An approach to proteomic analysis of human tumors

A strategy for proteomic analysis of microdissected cells derived from huma n tumor specimens is described and demonstrated by using esophageal cancer as an example. Normal squamous epithelium and corresponding tumor cells fro m two patients were procured by laser-capture microdissection and studied b y two-dimensional polyacrylamide gel electrophoresis (2D-PAGE). Fifty thous and cells resolved approximately 675 distinct proteins (or isoforms) with m olecular weights ranging between 10 and 200 kDa and isoelectric points of p H 3-10. Comparison of the microdissected protein profiles showed a high deg ree of similarity between the matched normal-tumor samples (98% identical). However, 17 proteins showed tumor-specific alterations, including 10 that were uniquely present in the tumors and seven that were observed only in th e normal epithelium. Two of the altered proteins were characterized by mass spectrometry and immunoblot analysis and were identified as cytokeratin 1 and annexin I. Acquisition of 2D-PAGE protein profiles, visualization of di sregulated proteins, and subsequent determination of the identity of select ed proteins through high-sensitivity MS-MS microsequencing are possible fro m microdissected cell populations. These separation and analytical techniqu es are uniquely capable of detecting tumor-specific alterations. Continued refinement of techniques and methodologies to determine the abundance and s tatus of proteins in vivo holds great promise for future study of normal ce lls and associated neoplasms. Mol. Carcinog. 27:158-165, 2000. Published by Wiley-Liss Inc.