Biology Reference
In-Depth Information
Chapter 18
Application of Saturation Labeling
in Lung Cancer Proteomics
Gereon Poschmann , Barbara Sitek , Bence Sipos , and Kai Stühler
Abstract
Cancer is a quite heterogeneous disease and each cancer type can be divided in different subentities. Normally
this is done by pathologist using classical dye-staining protocols or considering specifi c biomarkers. To
identify new biomarkers, allowing a more specifi c diagnosis clinical tissue specimen is the material of
choice. But the amount of clinical material obtained by resection or biopsy is often limited. In order to
perform analytical studies with such scarce sample material, a sensitive analysis method is required. Using
two-dimensional electrophoresis (2DE) for the analysis of small protein amounts, protein saturation labeling
using fl uorescence dyes has been successfully applied. Here, we describe the application of saturation
labeling in combination with microdissection for the analysis of lung tumor cells and bronchial epithelium
cells. The presented study demonstrates all relevant steps of differential proteome analysis with scarce pro-
tein amount: experimental design, manual microdissection, optimization of saturation labeling, 2DE,
protein identifi cation and validation. As a result, 32 non-redundant proteins could be identifi ed to be
differentially regulated between the respective tissue types and are candidate biomarkers for describing
lung cancer in more detail.
Key words:
DIGE, Saturation labeling, Cancer proteomics, Microdissection, Reference proteome
1. Introduction
Cancer is a quite heterogeneous disease. In the case of lung cancer,
different tumor types, e.g., squamous cell carcinoma (SCC), adeno-
carcinoma, small cell lung cancer, and large cell carcinoma, can be
pathologically discriminated. Each tumor type differs in its behavior
concerning progression, metastasis, and treatment and has its own
morphological and cellular properties. Even a single tumor type
offers large tissue heterogeneity: tumor and stroma areas must be
distinguished, certain areas—even in a single tumor—could con-
sist of cells of several differentiation grades (good, moderately, or
poorly differentiated), and cells in central areas of the tumor could
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