Prediction of molecular target drug effect using quantitative phosphoproteome analysis of patient derived colorectal cancer cells

• Project/Area Number: 26670614
• Research Category: Grant-in-Aid for Challenging Exploratory Research
• Allocation Type: Multi-year Fund
• Research Field: Digestive surgery
• Research Institution: National Institutes of Biomedical Innovation, Health and Nutrition
• Principal Investigator: Tomonaga Takeshi 国立研究開発法人医薬基盤・健康・栄養研究所, プロテオームリサーチプロジェクト, プロジェクトリーダー (80227644)
• Project Period (FY): 2014-04-01 – 2016-03-31
• Project Status: Completed (Fiscal Year 2015)
• Budget Amount: ¥3,640,000 (Direct Cost: ¥2,800,000、Indirect Cost: ¥840,000); Fiscal Year 2015: ¥2,210,000 (Direct Cost: ¥1,700,000、Indirect Cost: ¥510,000); Fiscal Year 2014: ¥1,430,000 (Direct Cost: ¥1,100,000、Indirect Cost: ¥330,000)
• Keywords: リン酸化プロテオミクス / 薬効予測 / EGFR抗体 / 大腸がん / プロテオミクス / リン酸化タンパク質 / 初代培養細胞 / リン酸化タンパク

Outline of Final Research Achievements

Molecular target drugs such as kinase inhibitors for cancer treatment are not uniformly clinically effective, thus sorting the patients that will benefit from the treatments is critical. Moreover, acquired resistance for the drugs is also a critical problem. Therefore, the identification of mechanisms underlying the resistance is urgent need. Systematic quantification of kinase activation is potentially predictive of the response of kinase inhibitors and it can be quantitated by phosphorylation level of their substrates. In this study, we developed a large-scale phosphoproteome quantification method for the kinase substrates and applied for prediction of the kinase activities and drug response. We also examined the mechanism of drug resistance. By the phosphoproteome analysis of several lung cancer cell lines which are sensitive or resistant for the drug currently used in clinic, cetuximab, we identified several phosphoproteins and kinases which are able to predict drug sensitivity.

