Proteomic analysis of IgA-deposits on glomeruli of biopsy samples of IgA nephropathy

• Project/Area Number: 25461212
• Research Category: Grant-in-Aid for Scientific Research (C)
• Allocation Type: Multi-year Fund
• Section: 一般
• Research Field: Kidney internal medicine
• Research Institution: Niigata University
• Principal Investigator: Yoshida Yutaka 新潟大学, 研究推進機構, 特任専門職員 (40182795)
• Co-Investigator(Kenkyū-buntansha): YAOITA Eishin 新潟大学, 大学院医歯学総合研究科, 准教授 (00157950) ; YAMAMOTO Tadashi 新潟大学, 産学地域連携推進機構, 特任教授 (30092737)
• Project Period (FY): 2013-04-01 – 2016-03-31
• Project Status: Completed (Fiscal Year 2015)
• Budget Amount: ¥4,810,000 (Direct Cost: ¥3,700,000、Indirect Cost: ¥1,110,000); Fiscal Year 2015: ¥1,170,000 (Direct Cost: ¥900,000、Indirect Cost: ¥270,000); Fiscal Year 2014: ¥2,600,000 (Direct Cost: ¥2,000,000、Indirect Cost: ¥600,000); Fiscal Year 2013: ¥1,040,000 (Direct Cost: ¥800,000、Indirect Cost: ¥240,000)
• Keywords: IgA腎症 / IgA免疫複合体 / 凍結腎生検標本 / 単離糸球体 / スリット膜 / EMARS法 / プロテオミクス / 腎臓学 / 糸球体

Outline of Final Research Achievements

EMARS method can label proteins in the immediate vicinity of a target membrane protein with fluorescein without destruction of cells or tissue integrity. We aimed to identify IgA deposits on glomerulus of biopsy samples of patients with IgA nephropathy bur found problems in specificity of labeling and low recovery of proteins. We, therefore, used glomeruli highly purified from rat kidneys and nephrin as a target protein to improve EMARS method. By using fluorescein-tyramide as a labeling reagent, labeling specificity was much improved and we succeeded in identification of many membrane proteins associates with nephrin in the slit diaphragm, but also find a low recovery and low specificity of labeled proteins in the step of collection of labeled proteins.

