Abstract

Rationale

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 the post genomic era most biomarker studies aim to measure abundances instead of real enzymatic activities. Therefore crucial changes in enzymatic activities during tumor progression and treatment response might not be detected. In order to circumvent these limitations a new methodology termed Activity Based Protein Profiling (ABPP), developed by Professor B. Cravatt and colleagues, may be a promising option. The methodology employs so-called Activity Based Probes (ABPs) that selectively bind to active sites of members of distinct enzyme superfamilies, thereby making an activity read-out of any given proteome possible. Using ABPs targeting serine hydrolases, a large and diverse class of enzymes that have previously been linked to lung cancer development, we introduced ABPP as a screening platform in a clinical setting.

Methods

A directed mass spectrometric approach was used for qualitative and quantitative analysis of ABP labeled proteomes. Samples were analyzed on an FTICR mass spectrometer (LTQ-FTMS, Thermo Finnigan, Bremen, Germany). Mass spectrometric data were searched against a recently updated human database (UniProt) using the Mascot search engine (version 2.2). SuperHirn v0.3 was used for label-free quantitation. Inclusion/exclusion lists were generated based on data derived from discovery-driven experiments in data-dependent acquisition mode.

Results

Approximately 30 serine hydrolases - mostly esterases and proteases - were identified per investigated proteome of the human lung adenocarcinoma cell line CaLu-3. Certain enzymes like Fatty Acid Synthase (FASN) or Kallikrein-6 (KLK6) have previously been associated with lung cancer development or lung cancer diagnosis, respectively. However, other enzymes like Neutral cholesterol ester hydrolase 1 (NCEH1) have not been linked to lung cancer so far or even represent uncharacterized proteins (Abhydrolase domain-containing protein 10, ABHD10). Interestingly, several threonine proteases were identified, indicating that this class of enzymes is also susceptible to the ABP targeting serine hydrolases.

Conclusion

ABPP allows fast and semi-quantitative analysis of enzymatic activity profiles in cell lines and primary human specimen. We aim to apply the established methodology on >100 pairs of fresh-frozen human lung adenocarcinoma biopsies and corresponding normal lung tissues from our tumor bank and link activity profiles of serine hydrolases to clinical follow-up data. The results of this study will ideally allow the discrimination of low-/ high-risk lung adenocarcinoma patients.

Note: This abstract was not presented at the AACR 101st Annual Meeting 2010 because the presenter was unable to attend.