApoE mutant proteins registered to date with Online Mendelian Inheritance in Man, such as ApoE2 and ApoE4, involve lysine and arginine mutations. Digestion of mutant ApoE with trypsin will thus result in fragments that differ substantially from wild-type ApoE3 in terms of mass, making serotyping ideally suited to mass spectrometry analysis. Results The mean coverage of the amino acid sequence of full-length ApoE was 91.6% in the protein resequence. Residues 112 and 158 (which are mutated in ApoE2 and ApoE4) were covered in all samples, and the protein sequences were used for serotyping. Serotypes including all heterozygous combinations (ApoE2/E3, E2/E4, E3/E4) corresponded exactly to the APOE genotyping results in each of the subjects. Conclusion Our novel ApoE serotyping method with protein resequencing requires no synthesis of stable isotope-labeled peptides or genome analysis. The method can use residual blood from samples collected for routine clinical tests, thus enabling retrospective studies with preserved body fluids. The test could be applied to samples from subjects whose DNA is unavailable. In future studies, we hope to demonstrate the capability of our method to detect rare ApoE mutations.
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Affiliation(s)
- Motoi Nishimura
- Department of Molecular Diagnosis, Graduate School of Medicine, Chiba University, Chiba, Japan
- Division of Laboratory Medicine and Clinical Genetics, Chiba University Hospital, Chiba, Japan
- Clinical Proteomics Research Center, Chiba University Hospital, Chiba, Japan
- * E-mail:
| | - Mamoru Satoh
- Department of Molecular Diagnosis, Graduate School of Medicine, Chiba University, Chiba, Japan
- Clinical Proteomics Research Center, Chiba University Hospital, Chiba, Japan
| | - Satomi Nishimura
- Department of Molecular Diagnosis, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Shoko Kakinuma
- Department of Molecular Diagnosis, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Kenichi Sato
- Division of Laboratory Medicine and Clinical Genetics, Chiba University Hospital, Chiba, Japan
| | - Setsu Sawai
- Department of Molecular Diagnosis, Graduate School of Medicine, Chiba University, Chiba, Japan
- Division of Laboratory Medicine and Clinical Genetics, Chiba University Hospital, Chiba, Japan
| | - Sachio Tsuchida
- Department of Molecular Diagnosis, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Takeshi Kazama
- Division of Laboratory Medicine and Clinical Genetics, Chiba University Hospital, Chiba, Japan
| | - Kazuyuki Matsushita
- Department of Molecular Diagnosis, Graduate School of Medicine, Chiba University, Chiba, Japan
- Division of Laboratory Medicine and Clinical Genetics, Chiba University Hospital, Chiba, Japan
- Clinical Proteomics Research Center, Chiba University Hospital, Chiba, Japan
| | - Sayaka Kado
- Chemical Analysis Center, Chiba University, Chiba, Japan
| | - Yoshio Kodera
- Clinical Proteomics Research Center, Chiba University Hospital, Chiba, Japan
- Laboratory of Biomolecular Dynamics, Department of Physics, School of Science, Kitasato University, Sagamihara, Japan
| | - Fumio Nomura
- Department of Molecular Diagnosis, Graduate School of Medicine, Chiba University, Chiba, Japan
- Division of Laboratory Medicine and Clinical Genetics, Chiba University Hospital, Chiba, Japan
- Clinical Proteomics Research Center, Chiba University Hospital, Chiba, Japan
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Angiotensin-converting enzyme inhibition curbs tyrosine nitration of mitochondrial proteins in the renal cortex during the early stage of diabetes mellitus in rats. Clin Sci (Lond) 2013; 124:543-52. [PMID: 23130652 PMCID: PMC3540783 DOI: 10.1042/cs20120251] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Experiments were performed to evaluate the hypothesis that ACE (angiotensin-converting enzyme) inhibition (enalapril) suppresses 3-NT (3-nitrotyrosine) production in the renal cortex during the early stage of Type 1 DM (diabetes mellitus) in the rat. Enalapril was administered chronically for 2 weeks to subsets of STZ (streptozotocin)-induced DM and vehicle-treated sham rats. O2− (superoxide anion) and NOx (nitrate+nitrite) levels were measured in the media bathing renal cortical slices after 90 min incubation in vitro. SOD (superoxide dismutase) activity and 3-NT content were measured in the renal cortex homogenate. Renal cortical nitrated protein was identified by proteomic analysis. Renal cortical production of O2− and 3-NT was increased in DM rats; however, enalapril suppressed these changes. DM rats also exhibited elevated renal cortical NOx production and SOD activity, and these changes were magnified by enalapril treatment. 2-DE (two-dimensional gel electrophoresis)-based Western blotting revealed more than 20 spots with positive 3-NT immunoreactivity in the renal cortex of DM rats. Enalapril treatment blunted the DM-induced increase in tyrosine nitration of three proteins ACO2, GDH1 and MMSDH (aconitase 2, glutamate dehydrogenase 1 and methylmalonate-semialdehyde dehydrogenase), each of which resides in mitochondria. These data are consistent with enalapril preventing DM-induced tyrosine nitration of mitochondrial proteins by a mechanism involving suppression of oxidant production and enhancement of antioxidant capacity, including SOD activation.
