There have been vast advances in research due to constantly improving proteomic technologies. Clinically, proteomics has the potential to improve the process and time taken in validating and discovering protein biomarkers. Biomarkers are used as an indicator to signal activities in biological samples. They can help to improve the development and discovery of new therapies and personalise the treatment and prevention of diseases. However, even with considerable developments in technology, some problems remain. For example, if the sensitivity of detection of proteins in mixture is greater and cost-effective assay is made more easily available, proteomics would then have made an even more significant difference in the field.
Proteomics techniques used in discovery of biomarkers
Separation techniques, together with technologies of mass spectrometry, aid in identification, quantification and characterization of proteins. With proteomics techniques, many types of proteins are now able to be identified from mixtures.
One example is the complexity of human plasma. Not all peptides will be detected by the mass spectrometer as some are only present in low abundance. Hence, this will reduce the number of proteins that can be identified (J.P. Wery, 2007). In order to solve this problem, multi-dimensional separation techniques were used.
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One- or two-dimensional sodium dodecyl sulphate polyacryamide gel electrophoresis (1D or 2D SDS-PAGE) separates proteins according to their molecular weight and isoelectric points (pI). In the process of isoelectric focusing (IEF), proteins travel along a stable pH gradient just to find a position where they can remain in a state with no net charge. A stable pH gradient can be generated with immobilized pH gradient (IPG) or carrier ampholytes. However, IPG strips are more preferred over carrier ampholytes as it improves the reproducibility of such protein separation method.
Other methods include reverse phase (RP) high performance liquid chromatography (HPLC) and prefractionating samples chromatographically or electrophoretically before RP separations (J.P. Wery, 2007).
Using better separation techniques, acquiring the data for analysis of proteomics samples is equally important. MALDI (matrix assisted laser desorption ionization) can be used to obtain the ion spectra of the samples. MALDI uses molecules that absorb energy at laser wavelength. In addition, another method is to use electrospray ionization (ESI). In this method, analyte will be ionised from a solution and transferred to a gas phase (A. Vlahou, 2004).
Biomarkers in cancer
Biomarkers in cancer are produced by either the tumour or the host system that responses to the tumour. It can be quantified and used as an indicator of any potential or future disease state. These biomarker molecules detect tumour and allow treatment to be carried out appropriately through therapeutic interventions (Ullah and Aatif, 2009).
Cysteine protease and serine protease are two examples of cancer biomarkers. The former is usually upregulated in many types of human cancer and the latter can be found in many types of tissues. Cancer development has been proven to correlate with localization and differential expression of cysteine cathespins. A variation in the level of it indicates a few pathological states such as cancer (Ullah and Aatif, 2009). Serine proteases are used to associate with a variety of normal physiological functions (Ullah and Aatif, 2009).
Biomarkers in cardiovascular disease
Cardiovascular disease has been a serious health problem in developed countries as it is a major cause of death. Usually, a complication of thrombus plus thickening of arterial wall will cause stroke or acute coronary syndrome (MartÃn-Ventura JL et al., 2009). Hence, to find a method to predict the risk of an individual suffering from such a cardiovascular disease is a huge challenge.
Since blood is involved in formation of thrombus, molecules released from the vascular wall into the bloodstream can be used to show the pathological processes taking place there. Theoretically, the biomarkers for cardiovascular diseases could be molecules that are involved in pathological processes in atherosclerosis (MartÃn-Ventura JL et al., 2009.
Biomarkers in diabetes
The state of pre-diabetes and type 2 diabetes mellitus (DM2) are caused by glucose intolerance (GI). Peripheral resistance to insulin is proven to be involved in cause of heart diseases and development of endothelial dysfunction (E.C. Pereira et al., 2008). A decrease in nitric oxide (NO) and inactivation of it by other lipid peroxidation products will result in hyperglycemia. Thus, a concentration of nitrate and blood plasma nitrite, known as NOx, is used as a biomarker for diabetes by indicating activity of nitric oxide synthase and production of NO (E.C. Pereira et al., 2008).
Biomarkers in neurological disorders
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Lastly, like all the other types of biomarkers mentioned above, the identification of biomarkers for neurological disorders also has its own set of challenges. Example of some of the challenges is that the complexity of the brain makes the techniques for diagnosis of diseases tough and there is a lack of models for validating biomarkers for neurological diseases (Dunckley et al., 2005). The availability of tissue at the site of pathology is also another problem.
In the discovery of biomarkers for neurological disorders, proteomics techniques such as 2D gel electrophoresis (2DE) and liquid chromatography are used to identify the cause of diseases. (Dunckley et al., 2005)
Discovery of various biomarkers for the different diseases has been hindered by various challenges and limitations. However, with a combination of different methods to identify biomarkers such as modern proteomics and metabolic technologies, faster identification of biomarkers would be possible and clinical diagnosis of patients would accelerate.