Abstract 5101: Biomarker identification in non-small cell lung cancer (NSCLC) with activity-based proteomics

Abstract

Abstract Background: Lung cancer is the leading cause of all cancer related deaths and treatment is still suboptimal. Novel biomarkers with a reliable predictive significance which may additionally represent therapeutic targets are therefore of utmost importance. In biomarker discovery studies transcript or protein abundances are typically compared in normal versus disease states. However, crucial changes in enzymatic activities remain undetected. Based on the work of Prof. Cravatt and others, activity-based proteomics has become a promising option to circumvent this limitation. This study aims to establish a robust and high throughput activity-based proteomics platform and to investigate the role of serine hydrolase activity profiles as prognostic biomarkers in lung cancer. Methods: A fluorophosphate derivate (CAS-Number: 353754-93-5) was used to covalently target serine hydrolases in proteomes derived from human lung adenocarcinoma biopsies and corresponding normal lung tissues (tumor cell content: >50%, TNM-stage: I-IV). Tagged proteins were subsequently affinity purified and analyzed using a directed mass spectrometry based approach (LTQ-FTMS, Thermo Finnigan). Data were qualitatively analyzed using the Mascot 2.2 search engine and Progenesis LC-MS version 2.5 (Nonlinear Dynamics) was employed for relative quantification. Results: The strategy described above results in the simultaneous qualitative and quantitative analysis of serine hydrolase activities in complex proteomes, thereby representing a valid alternative to activity-based proteomics approaches described so far. The analysis of 40 pairs of fresh frozen malignant and corresponding normal lung tissues in combination with clinical follow-up data led to the identification of two biomarker candidates that have previously not been associated with lung cancer. Conclusion & Outlook: Based on the results obtained in this study we conclude that activity-based proteomics represents a powerful strategy in the seek for novel biomarker candidates in human lung adenocarcinoma. Future research will involve data validation with additional samples from our tumor bank using advanced quantitative Multiple Reaction Monitoring (MRM) technology. Liu, Y., Patricelli, M.P. & Cravatt, B.F. Activity-based protein profiling: the serine hydrolases. Proceedings of the National Academy of Sciences of the United States of America 96, 14694-14699 (1999). Jessani, N., et al. A streamlined platform for high-content functional proteomics of primary human specimens. Nature methods 2, 691-697 (2005). Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 5101. doi:10.1158/1538-7445.AM2011-5101