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Yamada M, Satoh M, Seimiya M, Sogawa K, Itoga S, Tomonaga T, Nomura F. Combined proteomic analysis of liver tissue and serum in chronically alcohol-fed rats. Alcohol Clin Exp Res 2012; 37 Suppl 1:E79-87. [PMID: 23083309 DOI: 10.1111/j.1530-0277.2012.01883.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2011] [Accepted: 05/16/2012] [Indexed: 12/31/2022]
Abstract
BACKGROUND Proteomic approaches may provide new insights into pathological conditions associated with alcoholism. The aim of this study was to conduct a proteomic analysis of liver tissue and serum in chronically alcohol-fed rats using agarose 2-dimensional gel electrophoresis (2-DE) and 3-step serum proteome analysis. METHODS A total of 12 rats were pair-fed nutritionally adequate liquid diet containing ethanol as 36% of the total energy or an isocaloric control diet for 2 months. Rat liver homogenates and cytosol fractions were subjected to agarose 2-DE. Serum samples were subjected to 3-step serum proteome analysis involving immunodepletion of abundant proteins followed by fractionation using reverse-phase high-performance liquid chromatography and 1-dimensional sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE). Candidate proteins were digested with trypsin and identified using mass spectrometry. Observed differences in protein expression levels were confirmed using Western blotting. RESULTS A total of 46 protein spots were found to be differentially expressed in the liver homogenates and cytosol fractions of alcohol-fed rats relative to pair-fed controls. The most notable change was down-regulation of a 29-kDa protein, which was subsequently identified as carbonic anhydrase III (CA III). Down-regulation of this protein in alcohol-fed rats was confirmed by Western blotting. The messenger RNA level of CA III was decreased as well. In rat serum, a total of 41 proteins were differentially expressed. Of these proteins, only betaine-homocysteine methyltransferase (BHMT) was also found to be differentially expressed in the liver. CONCLUSIONS A combined proteomic analysis of liver tissue and serum in chronically alcohol-fed rats revealed that the expression of CA III is significantly down-regulated in the liver of alcohol-fed rats. Our results also showed that BHMT expression is up-regulated in both the liver and serum of alcohol-fed rats.
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Affiliation(s)
- Mako Yamada
- Department of Molecular Diagnosis, Graduate School of Medicine, Chiba University, Chiba, Japan
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Bousette N, Gramolini AO, Kislinger T. Proteomics-based investigations of animal models of disease. Proteomics Clin Appl 2012; 2:638-53. [PMID: 21136864 DOI: 10.1002/prca.200780043] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Cells contain a large yet, constant genome, which contains all the coding information necessary to sustain cellular physiology. However, proteins are the end products of genes, and hence dictate the phenotype of cells and tissues. Therefore, proteomics can provide key information for the elucidation of physiological and pathophysiological mechanisms by identifying the protein profile from cells and tissues. The relatively novel techniques used for the study of proteomics thus have the potential to improve diagnostic, prognostic, as well as therapeutic avenues. In this review, we first discuss the benefits of animal models over the use of human samples for the proteomic analysis of human disease. Next, we aim to demonstrate the potential of proteomics in the elucidation of disease mechanisms that may not be possible by other conventional technologies. Following this, we describe the use of proteomics for the analysis of PTM and protein interactions in animal models and their relevance to the study of human disease. Finally, we discuss the development of clinical biomarkers for the early diagnosis of disease via proteomic analysis of animal models. We also discuss the development of standard proteomes and relate how this data will benefit future proteomic research. A comprehensive review of all animal models used in conjunction with proteomics is beyond the scope of this manuscript. Therefore, we aimed to cover a large breadth of topics, which together, demonstrate the potential of proteomics as a powerful tool in biomedical research.
