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

• 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
• Project Status: Completed (Fiscal Year 2013)
• Budget Amount: ¥3,770,000 (Direct Cost: ¥2,900,000、Indirect Cost: ¥870,000); Fiscal Year 2012: ¥1,560,000 (Direct Cost: ¥1,200,000、Indirect Cost: ¥360,000); Fiscal Year 2011: ¥2,210,000 (Direct Cost: ¥1,700,000、Indirect Cost: ¥510,000)
• Keywords: 腎臓 / プロテオミクス / ラベルフリー定量 / 膜性腎症 / レベル フリー / FFPE / レーザーマイクロディセクション / 質量分析計 / 糸球体 / 腎生検FFPE試料 / Laser microdissection / LC-MS/MS

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 3rd, Yamamoto T
  • Journal Title: J Proteome Res. Volume: 13 Issue: 3 Pages: 1636-46
  • DOI: 10.1021/pr401122m
  • Peer Reviewed / Open Access / Acknowledgement Compliant
• [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 (Carlton) Volume: 19 Issue: 4 Pages: 195-201
  • DOI: 10.1111/nep.12207
  • Peer Reviewed / Open Access / Acknowledgement Compliant
• [Journal Article] Decreased urinary calbindin 1 levels in proteinuric rats and humans with distal nephron segment injuries. (2014)
  • 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: 18 Issue: 3 Pages: 432-43
  • DOI: 10.1007/s10157-013-0835-3
  • Peer Reviewed / Open Access / Acknowledgement Compliant
• [Journal Article] .Basics and recent advances of two dimensional- polyacrylamide gel electrophoresis (2014)
  • Author(s): Magdeldin S, Enany S, Yoshida Y, Xu B, Zhang Y, Zureena Z, Lokamani I, Yaoita E, Yamamoto T
  • Journal Title: Clin Proteomics Volume: 11 Issue: 1 Pages: 16-16
  • DOI: 10.1186/1559-0275-11-16
  • Peer Reviewed / Open Access / Acknowledgement Compliant
• [Journal Article] Profiling and annotation of human kidney glomerulus proteome (2013)
  • Author(s): Cui Z, Yoshida Y, Xu B, Zhang Y, Nameta M, Magdeldin S, Makiguchi T, Ikoma T, Fujinaka H, Yaoita E, Yamamoto T
  • Journal Title: Proteome Sci Volume: 11 Issue: 1 Pages: 13-13
  • DOI: 10.1186/1477-5956-11-13
  • Peer Reviewed
• [Journal Article] Toward deciphering proteomes of formalin-fixed paraffinembedded (FFPE) tissues (2012)
  • Author(s): Magdeldin S
  • Journal Title: Proteomics Volume: 12 Issue: 7 Pages: 1045-1058
  • DOI: 10.1002/pmic.201100550
  • Peer Reviewed
• [Journal Article] Extensive proteomic profiling of the secretome of European community acquired methicillin resistant Staphylococcus aureus clone (2012)
  • Author(s): Enany S, Yoshida Y, Magdeldin S, Zhang Y, Xu B, Yamamoto T
  • Journal Title: Peptides Volume: 37 Issue: 1 Pages: 128-37
  • DOI: 10.1016/j.peptides.2012.06.011
  • Peer Reviewed
• [Journal Article] Proteomic approach to human kidney glomerulus prepared by laser microdissection from frozen biopsy specimens: exploration of proteome after removal of blood-derived proteins (2012)
  • Author(s): Yoshida Y, Nameta M, Kuwano M, Zhang Y, Bo X, Magdeldin S, Cui Z, Fujinaka H, Yaoita E, Tomonaga T, Yamamoto T
  • Journal Title: Proteomics Clin Appl Volume: 6 Issue: 7-8 Pages: 412-417
  • DOI: 10.1002/prca.201200016
  • Peer Reviewed
• [Journal Article] Murine colon proteome and characterization of the protein pathways. (2012)
  • Author(s): Magdeldin S
  • Journal Title: BioData Min. Volume: 5 Issue: 1 Pages: 11-11
  • DOI: 10.1186/1756-0381-5-11
  • Peer Reviewed
• [Journal Article] Comparison of human glomerulus proteomic profiles obtained from low quantities of samples by different mass spectrometry with the comprehe nsive database (2011)
  • Author(s): Ying Zhang
  • Journal Title: Proteome Science Volume: VOL.9 Issue: 1 Pages: 47-57
  • 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
• [Presentation] Deep Proteome Mapping of Mouse Kidney Based on OFFGel Prefractionation Reveals Remarkable Protein Post- Translational Modifications. (2013)
  • Author(s): Sameh Magdeldin
  • Organizer: Hupo 2013
  • Place of Presentation: Yokohama, Japan
• [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.
• [Presentation] Optimization of protein extraction and LC/MS analysis from fomalin-fixed-paraffin embedded specimens. (2012)
  • Author(s): Sameh Magdeldin, Yutaka Yoshida, Bo Xu, Ying Zhang, Eishin Yaoita, Tadashi Yamamoto
  • Organizer: 第５５回日本腎臓学術総会
  • Place of Presentation: 横浜
• [Presentation] Multi enzyme direct digestion and uHPLC-MS/MS analysis of formalin-fixed, paraffin-embedded laser microdissected specimens. (2012)
  • Author(s): Sameh Magdeldin, Yutaka Yoshida, Bo Xu, Ying Zhang, Eishin Yaoita, Tadashi Yamamoto
  • Organizer: 第11回国際ヒトプロテオーム機構学術集会
  • Place of Presentation: ボストン（アメリカ合衆国）
• [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
• [Presentation] Characterization and building up a comprehensive murine colon proteome catalogue (2011)
  • Author(s): Magdeldin S, Li H, Yoshida Y, Enany S, Xu B, Zhang Y, Yaoita E, Yamamoto T
  • Organizer: HUPO 2011 Annual World Congress
  • Place of Presentation: Geneva, Palexpo Convention hall
• [Book] Clin Proteomics (2014)
  • Author(s): Magdeldin S, Enany S, Yoshida Y, Xu B, Zhang Y, Zureena Z, Lokamani I, Yaoita E, Yamamoto T
  • 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
• [Remarks]
  • URL: http://www.hkupp.org/