Proteomic Strategies for the Characterization and the Early Detection of Lung Cancer  Pierre P. Massion, MD, Richard M. Caprioli, PhD  Journal of Thoracic Oncology  Volume 1, Issue 9, Pages 1027-1039 (November 2006) DOI: 10.1016/S1556-0864(15)31639-7 Copyright © 2006 International Association for the Study of Lung Cancer Terms and Conditions

FIGURE 1 Schematic representation of identification of the components of a complex protein mixture through top-down and bottom-up proteomic approaches. 2D-Page, two-dimensional polyacrylamide gel electrophoresis; MS-MS, tandem mass spectrometry; MALDI TOF MS; matrix-assisted laser desorption time-of-flight mass spectrometry; LC MS-MS, liquid chromatography tandem mass spectrometry; Thermo LTQ, linear ion trap mass spectrometer. Journal of Thoracic Oncology 2006 1, 1027-1039DOI: (10.1016/S1556-0864(15)31639-7) Copyright © 2006 International Association for the Study of Lung Cancer Terms and Conditions

FIGURE 2 Schematic representation of matrix-assisted desorption ionization mass spectrometry. Fresh tissue is sectioned and mounted on a conductive metal plate. The sample is coated with matrix in a raster design, typically sinapinic acid, and directly analyzed in the mass spectrometer. The relative intensity of any of the signals in the spectrum is measured over the entire tissue at higher image resolution. If a small number of discrete areas are to be analyzed, then these are ablated individually in a profiling mode. If the relative intensity of any of the signals in the spectrum is to be measured over the entire tissue at higher image resolution, then a raster is performed to provide a matrix of pixels in an imaging mode. An image representing the intensity of a given peak in each pixel in the array is then generated. Journal of Thoracic Oncology 2006 1, 1027-1039DOI: (10.1016/S1556-0864(15)31639-7) Copyright © 2006 International Association for the Study of Lung Cancer Terms and Conditions

FIGURE 3 (A), 2D-PAGE gel separation of proteins identified with silver staining from a stage I lung adenocarcinoma. The proteins are separated by isoelectric point (PI) in the first dimension and by molecular weight (MW) in the second dimension. (B–F), the outlined areas of (A) showing proteins significantly increased in lung adenocarcinoma (Chen G, Gharib TG, Huang CC, et al. Proteomic analysis of lung adenocarcinoma: identification of a highly expressed set of proteins in tumors. Clin Cancer Res 2002;8:2298–2305. Reprinted by permission. Journal of Thoracic Oncology 2006 1, 1027-1039DOI: (10.1016/S1556-0864(15)31639-7) Copyright © 2006 International Association for the Study of Lung Cancer Terms and Conditions

FIGURE 4 Tissue microarrays (TMAs) of lung cancer specimens. TMAs are comprised of core biopsies 0.6 mm in diameter of different tumors and of uninvolved lung from the same individuals. TMAs allow high-throughput analysis of molecular markers identified in lung cancer and control samples. Clinical annotation of these specimens allows rapid assessment of clinical outcomes (e.g., survival) as schematically represented by Kaplan-Meier survival curves. FISH, fluorescent in situ hybridization; IHC, immunohistochemistry. Journal of Thoracic Oncology 2006 1, 1027-1039DOI: (10.1016/S1556-0864(15)31639-7) Copyright © 2006 International Association for the Study of Lung Cancer Terms and Conditions

FIGURE 5 Detection of the optimal discriminatory biomarker sets in lung tumors. (Top), Representative MALDI-TOF-MS spectra obtained from tumor and normal lung tissue samples with molecular weight calculation (m/z values). *Examples of the MS peaks identified by the statistical analyses as optimal discriminatory patterns between normal and tumor. (Bottom), Hierarchical cluster analysis of 42 lung tumors and eight normal lung tissues in the training cohort according to the protein expression patterns of 82 MS signals. Each row represents an individual proteomic signal, and each column represents an individual sample. The dendrogram at the top shows the similarity in protein expression profiles of the samples. Substantially raised (red) expression of the proteins is noted in individual tumor and normal lung tissue samples. AD, adenocarcinoma; SQ, squamous cell carcinoma; LA, large cell carcinoma; META, metastases to lung from other sites; REC, recurrent non-small cell lung cancer; CAR, pulmonary carcinoid; NL, normal lung. (Yanagisawa K, Shyr Y, Xu BJ, et al. Proteomic patterns of tumour subsets in non-small-cell lung cancer. Lancet 2003; 362:433–439. Reprinted by permission.) Journal of Thoracic Oncology 2006 1, 1027-1039DOI: (10.1016/S1556-0864(15)31639-7) Copyright © 2006 International Association for the Study of Lung Cancer Terms and Conditions