2D gel blood serum biomarkers reveal differential clinical proteomics

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The review will discuss how the application of quantitative 2D gel electrophoresis, combined with appropriate single-variable and multivariate biostatistics, ...

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2D gel blood serum biomarkers reveal differential clinical proteomics of the neurodegenerative diseases Essam A Sheta, Stanley H Appel and Ira L Goldknopf †

References

This review addresses the challenges of neuroproteomics and recent progress in biomarkers and tests for neurodegenerative diseases, including Alzheimer’s disease, Parkinson’s disease and amyotrophic lateral sclerosis. The review will discuss how the application of quantitative 2D gel electrophoresis, combined with appropriate single-variable and multivariate biostatistics, allows for selection of disease-specific serum biomarkers. It will also address how the use of large cohorts of specifically targeted patient blood serum samples and complimentary age-matched controls, in parallel with the use of selected panels of these biomarkers, are being applied to the development of blood tests to specifically address unmet pressing needs in the differential diagnosis of these diseases, and to provide potential avenues for mechanism-based drug targeting and treatment monitoring. While exploring recent findings in this area, the review discusses differences in critical pathways of immune/inflammation and amyloid formation between Parkinson’s disease and amyotrophic lateral sclerosis, as well as discernable synergistic relationships between these pathways that are revealed by this approach. The potential for pathway measurement in blood tests for differential diagnosis, disease burden and therapeutic monitoring is also outlined.

Affiliations

Expert Rev. Proteomics 3(1), 45–62 (2006)

CONTENTS Why neurodegenerative diseases? Alzheimer’s disease Parkinson’s disease Amyotrophic lateral sclerosis Challenges of neuroproteomics Expert commentary Five-year view Key issues



Author for correspondence Power3 Medical Products, Inc., 3400 Research Forest Drive, The Woodlands, TX 77384, USA Tel.: +1 281 466 1600 Fax: +1 281 466 1481 [email protected] KEYWORDS: 2D, ALS, Alzheimer’s, biomarkers, biostatistics, inflammation, multivariate, neurodegenerative, Parkinson’s, proteomics

www.future-drugs.com

Much like genomics, proteomics is more of a concept than a specifically defined technology, as it refers to any type of technology that focuses upon the wide-scale analysis of proteins. These technologies range from those designed to study a single protein (i.e., mapping of sites of post-translational modifications) to those for the analysis of hundreds to thousands of proteins in a single experiment (e.g., 2D gel electrophoresis, protein arrays or isotope-coded affinity tags and various iterations of mass spectrometry [MS], to name a few). Although several methods have emerged for automated protein separation and identification, it remains an unsolved challenge to analyze and interpret the enormous volumes of proteomic data that arise from these approaches. To complicate matters further, more than 75%

10.1586/14789450.3.1.45

of the predicted proteins in multicellular organisms have unknown cellular functions. However, unmet medical needs challenge proteomics to provide avenues for superior diagnostics and therapeutics. Proteomic research is currently focused on two contrasting but complementary strategies. The first strategy, termed cell mapping proteomics, aims to define protein–protein interactions to build a picture of the intricate networks that constitute intercellular signaling pathways. The second strategy, protein expression proteomics, monitors global expression of large numbers of proteins within a cell type, tissue or in biological fluids, and quantitatively identifies how patterns of expression change in different circumstances. The latter approach is the focus of this review.

© 2006 Future Drugs Ltd

ISSN 1478-9450

45

Sheta, Appel & Goldknopf

2D gel electrophoresis has been used in research laboratories for biomarker discovery since the 1970s [1–3]. The advent of much faster identification of protein spots by in-gel digestion and MS ushered in the accelerated development of proteomic science through large-scale application of these techniques [4,5]. With the advent of bioinformatics, progression of proteomics towards diagnostics and personalized medicine has become feasible [6–8]. Although still in its infancy, the application of proteomics in neurodegenerative disease studies is maturing into a powerful approach for comprehensive analyses of disease mechanisms and disease markers. Amyotrophic lateral sclerosis (ALS), Parkinson’s disease (PD) and Alzheimer’s disease (AD) are among those devastating disorders where disease markers are particularly needed. Why neurodegenerative diseases?

Neurodegenerative diseases are a varied assortment of CNS disorders characterized by the progressive loss of neural tissues. The estimated cost to society of three of these devastating diseases exceeds US$100 billion (TABLE I). Generally, the diagnosis of AD, PD or ALS is based on clinical criteria and the results of electrodiagnostic studies. Numerous neurological imaging, blood and CSF studies may be performed, mostly to rule out the presence of other medical conditions that may mimic the clinical appearance of the three diseases. The genetic based diagnostics for AD, PD and ALS are associated with the less common familial forms of the diseases, while minimal diagnostics are available for the more common sporadic forms of the diseases. Available proteinbased diagnostic tests are limited to cerebrospinal fluid (CSF), using commercially available immunoassay kits for amyloid β (Aβ), Tau protein and phosphorylated Tau, as risk factors for AD. Absolute dependence on individual markers for diagnosis is problematic as concentrations vary among individuals according to their age, sex and genetic profile. In fact, in AD, the only objective definitive diagnostics requires tissue examination, which is usually delayed until autopsy. Alzheimer’s disease

AD is one of the most common causes of mental deterioration in elderly people, accounting for approximately 50–60% of the overall cases of dementia among persons over 65 years of age.

The rate of occurrence of AD doubles every 5 years for those between 65 and 85 years of age [9]. It is estimated that there are currently 18 million people worldwide with AD. This figure is projected to nearly double to 34 million by 2025. AD is characterized by global cognitive decline and the accumulation of the Aβ deposits and neurofibrillary tangles in the brain. Progress in understanding the biochemical and pathological alterations in AD is due to the finding of numerous genetic mutations. Early-onset familial AD represents a small fraction of all AD cases (≤5%), dominates in younger age (

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