Research Products

• [Journal Article] Cell surface localization of importin α1/KPNA2 affects cancer cell proliferation by regulating FGF1 signalling (2016)
  • Author(s): Yamada K., Miyamoto Y., Tsujii A., Moriyama T., Ikuno Y., Shiromizu T., Serada S., Fujimoto M., Tomonaga T., Naka T., Yoneda Y., Oka M.
  • Journal Title: Scientific Reports Volume: 6 Issue: 1 Pages: 231410-231410
  • DOI: 10.1038/srep21410
  • Peer Reviewed / Open Access
• [Journal Article] Cell surface localization of importin α1/KPNA2 affects cancer cell proliferation by regulating FGF1 signalling. (2016)
  • Author(s): Yamada K., Miyamoto Y., Tsujii A., Moriyama T., Ikuno Y., Shiromizu T., Serada S., Fujimoto M., Tomonaga T., Naka T., Oka M.
  • Journal Title: Sci Rep Volume: 6 Issue: 1 Pages: 24823-24823
  • DOI: 10.1038/srep24823
  • Peer Reviewed / Open Access
• [Journal Article] Targeted Phosphoproteome Analysis Using Selected/Multiple Reaction Monitoring (SRM/MRM). (2016)
  • Author(s): Adachi, J., Narumi, R., Tomonaga, T
  • Journal Title: Methods Mol Biol Volume: 1394 Pages: 87-100
  • DOI: 10.1007/978-1-4939-3341-9_7
  • ISBN: 9781493933396, 9781493933419
  • Peer Reviewed
• [Journal Article] Quantitative Analysis of Tissue Samples by Combining iTRAQ Isobaric Labeling with Selected/Multiple Reaction Monitoring (SRM/MRM). (2016)
  • Author(s): Narumi, R., Tomonaga, T
  • Journal Title: Methods Mol Biol Volume: 1355 Pages: 85-101
  • DOI: 10.1007/978-1-4939-3049-4_6
  • ISBN: 9781493930487, 9781493930494
  • Peer Reviewed
• [Journal Article] Data for Proteomic Analysis of ATP-Binding Proteins and Kinase Inhibitor Target Proteins Using an ATP Probe. (2015)
  • Author(s): Adachi, J., Kishida, M., Watanabe, S., Hashimoto, Y., Fukamizu, K., and Tomonaga, T.
  • Journal Title: Data in Brief Volume: 5 Pages: 726-729
  • DOI: 10.1016/j.dib.2015.10.018
  • Peer Reviewed / Open Access
• [Journal Article] Nuclear accumulation of annexin A2 contributes to chromosomal instability by coilin-mediated centromere damage (2015)
  • Author(s): Kazami, T., Nie, H., Satoh, M., Kuga, T., Matsushita, K., Kawasaki, N., Tomonaga, T*., and Nomura, F
  • Journal Title: Oncogene Volume: in press Issue: 32 Pages: 4177-4189
  • DOI: 10.1038/onc.2014.345
  • Peer Reviewed
• [Journal Article] Differential Proteome Analysis Identifies TGF-beta-Related Pro-Metastatic Proteins in a 4T1 Murine Breast Cancer Model. (2015)
  • Author(s): Sato, M., Matsubara, T., Adachi, J., Hashimoto, Y., Fukamizu, K., Kishida, M., Yang, Y.A., Wakefield, L.M., and Tomonaga, T
  • Journal Title: PloS One Volume: 10 Issue: 5 Pages: e0126483-e0126483
  • DOI: 10.1371/journal.pone.0126483
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] c-Abl induces stabilization of histone deacetylase 1 (HDAC1) in a kinase activity-dependent manner. (2015)
  • Author(s): Kazumasa Aoyama, Noritaka Yamaguchi, Ryuzaboro Yuki, Mariko Morii, Sho Kubota, Kensuke Hirata, Kohei Abe, Takuya Honda, Takahisa Kuga, Yuuki Hashimoto, Takeshi Tomonaga, and Naoto Yamaguchi
  • Journal Title: Cell Biology International Volume: 39 Issue: 4 Pages: 446-456
  • DOI: 10.1002/cbin.10413
  • Peer Reviewed / Acknowledgement Compliant
• [Journal Article] Role for Tyrosine Phosphorylation of A-kinase Anchoring Protein 8 (AKAP8) in its Dissociation from Chromatin and the Nuclear Matrix (2015)
  • Author(s): Kubota S, Morii M, Yuki R, Yamaguchi N, Yamaguchi H, Aoyama K, Kuga T, Tomonaga T, Yamaguchi N.
  • Journal Title: J Biol Chem Volume: 290 Issue: 17 Pages: 10891-904
  • DOI: 10.1074/jbc.m115.643882
  • Peer Reviewed / Open Access
• [Journal Article] c-Abl-mediated tyrosine phosphorylation of JunB is required for Adriamycin-induced expression of p21. (2015)
  • Author(s): Noritaka Yamaguchi, Ryuzaburo Yuki, Sho Kubota, Kazumasa Aoyama, Takahisa Kuga, Yuuki Hashimoto, Takeshi Tomonaga, and Naoto Yamaguchi.
  • Journal Title: Biochemical Journal Volume: 471 Issue: 1 Pages: 67-77
  • DOI: 10.1042/bj20150372
  • Peer Reviewed / Acknowledgement Compliant
• [Journal Article] Transcriptional Dynamics of Immortalized Human Mesenchymal Stem Cells during Transformation. (2015)
  • Author(s): Takeuchi, M., Higashino, A., Takeuchi, K., Hori, Y., Koshiba-Takeuchi, K., Makino, H., Monobe, Y., Kishida, M., Adachi, J., Takeuchi, J., Tomonaga, T., Umezawa, A., Kameoka, Y., and Akagi, K.
  • Journal Title: PloS one Volume: 10 Issue: 5 Pages: 0126562-0126562
  • DOI: 10.1371/journal.pone.0126562
  • NAID: 120005947126
  • Peer Reviewed / Open Access
• [Journal Article] Differential proteome analysis identifies TGF-β-related pro-metastatic proteins in a 4T1 murine breast cancer model. (2015)
