Analysis of protein expression patterns in Barrett's esophagus using MALDI mass spectrometry, in search of malignancy biomarkers

Quantitative Shotgun Proteomics Unveils Candidate Novel Esophageal Adenocarcinoma (EAC)-specific Proteins

Esophageal cancer is the eighth most common cancer worldwide and the majority of patients have systemic disease at presentation. Esophageal adenocarcinoma (OAC), the predominant subtype in western countries, is largely resistant to current chemotherapy regimens. Selective markers are needed to enhance clinical staging and to allow targeted therapies yet there are minimal proteomic data on this cancer type. After histological review, lysates from OAC and matched normal esophageal and gastric samples from seven patients were subjected to LC MS/MS after tandem mass tag labeling and OFFGEL fractionation. Patient matched samples of OAC, normal esophagus, normal stomach, lymph node metastases and uninvolved lymph nodes were used from an additional 115 patients for verification of expression by immunohistochemistry (IHC).

Over six thousand proteins were identified and quantified across samples. Quantitative reproducibility was excellent between technical replicates and a moderate correlation was seen across samples with the same histology. The quantitative accuracy was verified across the dynamic range for seven proteins by immunohistochemistry (IHC) on the originating tissues. Multiple novel tumor-specific candidates are proposed and EPCAM was verified by IHC.

This shotgun proteomic study of OAC used a comparative quantitative approach to reveal proteins highly expressed in specific tissue types. Novel tumor-specific proteins are proposed and EPCAM was demonstrated to be specifically overexpressed in primary tumors and lymph node metastases compared with surrounding normal tissues. This candidate and others proposed in this study could be developed as tumor-specific targets for novel clinical staging and therapeutic approaches.

Biomarkers in Barrett's Esophagus

Biomarkers are substances that can be used to indicate normal or diseased states. In clinical settings, the term biomarker generally refers to a molecular marker produced by tissues whose detection heralds a diseased state. For patients with Barrett's esophagus, there are at least three clinical settings in which the use of molecular biomarkers has been proposed including 1) stratifying the risk of neoplastic progression, 2) serving as an adjunct to aid in the diagnosis of dysplasia, and 3) predicting response to ablative therapies. Although the routine clinical use of biomarkers in any of these clinical settings is not yet recommended, it seems reasonable to assume that biomarker validation studies will be carried out in the coming years and that movement into the clinics will be inevitable. This article reviews the current progress in using biomarkers in each of the clinical settings described above with a focus on the molecular biomarkers which have advanced the farthest toward use in routine clinical practice.

Defining disease with laser precision: laser capture microdissection in gastroenterology

Laser capture microdissection (LCM) is an efficient and precise method for obtaining pure cell populations or specific cells of interest from a given tissue sample. LCM has been applied to animal and human gastroenterology research in analyzing the protein, DNA, and RNA from all organs of the gastrointestinal system. There are numerous potential applications for this technology in gastroenterology research, including malignancies of the esophagus, stomach, colon, biliary tract, and liver. This technology can also be used to study gastrointestinal infections, inflammatory bowel disease, pancreatitis, motility, malabsorption, and radiation enteropathy. LCM has multiple advantages when compared with conventional methods of microdissection, and this technology can be exploited to identify precursors to disease, diagnostic biomarkers, and therapeutic interventions.

High throughput techniques for characterizing the expression profile of Barrett's esophagus

Barrett's esophagus (BE) is the metaplastic change of the normal lined squamous epithelium of the distal esophagus to a columnar type of epithelium as a result of chronic long-standing gastroesophageal reflux disease. Patients with BE have a significantly increased risk of developing an esophageal adenocarcinoma, with an estimated annual incidence varying from 0.4 to 1.8%. Over the last 3 decades, the incidence of BE and its associated adenocarcinoma has increased in Western countries at a rate that exceeds that of any other malignancy. Despite all the research performed on BE, there is still an inadequate understanding of the biological basis of this mucosal transformation. With the upcoming modern high throughput technologies, important progression has been made in unraveling the expression profiles and gaining more insight in the biology of BE and esophageal adenocarcinoma. Several studies reported genome, transcriptome, proteome, and kinome investigations using high throughput techniques. These studies were conducted to find biomarkers that can be used to detect BE patients with increased risk for malignant progression or to obtain more insight in the mechanism underlying BE development. In the following review, we first discuss the different techniques that are currently available and summarize findings in this field, including several recent publications of our group.

Molecular changes in the progression of Barrett's oesophagus

Barrett's oesophagus is a frequent complication of gastro-oesophageal reflux disease predicting oesophageal adenocarcinoma. The majority of Barrett's patients will not develop cancer, so that specific methods of identification of those at risk are required. Recent molecular studies have identified a selection of candidate biomarkers that need validation in prospective studies. They reflect various changes in cell behaviour during neoplastic progression. The ASPECT trial in the UK aims to establish whether chemoprevention with aspirin and a proton pump inhibitor will reduce adenocarcinoma development and mortality in patients with Barrett's oesophagus. It will also validate biomarkers for progression and clinical response and further study disease pathogenesis.

Comparison of Kinome Profiles of Barrett's Esophagus with Normal Squamous Esophagus and Normal Gastric Cardia

The precursor metaplastic mucosal lesion that predisposes for esophageal adenocarcinoma is Barrett's esophagus. Because the signal transduction events that occur in Barrett's esophagus are poorly understood, this study aimed at generating a comprehensive description of cellular kinase activity in Barrett's esophagus, normal squamous esophagus, and gastric cardia to gain more insight into the pathogenesis of Barrett's esophagus. Peptide arrays, exhibiting 1,176 specific consensus sequences for protein kinases, were used to produce a global analysis of cellular kinase activity in biopsies of Barrett's esophagus, and results were compared with the neighboring cardia and squamous epithelia. Several differences in kinase activity using immunoblot analysis and enzyme activity assays were validated in biopsies of 27 Barrett's esophagus patients. Three unique kinome profiles are described and compared. We identified cascades of activated kinases showing that mitogen-activated protein kinase and epidermal growth factor receptor activity are both significantly altered in Barrett's esophagus compared with squamous and gastric cardia epithelia. Another novel finding is that the glycolysis pathway is significantly up-regulated in Barrett's esophagus, which is illustrated by an up-regulated pyruvate kinase activity. Here, the unique kinome profile of Barrett's esophagus is made available as a comprehensive database. Several signaling pathways are revealed as specifically expressed in Barrett's esophagus when compared with the adjacent normal epithelia. These unique findings provide novel insight in the pathogenesis of Barrett's esophagus that will ultimately help to resolve the increasing problem of Barrett's esophagus and prevention of esophageal adenocarcinoma.

Laser-assisted microdissection for real-time PCR sample preparation

Laser-assisted microdissection (LMD) has been developed to procure precisely the cells of interest in a tissue specimen, in a rapid and practical manner. Together with real-time PCR and RT-PCR techniques, it is now feasible to study genetic alterations, gene expression features and proteins in defined cell populations from complex normal and diseased tissues. The process that brings from sample collection to the final quantitative results is articulated in several steps, each of which requires optimal choices in order to end up with high-quality nucleic acid or protein that allows successful application of the final quantitative assays. This review will describe shortly the development of LMD technologies and the principles they are based on. Trying to highlight the advantages and disadvantages of LMD, the main problems related to specimens collection and processing, section preparation and extraction of bio-molecules from microdissected tissue samples have been analysed.