Research Products

• [Journal Article] Avian podocytes, which lack nephrin, use adherens junction proteins at intercellular junctions. (2016)
  • Author(s): Yaoita E, Nishimura H, Nameta M, Yoshida Y, Takimoto H, Fujinaka H, Kawachi H, Magdeldin S, Zhang Y, Xu B, Oyama T, Nakamura F, Yamamoto T
  • Journal Title: J Histchem Cytochem Volume: 64 Issue: 1 Pages: 67-76
  • DOI: 10.1369/0022155415611708
  • Peer Reviewed / Acknowledgement Compliant
• [Journal Article] Unrestricted modification search reveals lysine methylation as major modification induced b tissue formalin fixation and paraffin embedding. (2015)
  • Author(s): Zhang Y, Muller M, Xu B, Yoshida Y, Horlacher O, Nikitin F, Garessus S, Magdeldin S, Kinoshita N, Fujinaka H, Yaoita E, Hasegawa M, Lisacek F, Yamamoto T
  • Journal Title: Proteomics Volume: 15 Issue: 15 Pages: 2568-2579
  • DOI: 10.1002/pmic.201400454
  • Peer Reviewed / Int'l Joint Research / Acknowledgement Compliant
• [Journal Article] Label-free quantitative proteomic analysis reveals strong involvement of complement alternative and terminal pathways in human glomerular sclerotic lesions. (2015)
  • Author(s): Zhang Y, Xu B, Kinoshita N, Yoshida Y, Tasaki M, Fujinaka H, Magdeldin S, Yaoita E, Yamamoto T.
  • Journal Title: J Proteomics. Volume: 123 Pages: 89-100
  • DOI: 10.1016/j.jprot.2015.03.024
  • Peer Reviewed
• [Journal Article] Complementary protein and peptide OFFGEL fractionation for high-throughput proteomic analysis. (2015)
  • Author(s): Magdeldin S, Elguoshy A, Yoshida Y, Hirao Y, Xu B, Zhang Y, Yamamoto K, Takimoto H, Fujinaka H, Kinoshita N, Yamamoto T
  • Journal Title: Anal Chem Volume: 87 Pages: 8481-8488
  • Peer Reviewed / Int'l Joint Research / Acknowledgement Compliant
• [Journal Article] Datasets from label-free quantitative proteomic analysis of human glomeruli with sclerotic lesions. (2015)
  • Author(s): Zhang Y, Xu B, Kinoshita N, Yoshida Y, Tasaki M, Fujinaka H, Magdeldin S, Yaoita E, Yamamoto T
  • Journal Title: Data Brief Volume: 4 Pages: 180-185
  • DOI: 10.1016/j.dib.2015.05.013
  • Peer Reviewed / Open Access / Int'l Joint Research / Acknowledgement Compliant
• [Journal Article] Exploring extra-cellular proteins in methicillin susceptible and methicillin resistant Staphylococcus aureus by liquid chromatography-tandem mass spectrometry. (2014)
  • Author(s): Enany S, Yoshida Y, Yamamoto T
  • Journal Title: World J Microbiol Biotechnol Volume: 30 Pages: 1269-1283
  • Peer Reviewed / Open Access
• [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] 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] .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] Tor and the Sin3-Rpd3 complex regulate expression of the mitophagy receptor protein Atg32 in yeast. (2014)
  • Author(s): Aihara M, Jin X, Kurihara Y, Yoshida Y, Matsushima Y, Oku M, Hirota Y, Saigusa T, Aoki Y, Uchiumi T, Yamamoto T, Sakai Y, Kang D, Kanki T.
  • Journal Title: Journal of Cell Science Volume: 127 Pages: 3184-96
  • DOI: 10.1242/jcs.153254
  • Peer Reviewed / Open Access
• [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] Profiling of kidney vascular endothelial cell plasma membrane proteins by liquid chromatography-tandem mass spectrometry (2012)
  • Author(s): Liu Z, Xu B, Nameta M, Zhang Y, Magdeldin S, Yoshida Y, Yamamoto K, Fujinaka H, Yaoita E, Tasaki M, Nakagawa Y, Saito K, Takahashi K, Yamamoto T
  • Journal Title: Clin Exp Nephrol Volume: 掲載予定 Issue: 3 Pages: 327-337
  • DOI: 10.1007/s10157-012-0708-1
  • NAID: 10031184238
  • Peer Reviewed
• [Presentation] EMARS法によるタンパク質複合体解析：腎糸球体上皮細胞足突起間接着装置を構成するタンパク質群の同定 (2016)
  • Author(s): 吉田 豊，瀧本裕基，小谷典弘，矢尾板永信
  • Organizer: 日本プロテオーム学会2016年年会
  • Place of Presentation: 東京都港区 北里大学
  • Year and Date: 2016-07-28
• [Presentation] 培養ポドサイトおける一次突起の誘導 (2016)
  • Author(s): 矢尾板永信，吉田 豊，瀧本裕基
  • Organizer: 第59回日本腎臓学会学術総会
  • Place of Presentation: 横浜市 パシフィコ横浜
