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Repertoire of self antigens eliciting immune response in patients with well-differentiated thyroid tumors is largely unexplored. To begin systematic analysis of this issue, we performed serological proteome analysis using sera of patients with benign and malignant thyroid neoplasms to identify protein targets of humoral anti-tumor immune response expressed in papillary and follicular thyroid cancer cell lines (K1 and FTC133, respectively). Combined autoantigenic profile of two cell lines comprised several dozens of reproducibly reactive protein spots in two-dimensional Western blot analysis, 15 of them being recurrently reactive in thyroid neoplasms vs healthy donors, malignant vs benign (or vice versa) fashion and/or associated with a particular tumor histotype. NanoLC-ESI-MS/MS analysis of tryptic fragments was performed to identify targets of thyroid tumor-specific immune responses. Although the molecular chaperones (particularly heat shock proteins) was the top subgroup enriched in the identified protein set (5 out of 15 antigens), other identified proteins with miscellaneous functions seem to be more relevant to the biology and diagnostic/therapeutic aspects of these neoplasms; possible causes of immunogenicity and diagnostic potential of identified antigens will be discussed. Identified autoantibody signature may provide novel tools for differential diagnostics of benign and malignant thyroid tumors, as well as give some clues about molecular pathogenesis of differentiated thyroid neoplasm.