Protein Arrays, Biochips, and Proteomics: The Next Phase of Genomic Discovery
Immobilization of proteins on the surface of arrays and neutralizing reactive areas after the immobilization are important practical issues in protein array. Many different types of proteins arrays such as antibody arrays and peptide arrays have been reported [ 73 ].
It starts research in breast cancer and leukemia [ 74 , 75 ]. Recently, one of the protein array technologies is the magneto-nanosensor array where giant magnetoresistive GMR [ 76 ] sensors are used to quantitatively measure analyte of interest proteins which are labeled with magnetic nanoparticles MNP. Another emerging protein array technology is Nucleic Acid Programmable Protein Arrays NAPPA [ 77 ], which have thousands of protein features directly expressed by nucleic acids on array surface.
More attentions have been paid to the role of protein arrays in medicine. They can be used for early detection of diseases, diagnosis of stages, stratification of patients, and prediction of therapeutic effects, and are increasing realization of the vision of personalized medicine. For cytokine measurements, protein arrays should be improved in both functional sensitivity and probe density.
Till now, the arrays have two major drawbacks: first, they are biased, because antigen selection is based on their potential to play a role in disease. Secondly, the analytical comprehensiveness of this technique is limited because only the molecules represented on the array can be identified. In the past few decades, the paradigm of biomarker research has shifted from a hypothesis-driven approach to a discovery-driven approach. Mass spectrometry and separation techniques and proteomics methods have been fully developed and have been common. These methods greatly increase the comprehensiveness of protein identification.
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Identify disease-associated antigens can elicit through immune responses by combining protein separation 2-DE, gel-free separation , immunological detection Western blotting and MS, or combining immunocapture and MS [ 78 ]. Proteins derived from cells or tissues e. In order to identify immunogenic proteins, the corresponding spots are separated from the gel and gels were digested. MS or tandem mass spectrometry is used for analysis and then analyzed by peptide fingerprinting or sequence tags method. LC—MS makes identification and quantification of target protein possible in a large and complex sample and most of the time it may not be achieved in the clinical work.
However, it will be useful when proteins are limited in a sample and at present this method will be considered as a supplement to 2-DE gel [ 79 , 80 ]. Antigen analysis of immunocapture MS is derived from the immobilization of antibodies in the serum of patients.
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Almost all antibodies are captured on protein A or G, which is a bacterial derived protein with specific affinity for the Fc domain of the antibody. Protein mixtures cell or tissue lysates are applied to a column or bead immobilized with antibodies to capture specific antigens of antibodies present in patient samples.
It can be a fully automated system allowing high-throughput and rapid identification. MS afford a method to identify a protein even from a complex mixture of proteins [ 81 , 82 ]. It is preferred and an applicable for a pure protein or a single spot for 2-DE gel.
Chemical defined or antibodies-coated protein biochip arrays for rapid protein detection. This system is used when small amount of samples is available. Very high surface expression of the immunoglobulin binding protein proACTR as the antigen capture and transfer reagent [ 83 ]. ProACTR can immobilize the antibody through the Fc region of antibody, and allows for higher capture capacity than antibody-coated beads.
It starts its diagnosis research with post-translationally modified proteins and high-throughput technique in breast cancer, lung cancer and prostate cancer. Unfortunately, it does not allow reliable protein sometimes [ 84 , 85 ].
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To the best of our knowledge, immunoproteomics with proACTR has not yet been applied to profile antigens associated with a certain disease, but mainly to the quantification of a single target [ 86 , 87 ]. The 2-DE for tissue sample is more complex than that for serum. Tissue from ovarian chocolate cysts or from eutopic endometrium contains connective tissues, red blood cells, epithelial cells and stromal cells.
Stringent protocols are adopted to ensure uniformity throughout the process to facilitate the protein maps. However, the development of robust assay platforms and standardized protocols are required before MS-based antigen profiling can be performed in the clinical setting. However, 12 cases of non-EMs ascites were analyzed as control 6 cases of infertility, 6 cases of normal fertile. There was no significant difference between the infertile controls and the normal fertile control group. However, the patients with mild EMs had protein reductions associated with several peritoneal protein spots of approximate molecular weights of 35—40 kD and pI close to 5.
Most of these proteins have not been further described in the existing literatures, so it is still unclear whether the aforementioned results can be used as diagnostic markers for EMs.
Compared with the controls, one beta chain isoform HpbetaE; molecular weight But the expression of HpbetaE in the control group was obtained to be related to the stage of menstrual cycle. The above studies indicate that changes in the protein expression profile of patients with endometriosis.
Protein Arrays, Biochips and Proteomics: The Next Phase of Genomic Discovery
The endometriosis diagnostic model had a sensitivity of The sensitivity was It provides an approach for screening the plasma markers of endometriosis. Several molecules had aberrant expression in peritoneal fluid of women with endometriosis may be useful for a better understanding of the pathogenesis of this disease. The normal human serum and patient serum were compared with the total protein of endometriosis.
In patients with endometriosis, 13 protein spots were associated with 11 known proteins, while 11 protein spots were found differently expressed in the endometrium of patients with and without endometriosis.
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Some proteins may be cytoskeleton, some may regulate in cell cycle, signal transduction or immune function participation. The hybridization of vimentin, beta-actin and ATP synthase beta subunit in serum of patients with endometriosis was significantly different from that of normal serum. ATP synthase may play an important role in ectopic endometrium as it needs invasive, and cell adhesion and cytoskeletal remodeling.
Studies have shown that the expression of these proteins is up-regulated in the endometrium in patients with endometriosis. These proteins have a certain effect on the formation of endometriotic lesions. Given that the occurrence of endometriosis may be due to an abnormality of eutopic endometrium itself.
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