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Affiliation(s)
- Nicolas Bousette
- Department of Physiology, University of Toronto, Toronto, Ontario, Canada; Heart and Stroke/Richard Lewar Centre of Cardiovascular Excellence, Toronto, Ontario, Canada
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The application of a three-step proteome analysis for identification of new biomarkers of pancreatic cancer. INTERNATIONAL JOURNAL OF PROTEOMICS 2011; 2011:628787. [PMID: 22091389 PMCID: PMC3199071 DOI: 10.1155/2011/628787] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/31/2011] [Accepted: 08/02/2011] [Indexed: 01/04/2023]
Abstract
We searched for novel tumor markers of pancreatic cancer by three-step serum proteome analysis. Twelve serum abundant proteins were depleted using immunoaffinity columns followed by fractionation by reverse-phase high-performance liquid chromatography. Proteins in each fraction were separated by two-dimensional gel electrophoresis. Then the gel was stained by Coomassie Brilliant Blue. Protein spots in which the expression levels were significantly different between cancer and normal control were identified by LC-MS/MS. One hundred and two spots were upregulated, and 84 spots were downregulated in serum samples obtained from patients with pancreatic cancers, and 58 proteins were identified by mass spectrometry. These candidate proteins were validated using western blot analysis and enzyme-linked immunosorbent assay (ELISA). As a result of these validation process, we could confirm that the serum levels of apolipoprotein A-IV, vitamin D-binding protein, plasma retinol-binding protein 4, and tetranectin were significantly decreased in patients with pancreatic cancer.
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Adsorption of urinary proteins on the conventionally used urine collection tubes: possible effects on urinary proteome analysis and prevention of the adsorption by polymer coating. INTERNATIONAL JOURNAL OF PROTEOMICS 2011; 2011:502845. [PMID: 22229090 PMCID: PMC3200127 DOI: 10.1155/2011/502845] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/01/2011] [Accepted: 07/05/2011] [Indexed: 11/18/2022]
Abstract
One possible factor determining recovery of trace amount of protein biomarker candidates during proteome analyses could be adsorption on urine tubes. This issue, however, has not been well addressed so far. Recently, a new technical device of surface coating by poly(2-methacryloyloxyethyl phosphorylcholine (MPC)-co-n-butyl methacrylate (BMA)) (poly(MPC-co-BMA)) has been developed mainly to prevent the adsorption of plasma proteins. We assessed whether conventionally used urine tubes adsorb trace amount of urinary proteins and, if any, whether the surface coating by poly(MPC-co-BMA) can minimize the adsorption. Proteinuric urine samples were kept in poly(MPC-co-BMA)-coated and noncoated urine tubes for 15 min and possibly adsorbed proteins and/or peptides onto urine tubes were analyzed by SDS-PAGE, 2-DE, and the MALDI-TOF MS. It was found that a number of proteins and/or peptides adsorb on the conventionally used urine tubes and that surface coating by poly(MPC-co-BMA) can minimize the adsorption without any significant effects on routine urinalysis test results. Although it remains to be clarified to what extent the protein adsorption can modify the results of urinary proteome analyses, one has to consider this possible adsorption of urinary proteins when searching for trace amounts of protein biomarkers in urine.
