Exploring the pathogenic antigens implicated in membranous glomerulonephritis by proteomics and bioinformatics using "All and None" approach strategy

2013 Fiscal Year Final Research Report

• Project/Area Number: 23790933
• Research Category: Grant-in-Aid for Young Scientists (B)
• Allocation Type: Multi-year Fund
• Research Field: Kidney internal medicine
• Research Institution: Niigata University
• Principal Investigator: ABDELGAWWAD Sameh 新潟大学, 医歯(薬)学総合研究科, 研究員 (50529469)
• Project Period (FY): 2011 – 2012
• Keywords: 腎臓 / プロテオミクス / ラベルフリー定量 / 膜性腎症

Research Abstract

We aimed at disclosing the antigens implicated in membranous nephropathy. Using shotgun proteomics combined with laboratory-made software (All and None), we analyzed 30 membranous nephropathy kidney biopsy samples. We collected 50 glomeruli sections for analysis by LC-MS/MS. Mascot or ProluCID were used as search engines to discriminate protein differences in these samples compared to control groups. We depicted an initial proteome profile for the possible dysregulated proteins implicated in this disease, and analyzed these proteins by using gene ontology for identification of biological processes relevant to the disease. In addition, we generated a database for further use, which would be integrated in the Human Kidney Urine Proteome Project (HKUPP).

Research Products

• [Journal Article] Deep proteome mapping of mouse kidney based on OFFGel prefractionation reveals remarkable protein post-translational modifications (2014)
  • Author(s): Magdeldin S, Yamamoto K, Yoshida Y, Xu B, Zhang Y, Fujinaka H, Yaoita E, Yates JR III, Yamamoto T
  • Journal Title: J Proteome Res Volume: 13 Pages: 1636-1646
  • DOI: 10.1021/pr401122m
  • Peer Reviewed
• [Journal Article] Heparin increasing podocyte-specific gene expressions (2014)
  • Author(s): Yaoita E, Yoshida Y, Nameta M, Zhang Y, Fujinaka H, Magdeldin S, Xu B, Yamamoto T
  • Journal Title: Nephrology Volume: 19 Pages: 195-201
  • DOI: 10.1111/nep.12207
  • Peer Reviewed
• [Journal Article] Profiling and annotation of human kidney glomerulus proteome (2013)
  • Author(s): Cui Z, Yoshida Y, Xu B, Zhang Y, Nameta Mm Magdeldin S, Makiguchi T, Ikoma T, Fujinaka H, Yaoita E, Yamamoto T
  • Journal Title: Proteome Sci Volume: 11 Pages: 13
  • DOI: 10.1186/1477-5956-11-13
  • Peer Reviewed
• [Journal Article] Decreased urinary calbindin 1 levels in proteinuric rats and humans with distal nephron segment injuries (2013)
  • Author(s): Iida T, Fujinaka H, Xu B, Zhang Y, Magdeldin S, Nameta M, Liu Z, Yoshida Y, Yaoita E, Tomizawa S, Saito A, Yamamoto T
  • Journal Title: Clin Exp Nephrol Volume: (Epub ahead of print)
  • DOI: 10.1007/s10157-013-0835-3
  • Peer Reviewed
• [Journal Article] Toward deciphering proteomes of formalin-fixed paraffin-embedded (FFPE) tissues (2012)
  • Author(s): Magdeldin S, Yamamoto T
  • Journal Title: Proteomics Volume: 12 Pages: 1045-1058
  • DOI: 10.1002/pmic.201100550
  • Peer Reviewed
• [Journal Article] Comparison of human glomerulus proteomic profiles obtained from low quantities of samples by different mass spectrometry with the comprehensive database (2011)
  • Author(s): Zhang Y, Yoshida Y, Xu B, Magdeldin S, Fujinaka H, Liu Z, Miyamoto M. Yaoita E, Yamamoto T
  • Journal Title: Proteom Sci Volume: 9 Pages: 47
  • DOI: 10.1186/1477-5956-9-47
  • Peer Reviewed
• [Presentation] Evaluation of OFFGel-based prefractionation approach in combination with in-solution or ultra-filtration protein digestion (2013)
  • Author(s): Magdeldin S, Yoshida Y, Xu B, Zhang Y, Yaoita E, Yamamoto T
  • Organizer: HUPO 12th Annual World Congress 2013
  • Place of Presentation: Yokohama, Japan
  • Year and Date: 20130914-18
• [Presentation] Multi enzyme direct digestion and uHPLC-MS/MS analysis of formalin-fixed, paraffin-embedded laser micro dissected specimens (2012)
  • Author(s): Magdeldin S, Yoshida Y, Xu B, Zhang Y, Yaoita E, Yamamoto T
  • Organizer: HUPO 11th Annual World Congress 2012
  • Place of Presentation: Boston, MA, U.S.A.
  • Year and Date: 20120909-13
• [Presentation] Characterization and building up a comprehensive murine colon proteome catalogue (2011)
  • Author(s): Magdeldin S, Yoshida Y, Xu B, Zhang Y, Yaoita E, Yamamoto T
  • Organizer: HUPO 10th Annual World Congress 2011
  • Place of Presentation: Geneva, Switzerland
  • Year and Date: 20110904-07
• [Book] Clin Proteomics (2014)
  • Author(s): Magdeldin S, Enany S, Yoshida Y, Xu B, Zhang Y, Zureena Z, Lokamani I, Yaoita E, Yamamoto T
  • Total Pages: 11:16
  • Publisher: BioMed Central, London
• [Remarks] 新潟大学医歯学総合研究科腎研究施設構造病理学分野
  • URL: http://www.kidney-niigata.org/strpath/ind_j.html
• [Remarks] HumanKidneyandUrineProteomeProject(HKUPP)
  • URL: http://www.hekupp.org/DB.html