ArticlesProteomic patterns of tumour subsets in non-small-cell lung cancer
Introduction
Lung cancer is a challenging worldwide clinical problem and the leading cause of death from cancer in the USA for both men and women, with an estimated 171900 new cases and 157200 deaths in 2003. Its overall incidence is increasing, and despite complex aggressive approaches to treatment and great strides in understanding its biology and causes, corresponding improvements in outcome are not yet apparent.1, 2 The behaviour of individual non-small-cell lung cancer (NSCLC) tumours cannot be understood through the analysis of individual or small numbers of genes, so cDNA microarray analysis has been used, with some success, to simultaneously investigate thousands of RNA expression levels and begin to identify patterns associated with biological characteristics.3, 4, 5 However, mRNA expression is poorly correlated with levels of protein expression, and such analyses cannot detect important post-translational modifications of proteins—such as proteolytic processing, phos-phorylation, or glycosylation—all of which are important processes in determining protein function.6, 7 Accordingly, comprehensive analysis of protein expression patterns in tissues might improve our ability to understand the molecular complexities of tumour cells.
Matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry (MALDI-TOF MS) can profile proteins up to 50 kDa in size in tissues.8 This technology can not only directly assess peptides and proteins in sections of tumour tissue, but also can be used for high resolution imaging of individual biomolecules present in tissue sections.9, 10, 11 The protein profiles obtained can contain thousands of data points, necessitating sophisticated data analysis algorithms. Although available bioinformatics techniques have been used to study physiological outcomes and cluster samples according to gene expression patterns in microarray analysis,3, 4, 5, 12, 13 these methods are inadequate to extract this information from mass spectral profiles of large numbers of samples, especially with respect to aligning thousands of anonymous peaks present in hundreds of independent mass spectra.
We aimed to use MALDI-TOF MS to assess protein expression profiles in a few hundred cells from single frozen sections of surgically resected lung tumours, and to develop custom software to assess the resulting data.
Section snippets
Study population
Patients seen at the Vanderbilt University School of Medicine Hospital between March, 1998, and July, 2002, for NSCLC and metastases to lung were assessed for this study. Informed consent was received and the project was approved by the local Institutional Review Board. All NSCLC tumours resected for this study were carefully staged preoperatively and clinically felt to be N2 node negative with CT, positron emission tomography, or mediastinoscopy, and none received preoperative therapy. Surgery
Results
To detect proteomic patterns in lung tumours, we assessed the protein expression profiles of 50 tissue samples in a training cohort. These included 42 surgically resected lung tumours (34 primary tumours and two pulmonary metastases of previously resected NSCLC, one pulmonary carcinoid, and five metastases to the lung from other sites) and eight normal lung samples. Spectra were obtained from a region of about 1 mm diameter from a single fresh frozen tumour section selected by a lung
Discussion
In this study, we directly profiled protein expression from tumour tissue with MALDI-TOF MS, and defined profiles that enabled classification of surgically resected lung tumours into biologically meaningful groups.
Previous studies have defined subclasses and prognostic subsets of lung adenocarcinomas based on gene expression patterns.3, 4, 5 However, mRNA expression cannot always indicate which proteins are expressed or how their activity might be modulated after translation.6, 7 Accordingly,
References (33)
- et al.
Imaging mass spectrometry: a new tool to investigate the spatial organization of peptides and proteins in mammalian tissue sections
Curr Opin Chem Biol
(2002) Revisions in the International System for Staging Lung Cancer
Chest
(1997)- et al.
Direct analysis of laser capture microdissected cells by MALDI mass spectrometry
J Am Soc Mass Spectrom
(2002) Tightening the clinical trial
Control Clin Trials
(1993)- et al.
Use of proteomic patterns in serum to identify ovarian cancer
Lancet
(2002) - et al.
SUMO-1 modification of Mdm2 prevents its self-ubiquitination and increases Mdm2 ability to ubiquitinate p53
Cell
(2000) - et al.
Isolation of tissue-type plasminogen activator, cathepsin H, and non-specific cross-reacting antigen from SK-PC-1 pancreas cancer cells using subtractive hybridization
FEBS Lett
(1996) - et al.
Thymosin-β4 regulates motility and metastasis of malignant mouse fibrosarcoma cells
Am J Pathol
(2002) The biology of lung cancer
Semin Oncol
(1997)Neoplasms of the lung
Gene-expression profiles predict survival of patients with lung adenocarcinoma
Nat Med
Classification of human lung carcinomas by mRNA expression profiling reveals distinct adenocarcinoma subclasses
Proc Natl Acad Sci USA
Diversity of gene expression in adenocarcinoma of the lung
Proc Natl Acad Sci USA
Current challenges and future applications for protein maps and post-translational vector maps in proteome projects
Electrophoresis
A comparison of selected mRNA and protein abundances in human liver
Electrophoresis
Molecular imaging of biological samples: localization of peptides and proteins using MALDI-TOF MS
Anal Chem
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