Functional proteomic studies

Over recent years, oncology has been a key focus of proteomic technologies as applied in both expression and functional studies. Expression proteomic studies are screening for differences in protein patterns between tumor and control tissues. Functional proteomic studies are defined as the combination of readouts with proteomics data from the same sample at different points of time (under different conditions), with the aim of detecting and prioritizing certain proteins or polypeptides of functional relevance. 

Most functional proteomic studies have been performed in cancer cell lines, that is, after exposition to toxicants, RNA inhibition, differentiation agents, viral transfection, and so on. These studies covered several aspects of mutagenesis, tumor promotion, and progression. In the recent years, it has been shown that repeated analysis of the proteome at different tumor stages also deliver distinct patterns and thus a functional picture of disease progression at the molecular level. 

Reymond MA, Steinert R, Kahne T, Sagynaliev E, Allal AS, Lippert H. Expression and functional proteomics studies in colorectal cancer. Pathol Res Pract 2004 200(2) 119-127. Review. 

The establishment of species- and tissue-specific protein databases provides a foundation for proteomics studies of diseases. Continual development will lead to functional proteomics studies, in which identification of protein modification in conjunction with functional data from established biochemical and physiological methods enables the examination of interplay between changes in a proteome and the progression of diseases. Recently, many investigations provided direct evidence for PTM in the pathophysiological progression of many diseases like diabetes, Alzheimer s diseases (AD), atherosclerosis, and oncogenesis. 

I. D. Wilson, J. K. Nicholson, J. Castro-Perez, J. H. Granger, K. A. Johnson, B. W. Smith, and R. S. Plumb. High Resolution Ultra Performance Liquid Chromatography Coupled to oa-TOF Mass Spectrometry as a Tool for Differential Metabolic Pathway Profiling in Functional Genomic Studies. J. Proteome Res., 4(2005) 591-598. 

There is now a growing interest in proteomic studies of brain synapses. Recent studies have revealed a high molecular complexity in the pre- and postsynaptic areas, with thousands of proteins [6]. An important investigation for the future is to identify posttranslational modifications, miscoded as well as misfolded proteins, likely to have an impact on different aspects of synaptic function as a response to the environment as well as to the lifestyle. The first challenge is to identify and quantify the presence and variation of different proteins in key structures of the pre- and postsynaptic areas in order to relate protein structures to synaptic function. Recently, a new model has been presented describing the molecular complexity of the synapse with important aspects in emotions, thinking, memory, and consciousness [7] (Fig. 17.2). 

Mass spectrometry has been applied mainly in proteome research, but also in discovery and quantitation of neuropeptides that are involved in pain mechanisms, such as nocistatin, substance P, or verification of, for example, the structure of endogenous morphine in the central nervous system. Some proteomics studies of pain are aimed at the search for pain markers in cerebrospinal fluid, as it may reflect changes in brain and spinal cord functioning. Another research area concerns proteome analysis in cancer pain using spinal cord tissue and animal models. 

The application of the improved MS techniques presented above with highly resolving separation methods, such as 2-D electrophoresis, capillary HPLC, and CE, resulted in the creation of a new science, proteomics63 While genomics, described by DNA databases, represents the ground stage of the cell, the study of the differential status of the cell, due to various stimuli or disease states, reflects the functional expression of protein products or proteomics. Proteomics studies are aimed at identifying the proteome, the network of proteins that define the... 

Hennessy BT, Lu Y, Gonzalez-Angulo AM et al (2010) A technical assessment of the utility of reverse phase protein arrays for the study of the functional proteome in non-microdis-sected hiunan breast cancers. Clin Proteomics 6 129-151... 

Research on microchip protein analysis has been very active for cellular protein functional assay, clinical diagnostics, and proteomics studies. Once again, the microfluidic technology plays an important role in protein assays. Immunoassay, protein separation, and enzymatic assay will be described in detail in subsequent sections. 

In contrast, Functional Proteomics concerns the manner in which proteins interact and, in turn, how these interactions determine function, both normal and abnormal. This approach is less reductionist than Expression Proteomics as proteins are studied in the context of their complex cellular interactions. Finally, Structural Proteomics is concerned with the primary through tertiary structure of proteins, and modifications therein, largely determined by x-ray and NMR analysis of protein crystals (20). In this chapter we will concern ourselves only with Expression and Functional Proteomics. 

As mentioned earlier, Functional Proteomics is concern with the manner in which proteins interact and, in turn, how these interactions ultimately determine function and dysfunction. This approach is less reductionist than Expression Proteomics because proteins are studied in the context of their complex cellular interactions. 

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