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Proteomics of Lympohoid Neoplasms - Proteome - mining for 2D Gel

Tadashi Kondo, Kazuyasu Fujii, Hideki Yokoo, Tesshi Yamada, Yoshihiro Matstuno, Keiji Iwatsuki, and Setsuo Hirohashi

Abstract

To identify the proteins useful for the differential diagnosis of lymphoid neoplasms, we studied the proteome of 42 cell lines from human lymphoid neoplasms. Two-dimensional difference gel electrophoresis (2D-DIGE) generated the protein expression profile of the cell lines from Hodgikin lymphoma (HL) (4 cell lines), B cell malignancies (19 cell lines), T cell malignancies (16 cell lines), and natural killer (NK) cell lymphoma (3 cell lines). The proteomic data of 83,977 protein spots are integrated into a text file, and studied by the methods of multivariate analysis and machine-learning methods. We identified the small number of spots, which discriminated 1) between HL cells and other cells (16 spots), 2) between the cells from B cell malignancies, T cell malignancies and NK cell lymphoma (11 spots), and 3) between HL ell and anaplastic large cell lymphoma (ALCL) cells (4 spots). Proteins corresponding to 389 spots were identified by mass spectrometric study and their expression level in the 42 lymphoid neoplasms was investigated. Among the proteins in the database, we found that 5 proteins grouped the cell lines according to their original histology using the decision tree classification algorithm. In conclusion, our results showed that the bioinformatics approach to proteomic data was useful to identify the key proteins for the histological subtypes of lymphoid neoplasms. We will develop our database for comprehensive understanding of the proteome of lymphoid neoplasms.

関連論文

  1. Kazuyasu Fujii, Tadashi Kondo, Masayo Yamada, Keiji Iwatsuki and Setsuo Hirohashi.
    Toward a comprehensive quantitative proteome database: protein expression map of lymphoid neoplasms by 2-D DIGE and MS. Proteomics, 6, 4856-4876, 2006. [PubMed](外部リンク)