  • Year and Date: 2016-06-17
• [Presentation] EMARS法を用いたポドサイトの細胞間接着装置の網羅的解析 (2016)
  • Author(s): 瀧本裕基，河内 裕，吉田 豊，矢尾板永信
  • Organizer: 第59回日本腎臓学会学術総会
  • Place of Presentation: 横浜市 パシフィコ横浜
  • Year and Date: 2016-06-17
• [Presentation] Comparable pathway analysis of IgA nephoritis glomeruli with normal one base on SWATH approach. (2014)
  • Author(s): Xu B, Zhang Y, Liu Y, Yoshida Y, Magdeldin S, Fujinaka H, Yaoita E, Abersold R, Yamamoto T
  • Organizer: HUPO 13th Annual World Congress
  • Place of Presentation: Madrid, Spain
  • Year and Date: 2014-10-05 – 2014-10-08
  • Invited
• [Presentation] 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 J,Yamamoto T
  • Organizer: HUPO 13th Annual World Congress
  • Place of Presentation: Madrid, Spain
  • Year and Date: 2014-10-05 – 2014-10-08
• [Presentation] Liquid chromatography and mass spectrometry for comparing clinical isolates of MRSA and MSSA (2014)
  • Author(s): Enany S, Yoshida Y, Magdeldin S, Yamamoto T
  • Organizer: HUPO 13th Annual World Congress
  • Place of Presentation: Madrid, Spain
  • Year and Date: 2014-10-05 – 2014-10-08
• [Presentation] HPPに向けてのHKUPPの取り組み (2014)
  • Author(s): 吉田 豊、山本 格
  • Organizer: 日本プロテオーム学会2014年会（JHUPO第12回大会）
  • Place of Presentation: つくば国際会議場（茨城県つくば市）
  • Year and Date: 2014-07-16 – 2014-07-18
  • Invited
• [Presentation] 3つの異なるプラットフォームでのSWATHデータ解析結果の比較 (2014)
  • Author(s): 許 波、張 エイ、吉田 豊、藤中 秀彦、矢尾板 永信、Yansheng Liu, Ruedi Aebersold, 山本 格
  • Organizer: 日本プロテオーム学会2014年会（JHUPO第12回大会）
  • Place of Presentation: つくば国際会議場（茨城県つくば市）
  • Year and Date: 2014-07-16 – 2014-07-18
• [Presentation] Profiling and annotation of human kidney glomerulus proteome. (2014)
  • Author(s): 吉田 豊、崔 珍玉、許 波、藤中 秀彦、矢尾板 永信、山本 格
  • Organizer: 第57回日本腎臓学会学術集会
  • Place of Presentation: パシフィコ横浜（横浜市西区）
  • Year and Date: 2014-07-04 – 2014-07-06
• [Presentation] 質量分析計と抗体の両者で同定された高信頼ヒト糸球体プロテオーム (2014)
  • Author(s): 行田 正晃、吉田 豊、矢尾板 永信、許 波、張 エイ、山本 格
  • Organizer: 第57回日本腎臓学会学術集会
  • Place of Presentation: パシフィコ横浜（横浜市西区）
  • Year and Date: 2014-07-04 – 2014-07-06
• [Presentation] 質量分析計と免疫組織化学によるヒト糸球体プロテオームデータベースの比較 (2013)
  • Author(s): 行田正明、吉田 豊、矢尾板永信、許 波、張 エイ、山本 格
  • Organizer: 第56回日本腎臓学会学術総会
  • Place of Presentation: 東京国際フォーラム（東京都千代田区）
• [Presentation] ラット足細胞初代培養系におけるヘパリンの効果（2） (2013)
  • Author(s): 矢尾板永信、吉田 豊、山本 格
  • Organizer: 第56回日本腎臓学会学術総会
  • Place of Presentation: 東京国際フォーラム（東京都千代田区）
• [Presentation] Proteomic analysis of nephron segments of formalin-fixed paraffin-embedded human kidney tissues. (2013)
  • Author(s): Yamamoto T, Yamamoto K, Yoshida Y, Xu B, Zhang Y, Magdeldin S
  • Organizer: HUPO 12th Annual World Congress
  • Place of Presentation: パシフィコ横浜（横浜市西区）
• [Presentation] High confident human glomerulus proteome identified both by mass spectrometry- and antibody-based proteomics. (2013)
  • Author(s): Nameta M, Yoshida Y, Zhang Y, Xu B, Magdeldin S
  • Organizer: HUPO 12th Annual World Congress
  • Place of Presentation: パシフィコ横浜（横浜市西区）
• [Presentation] 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
  • Organizer: HUPO 12th Annual World Congress
  • Place of Presentation: パシフィコ横浜（横浜市西区）
• [Presentation] Accurate quantification of peptides for mass spectrometric analysis: a modified microscale bininchoninic acid assay. (2013)
  • Author(s): Yoshida Y, Hasegawa M, Lim LC, Shiromizu T, Hara Y, kanagawa A, Koyama Y, Yaoita E, Wakai T, Tomonaga T, Yamamoto T
  • Organizer: HUPO 12th Annual World Congress
  • Place of Presentation: パシフィコ横浜（横浜市西区）
• [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ホームページ
  • URL: http://www.kidney-niigata.org/strpath/ind_j.html
• [Remarks] Human Kidney and Urine Proteome Projectホームページ
  • URL: http://www.hkupp.org/
• [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ホームページ
  • URL: http://www.kidney-niigata.org/strpath/ind_j.html
• [Remarks] Human Kidney and Urine Proteome Organizationホームページ
  • URL: http://www.hkupp.org/