Clinical proteomic biomarkers: relevant issues on study design & technical considerations in biomarker development

Abstract

Biomarker research is continuously expanding in the field of clinical proteomics. A combination of different proteomic-based methodologies can be applied depending on the specific clinical context of use. Moreover, current advancements in proteomic analytical platforms are leading to an expansion of biomarker candidates that can be identified. Specifically, mass spectrometric techniques could provide highly valuable tools for biomarker research. Ideally, these advances could provide with biomarkers that are clinically applicable for disease diagnosis and/ or prognosis. Unfortunately, in general the biomarker candidates fail to be implemented in clinical decision making. To improve on this current situation, a well-defined study design has to be established driven by a clear clinical need, while several checkpoints between the different phases of discovery, verification and validation have to be passed in order to increase the probability of establishing valid biomarkers. In this review, we summarize the technical proteomic platforms that are available along the different stages in the biomarker discovery pipeline, exemplified by clinical applications in the field of bladder cancer biomarker research.

Figure 1

Main components of biomarker study design include definition of clinical need, sample selection and recruitment, statistical evaluation plan and selection of the analytical platform.

Figure 2

Representative workflow of the typical procedure to be followed regarding the sample biobanking. This multistep process includes sample tracking by electronic system, as well as integration of patients clinical characteristics and demographic data. Finally, the deposition of acquired data in public repositories is presented.

Figure 3

Schematic representation of proteomics platform applied in biomarker workflow. Initial discovery phase currently relies on untargeted MS-based approaches resulting in identification of vast number of potential biomarkers. Further verification requires targeted approach. Candidates should to be prioritized based on their functional/ biological relevance. Since the molecular changes underlying the pathological conditions are complex and heterogeneous, the ultimate solution to improve the accuracy of biomarkers appears to be the combination of biomarkers into a panel. The biomarker panel is evaluated in the verification step and further tested during the validation. Currently, immune-based approached are most commonly applied, although moderate selectivity of antibodies represents a significant problem. Alternatively, quantitative MS-based approach like MRM can be also introduced. Along with the advancements in biomarker workflow, the number of putative biomarkers is often decreasing, whereas the sample sets and general costs are increasing. In the validation phase, biomarker performance has to be assessed in a large cohort study in targeted population.