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Faergestad EM, Rye MB, Nhek S, Hollung K, Grove H. The use of chemometrics to analyse protein patterns from gel electrophoresis. ACTA CHROMATOGR 2011. [DOI: 10.1556/achrom.23.2011.1.1] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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Kadowaki M, Sangai T, Nagashima T, Sakakibara M, Yoshitomi H, Takano S, Sogawa K, Umemura H, Fushimi K, Nakatani Y, Nomura F, Miyazaki M. Identification of vitronectin as a novel serum marker for early breast cancer detection using a new proteomic approach. J Cancer Res Clin Oncol 2011; 137:1105-15. [PMID: 21253761 DOI: 10.1007/s00432-010-0974-9] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2010] [Accepted: 12/28/2010] [Indexed: 01/22/2023]
Abstract
PURPOSE Breast cancer is the most frequent malignancy in women. However, no useful serum markers with high sensitivity and specificity for the detection of early breast cancer have been identified. The search for biological markers of early breast cancer is of continual interest in experimental and clinical breast cancer research. We recently described a simple and highly reproducible three-step proteome analysis for identifying potential disease-marker candidates among the low-abundance serum proteins. METHODS Serum samples from breast ductal carcinoma in situ (DCIS) patients and normal controls were subjected to a three-step serum proteome analysis. The steps were the following: first, immunodepletion of most abundant proteins; second, fractionation using reverse-phase high-performance liquid chromatography; and third, separation using two-dimensional electrophoresis (2-DE). Differences revealed by protein staining were further confirmed by Western blotting, immunohistochemical staining, and enzyme-linked immunosorbent assays (ELISA). RESULTS Twenty-two upregulated and 26 downregulated spots were detected on the 2-DE gels, and a total of 33 proteins were identified by liquid chromatography and tandem mass spectrometry. Western blotting confirmed that the level of vitronectin was significantly increased in DCIS patients compared with that of normal controls. Immunohistochemical staining of vitronectin in breast cancer tissue revealed high expression in small vessel walls surrounding cancer cells and the extracellular matrix of stroma. Moreover, vitronectin serum concentrations, as measured by ELISA, were significantly increased in patients with DCIS or more advanced breast cancer compared with those of normal controls. CONCLUSIONS Vitronectin could serve as a promising serum marker for the detection of primary breast cancer.
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Affiliation(s)
- Masami Kadowaki
- Department of General Surgery, Graduate School of Medicine, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba, 260-8670, Japan.
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Abstract
To investigate changes in protein expression by proteomic analysis in the sera of patients with sepsis and to identify new biomarkers of sepsis. A total of 45 consecutive patients with severe sepsis or septic shock (sepsis group), 22 healthy volunteers, and 23 patients undergoing off-pump coronary artery bypass grafting (control group). Serum samples from eight patients of each group underwent proteomic analysis involving removal of 12 major proteins and subsequent reversed-phase high-performance liquid chromatography fractionation and one-dimensional electrophoresis. The intensity of 41 bands (with 12 proteins identified) increased and that of 42 bands (with 22 proteins identified) decreased in the sepsis group. Results of proteomic analysis successfully validated by Western blotting and/or enzyme-linked immunosorbent assay for three proteins (YKL-40, lipocalin 2, and S100A9) increased in the sepsis group as well as two proteins (retinol-binding protein, vitamin D-binding protein) decreased. Serum YKL-40 levels (sYKL-40) on intensive care unit (ICU) admission were assessed by enzyme-linked immunosorbent assay between the two groups; resulting YKL-40 was significantly higher in the sepsis group (P < 0.001). Furthermore, sYKL-40 on ICU admission was significantly higher in patients with positive blood culture (P < 0.005), patients with septic shock (P < 0.05), and patients requiring continuous hemodiafiltration (P < 0.05) or hydrocortisone replacement therapy (P < 0.005) during subsequent treatment. A positive correlation between sYKL-40 and blood IL-6 level on ICU admission was noted in the sepsis group (r = 0.465, P < 0.01). YKL-40 identified by proteomic analysis is considered as a biomarker of sepsis. However, further investigation is needed to clarify its roles and clinical usefulness as a biomarker.