  • Author(s): Sato M, Matsubara T, Adachi J, Hashimoto Y, Kishida M, Yang Y, Wakefield LM, Tomonaga T*
  • Journal Title: PLoS One Volume: in press
  • Peer Reviewed / Open Access
• [Journal Article] Proteome-wide discovery of unknown ATP-binding proteins and kinase inhibitor target proteins using an ATP probe. (2014)
  • Author(s): Jun Adachi, Marina Kishida, Shio Watanabe, Yuuki Hashimoto, Kazuna Fukamizu, Takeshi Tomonaga.
  • Journal Title: Journal of proteome research Volume: 13 Issue: 12 Pages: 5461-5470
  • DOI: 10.1021/pr500845u
  • Peer Reviewed
• [Journal Article] Discovery of colorectal cancer biomarker candidates by membrane proteomic analysisand subsequent verification using selected reaction monitoring and tissue microarrayanalysis (2014)
  • Author(s): Kume H, Muraoka S, Kuga T, Adachi J, Narumi R, Watanabe S, Kuwano M, Kodera Y, Matsushita K, Fukuoka J, Masuda T, Ishihama Y, Matsubara H, Nomura F, Tomonaga T.
  • Journal Title: Mol Cell Proteomics. Volume: M113 Issue: 6 Pages: 37093-37093
  • DOI: 10.1074/mcp.m113.037093
  • Peer Reviewed
• [Presentation] プロテオミクスを用いたバイオマーカー探索とPrecision Medicineへの応用 (2016)
  • Author(s): 朝長 毅
  • Organizer: 第44回 京阪泌尿器腫瘍セミナー
  • Place of Presentation: 大阪
  • Year and Date: 2016-02-08
  • Invited
• [Presentation] 定量プロテオミクスの創薬及び個別化医療への応用 (2016)
  • Author(s): 朝長 毅
  • Organizer: 第13回 神戸ポートアイランド創薬フォーラム
  • Place of Presentation: 神戸臨床研究情報センター
  • Year and Date: 2016-01-26
  • Invited
• [Presentation] 定量プロテオミクスを用いた疾患バイオマーカー探索とその医療への応用 (2015)
  • Author(s): 朝長 毅
  • Organizer: 日本プロテオーム学会2015年会
  • Place of Presentation: くまもと森都心プラザ
  • Year and Date: 2015-07-23
  • Invited
• [Presentation] 定量プロテオミクスの医療への応用 (2015)
  • Author(s): 朝長 毅
  • Organizer: 第42回BMSカンファレンス
  • Place of Presentation: 岐阜グランドホテル
  • Year and Date: 2015-07-06
  • Invited
• [Presentation] Verification of predictive biomarker candidates of colorectal cancer metastasis in serum extracellular vesicles by selected reaction monitoring based targeted proteomics. (2015)
  • Author(s): Tomonaga T, Kume H
  • Organizer: International Extracellular Vesicles Conference
  • Place of Presentation: Washington DC, USA
  • Year and Date: 2015-04-23
  • Int'l Joint Research
• [Presentation] 定量プロテオミクスの医療への応用 (2015)
  • Author(s): 朝長 毅
  • Organizer: 第150回 質量分析関西談話会
  • Place of Presentation: 大阪
  • Year and Date: 2015-03-14
  • Invited
• [Presentation] Identification of predictive biomarker candidates of colorectal cancer metastasis in serum extracellular vesicles based on membrane quantitative proteomics of cancer tissues. (2014)
  • Author(s): Tomonaga T, Kume H
  • Organizer: Australasia Extracellular Vesicles Conference
  • Place of Presentation: Kerns, Australia
  • Year and Date: 2014-11-20
• [Presentation] Discovery of colorectal cancer biomarker candidates by membrane proteomic analysis and subsequent verification using selected reaction monitoring. (2014)
  • Author(s): Tomonaga T, Kume H
  • Organizer: Human Proteome Organization (HUPO) 13th Annual World Congress
  • Place of Presentation: Madrid, Spain
  • Year and Date: 2014-10-05 – 2014-10-08
• [Presentation] Discovery of colorectal cancer biomarker candidates by membrane proteomic analysis of human tissue samples and subsequent verification using SRM/MRM (2014)
  • Author(s): Tomonaga T
  • Organizer: The 13th HUPO World Congress Post Congress Workshop
  • Place of Presentation: Segovia, Spain
  • Year and Date: 2014-09-09
  • Invited
• [Presentation] 質量分析計を用いたバイオマーカー定量法の実用化（医療への応用） (2014)
  • Author(s): 朝長 毅
  • Organizer: レドックス・ライフイノベーション第170委員会
  • Place of Presentation: 宮崎
  • Year and Date: 2014-08-22
  • Invited
• [Presentation] 質量分析計を用いたバイオマーカー定量法の創薬への応用を目指して (2014)
  • Author(s): 朝長 毅
  • Organizer: 第12回日本プロテオーム学会2014年会
  • Place of Presentation: つくば
  • Year and Date: 2014-07-17
  • Invited
• [Presentation] 質量分析計を用いたバイオマーカー定量法の実用化（医療への応用） (2014)
  • Author(s): 朝長 毅
  • Organizer: 第14回日本蛋白質科学会
  • Place of Presentation: 神奈川
  • Year and Date: 2014-06-25
  • Invited
• [Presentation] 質量分析計を用いたバイオマーカー定量法の医療への応用 (2014)
  • Author(s): 朝長 毅
  • Organizer: 第10回日本臨床プロテオーム研究会
  • Place of Presentation: 東京
  • Year and Date: 2014-05-10
  • Invited
• [Remarks] 国立研究開発法人医薬基盤・健康・栄養研究所 プロテオームリサーチプロジェクト
  • URL: http://www.nibiohn.go.jp/proteome/index.html
• [Patent(Industrial Property Rights)] ペプチド又はタンパク質の分画方法 (2015)
  • Inventor(s): 朝長 毅、足立 淳、宮崎将太
  • Industrial Property Rights Holder: ジーエルサイエンス 株式会社
  • Industrial Property Rights Type: 特許
  • Industrial Property Number: 2015-134482
  • Filing Date: 2015-07-03