Proteomics in clinical trials and practice: present uses and future promise

Overview and introduction to clinical proteomics

As the field of clinical proteomics progresses, discovery of disease biomarkers becomes paramount. However, the immediate challenges are to establish standard operating procedures for both clinical specimen handling and reduction of sample complexity and to increase the ability to detect proteins and peptides present in low amounts. The traditional concept of a disease biomarker is shifting toward a new paradigm, namely, that an ensemble of proteins or peptides would be more efficient than a single protein/peptide in the diagnosis of disease. Because clinical proteomics usually requires easy access to well-defined fresh clinical specimens (including morphologically consistent tissue and properly pretreated body fluids of sufficient quantity), biorepository systems need to be established. Here, we address these questions and emphasize the necessity of developing various microdissection techniques for tissue specimens, multidimensional fractionation for body fluids, and other related techniques (including bioinformatics), tools which could become integral parts of clinical proteomics for disease biomarker discovery.

Microdissecting the proteome

The complexity of the proteome is extremely high, because every organ or even a part of it can differ considerably in its protein composition. Performing proteomic studies therefore means to separate these functional different tissue areas before analysis. Otherwise all gained results will be depending on the question whether they are incorrect or at least dubious and do they reflect the different functions of tissues at all. The separation of functional tissue areas can be achieved by laser-based microdissection. In this review we will discuss the compatibly of microdissected formalin or cryofixed tissue with different proteomic techniques like 2-DE, MS and protein arrays.

MYOMETRIAL ACTIVATION – COORDINATION, CONNECTIVITY AND CONTRACTILITY

One of the most important stages of pregnancy is the activation of uterine contractions that result in the expulsion of the fetus. The timely onset of labour is clearly important for a healthy start to life but incomplete understanding of the precise mechanisms regulating labour onset have prohibited the development of effective and safe treatments for preterm labour. This review explores the activation of the myometrium at labour onset, focussing on mechanisms of uterine contractility, including those proteins that play an important role in smooth muscle contractility. The review primarily focuses on human work but in the absence of human data describes animal studies. A broad overview of myometrial contraction mechanisms is provided before discussing more detailed aspects and identifying areas where uncertainty remains. Also discussed is the recent application of ‘omics’ based approaches to parturition research, which has facilitated an increase in the understanding of myometrial activation.

High-throughput antibody microarrays for quantitative proteomic analysis

The antibody microarray is an intrinsically robust and quantitative system that delivers high-throughput and parallel measurements on particular sets of known proteins. It has become an important proteomics research tool, complementary to the conventional unbiased separation-based and mass spectrometry-based approaches. This review summarizes the technical aspects of production and the application for quantitative proteomic analysis with an emphasis on disease proteomics, especially the identification of biomarkers. Quality control, data analysis methods and the challenges for quantitative assays are also discussed.

Challenges of cancer biomarker profiling

OBJECTIVES

New biomarkers are being developed to identify individuals at risk for cancer, detect disease earlier, determine prognosis, detect recurrence, predict response to particular agents, and monitor response to treatment. This article attempts to address some of the challenges facing the research and medical communities in the delivery of new biomarkers for individualized medicine.

METHODS

A variety of issues and barriers can affect the transfer of clinical tests from research to clinical practice. Differences in sample collection, handling or storage, and profiling techniques may influence the protein profile obtained by any method.

RESULTS

Standard procedures and quality check schemes are necessary because there is a lack of definition to guarantee reproducibility of new procedures. From technical and economic viewpoints, the assay has to be sufficiently robust to be completed in community-based hospitals. Although traditionally cancer patients were treated with drugs of low toxicity or of high tolerance regardless of their efficacy in a given patient if the benefits of that drug are proven in both experimental and clinical conditions, recent advances have provided opportunities to adapt "tailored" treatment modalities. The evolving trend is the usage of patterns of markers instead of a single marker. Further challenges in biomarker development are in finding the relevant markers that have the right degree of specificity and sensitivity and a reliable test to measure the outcome.

CONCLUSIONS

Discovery, testing, and validation of clinically appropriate and commercially useful tumor markers should permit individualization of therapy.

The ongoing evolution of proteomics in malignancy

The complementary fields of genomics and proteomics offer insights into the molecular mechanisms of diseases. While genomics seeks to define our genetic substrate, proteomics explores the structure and function of proteins, which are the end effectors of our genes. Proteomics has been revolutionized in the past decade by the application of techniques such as protein arrays, two-dimensional gel electrophoresis, and mass spectrometry. These techniques have tremendous potential for biomarker development, target validation, diagnosis, prognosis, and optimization of treatment in medical care, especially in the field of clinical oncology. We will discuss innovations in proteomic technologies and highlight their prospective applications to patient care.

A phase II and pharmacodynamic study of gefitinib in patients with refractory or recurrent epithelial ovarian cancer

BACKGROUND

The primary objective of this study was to evaluate the biochemical effects of gefitinib on its target signal-transduction pathways in patients with recurrent epithelial ovarian cancer (EOC). The secondary objectives included assessing clinical activity and toxicity and determining the association between biochemical and clinical outcomes.

METHODS

Twenty-four heavily pretreated patients with EOC who had good end-organ function and performance status and who had measurable disease received gefitinib 500 mg daily. Prospectively planned core-needle tumor biopsies were obtained before treatment and after 4 weeks. Protein expression of total and phosphorylated (p) epidermal growth factor receptor (EGFR), protein kinase B (AKT), and extracellular regulated kinase (ERK) was quantified in microdissected tumor cells using tissue lysate array proteomics.

RESULTS

All tumor samples had detectable levels of EGFR and p-EGFR. A decrease in the quantity of both EGFR and p-EGFR was observed with gefitinib therapy in >50% of patients. This was not associated with clinical benefit, nor were responses observed. However, trends for increased gastrointestinal and skin toxicity were observed with greater phosphorylation or quantities of EGFR, ERK, and AKT in tumor samples (P </= .05). Gefitinib had limited clinical activity as monotherapy despite documented target inhibition.

CONCLUSIONS

The results from this study demonstrated that gefitinib inhibited the phosphorylation of EGFR in EOC tumor cells, providing proof of target in a clinical setting. Combinatorial therapy with molecular therapeutics against complementary targets may prove successful.