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Lu J, Suzuki T, Satoh M, Chen S, Tomonaga T, Nomura F, Suzuki N. Involvement of aldolase A in X-ray resistance of human HeLa and UV(r)-1 cells. Biochem Biophys Res Commun 2008; 369:948-52. [PMID: 18328256 DOI: 10.1016/j.bbrc.2008.02.122] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2008] [Accepted: 02/27/2008] [Indexed: 10/22/2022]
Abstract
To find novel proteins involved in radio-resistance of human cells, we searched for nuclear proteins, whose expression levels alter after X-ray irradiation in HeLa cells, using agarose fluorescent two-dimensional differential gel electrophoresis following mass spectrometry. We identified 6 proteins, whose levels were increased in nuclei 24h after irradiation at 5Gy, including aldolase A. Nuclear aldolase A levels increased twofold after the irradiation, however, total aldolase A levels did not change. When the expression of aldolase A was suppressed by its specific siRNA, sensitization of the suppressed cells to X-ray-induced cell death was observed. In addition, UV(r)-1 cells with higher aldolase A expression exhibited lower sensitivity to X-ray-induced cell death than the parental RSa cells with lower aldolase A expression. These results suggest that aldolase A may play a role in the radio-response of human cells, probably in nuclei, in addition to its glycolytic role in the cytosol.
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Affiliation(s)
- Jun Lu
- Department of Environmental Biochemistry, Graduate School of Medicine, Chiba University, Inohana 1-8-1, Chuo-ku, Chiba 260-8670, Japan
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Oh-Ishi M, Kodera Y, Furudate SI, Maeda T. Disease proteomics of endocrine disorders revealed by two-dimensional gel electrophoresis and mass spectrometry. Proteomics Clin Appl 2008; 2:327-37. [DOI: 10.1002/prca.200780026] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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Meunier B, Dumas E, Piec I, Béchet D, Hébraud M, Hocquette JF. Assessment of Hierarchical Clustering Methodologies for Proteomic Data Mining. J Proteome Res 2006; 6:358-66. [PMID: 17203979 DOI: 10.1021/pr060343h] [Citation(s) in RCA: 119] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Hierarchical clustering methodology is a powerful data mining approach for a first exploration of proteomic data. It enables samples or proteins to be grouped blindly according to their expression profiles. Nevertheless, the clustering results depend on parameters such as data preprocessing, between-profile similarity measurement, and the dendrogram construction procedure. We assessed several clustering strategies by calculating the F-measure, a widely used quality metric. The combination, on logged matrix, of Pearson correlation and Ward's methods for data aggregation is among the best clustering strategies, at least with the data sets we studied. This study was carried out using PermutMatrix, a freely available software derived from transcriptomics.
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Affiliation(s)
- Bruno Meunier
- UR 1213, Unité de Recherches sur les Herbivores, Equipe Croissance et Métabolisme du Muscle, INRA de Clermont-Ferrand/Theix, F-63122 [corrected] Saint-Genès Champanelle, France.
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Yahiro K, Morinaga N, Satoh M, Matsuura G, Tomonaga T, Nomura F, Moss J, Noda M. Identification and characterization of receptors for vacuolating activity of subtilase cytotoxin. Mol Microbiol 2006; 62:480-90. [PMID: 16965518 DOI: 10.1111/j.1365-2958.2006.05379.x] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Some shiga toxin-producing Escherichia coli secrete a novel AB5 cytotoxin, named subtilase cytotoxin (SubAB), which induces vacuole formation in addition to cytotoxicity in susceptible cells. By immunoprecipitation with SubAB from Vero cells, we discovered proteins of 100 kDa, 135 kDa and 155 kDa as potential candidates for its receptor. These proteins were N-glycosylated in their extracellular domains, a modification that was necessary for interaction with SubAB. Biotinylated receptors were partially purified by Datura stramonium agglutinin affinity chromatography and avidin-agarose and analysed by TOF mass spectroscopy. The peptide sequences of p135 were identical to beta1 integrin, and its identification was confirmed with anti-integrin beta1 antibody. The p155 protein was identified as alpha2 integrin using anti-integrin alpha2 antibody. In addition, treatment of Vero cells with beta1 integrin RNAi before exposure to SubAB prevented vacuolating activity. These results suggested that SubAB recognizes alpha2beta1 integrin as a functional receptor; this first interaction may be an important key step leading to the SubAB-induced morphological changes in Vero cells.
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Affiliation(s)
- Kinnosuke Yahiro
- Departments of Molecular Infectiology, Graduate School of Medicine, Chiba University, Chiba, Japan
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Current Awareness on Comparative and Functional Genomics. Comp Funct Genomics 2005. [PMCID: PMC2447491 DOI: 10.1002/cfg.425] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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