Development of bioinformatic tools for cancer immunotherapy

2010 Fiscal Year Final Research Report

• Project/Area Number: 20700419
• Research Category: Grant-in-Aid for Young Scientists (B)
• Allocation Type: Single-year Grants
• Research Field: Medical systems
• Research Institution: Shizuoka Cancer Center Research Institute
• Principal Investigator: NAKAMURA Yoji Shizuoka Cancer Center Research Institute, 中央水産研究所・水産遺伝子解析センター, 研究員 (90463182)
• Project Period (FY): 2008 – 2010
• Keywords: 医療情報システム / 免疫治療

Research Abstract

I developed an integrated database of immunoglobulin (Ig or antibody) and T-cell receptor (TCR) data reported in cancer studies (the Cancer-related Immunological Gene Database [CIG-DB]). This database is designed as a platform to explore public human and murine Ig/TCR genes sequenced in cancer studies, and a total of 2,081 cancer-related Ig and TCR entries are tabularized. The CIG-DB is equipped with search engines for amino acid sequences and MEDLINE references, sequence analysis tools, and a 3D viewer. This database is accessible without charge or registration at http://www.scchr-cigdb.jp/, and the search results are freely downloadable.
In addition, I developed an in silico docking simulation assay system of binding affinity between HLA-A24 protein and A24-restricted peptides using two softwares, AutoDock and MODELLER, and a crystal structure of HLA-A24 protein in the Protein Data Bank (PDB). I compared the current assay system with the previous method in terms of the prediction capability using MHC stabilization and peptide-stimulated CTL induction assays for carcinoembryonic antigen (CEA) and other HLA-A24 peptides. The result suggested that the current in silico assay system have potential advantages in efficiency of epitope prediction over the previous method.

Research Products

• [Journal Article] Analysis of HLA-A24-restricted peptides of carcinoembryonic antigen using a novel structure-based peptide-HLA docking algorithm. (2011)
  • Author(s): Nakamura Y, Tai S, Oshita C, Iizuka A, Ashizawa T, Saito S, Yamaguchi S, Kondo H, Yamaguchi K, Akiyama Y.
  • Journal Title: Cancer Science. Vol.102 Pages: 690-696
• [Journal Article] Identification of melanoma antigens using a Serological Proteome Approach (SERPA). (2010)
  • Author(s): Suzuki A, Iizuka A, Komiyama M, Takikawa M, Kume A, Tai S, Ohshita C, Kurusu A, Nakamura Y, Yamamoto A, Yamazaki N, Yoshikawa S, Kiyohara Y, Akiyama Y.
  • Journal Title: Cancer Genomics Proteomics. Vol.7 Pages: 17-23
• [Journal Article] CIG-DB : the database for human or mouse immunoglobulin and T cell receptor genes available for cancer studies. (2010)
  • Author(s): Nakamura Y, Komiyama T, Furue M, Gojobori T, Akiyama Y
  • Journal Title: BMC Bioinformatics. Vol.11 Pages: 398
• [Presentation] 血清中のMAGE抗原及びCMV-pp65抗原に対する抗体価の測定及び標準化 (2009)
  • Author(s): 飯塚明、久米亜希子、小宮山優、中村洋路、来栖亜弓、清原祥夫、山口建、秋山靖人
  • Organizer: 第68回日本癌学会学術総会
  • Year and Date: 2009-10-03
• [Remarks] ホームページ等
  • URL: http://www.scchr-cigdb.jp/