Cancer remains a major public health challenge despite progress in detection and therapy. A large portion of the US population will develop cancer during their lifetime, with ΒΌ500 000 individuals dying annually from the disease. The race to obtain control over the disease process is gaining speed and focus. From biotechnology to chemistry, from applied physics to software, increasing resources are being brought to bear on the goals of prevention and reducing mortality. Innovations and applications of biotechnology have allowed the exploitation of biological processes in an effort to study pathogenesis at the molecular level. Novel technologies that are designed to advance the molecular analyses of healthy and diseased human cells are poised to revolutionize the field of health and disease. Advances in the fields of genomics and proteomics are hoped to provide insights into the molecular complexity of the disease process and thus enable the development of tools to help in treatment as well as in detection and prevention.

Among the important tools critical to detection, diagnosis, treatment, monitoring, and prognosis are biomarkers. Biomarkers are biological molecules that are indicators of physiologic state and also of change during a disease process. The utility of a biomarker lies in its ability to provide an early indication of the disease, to monitor disease progression, to provide ease of detection, and to provide a factor measurable across populations. The initial draft of the human genome has set the pace for biomarker discovery and provided the impetus for the next level of molecular inquiry, which is represented by functional genomics or proteomics. Proteomics is the study of the complete protein complement, or the proteome of the cell. In contrast to the genome, the proteome is dynamic and is in constant flux because of a combination of factors. These include differential splicing of the respective mRNAs, posttranslational modifications, and temporal and functional regulation of gene expression. Proteomic technologies allow for identification of the protein changes caused by the disease process in a relatively accurate manner. The inherent advantage afforded to proteomics is that the identified protein is itself the biological endpoint. At the protein level, distinct changes occur during the transformation of a healthy cell into a neoplastic cell, including altered expression, differential protein modification, changes in specific activity, and aberrant localization, all of which may affect cellular function. Identifying and understanding these changes is the underlying theme in cancer proteomics.

Genomics-based approaches to biomarker development include the measurements of expression of full sets of mRNA, such as differential display , serial analysis of gene expression, and large-scale gene expression arrays. However, interpreting the best data and adapting the results to a particular application remain challenging. Although studies of differential mRNA expression are informative, they do not always correlate with protein concentrations. Proteins are often subject to proteolytic cleavage or posttranslational modifications, such as phosphorylation or glycosylation. Cancer biomarker discovery strategies that target expressed proteins are becoming increasingly popular because proteomic approaches characterize the proteins, modified or unmodified, involved in cancer progression.

Two-dimensional gel electrophoresis has been the mainstay of electrophoretic technology for a decade and is the most widely used tool for separating proteins. Initially described 25 years ago, proteins in a two-dimensional gel are separated in the first dimension based on their isoelectric points and then in a second dimension based on their molecular masses. In many cases, two-dimensional gel electrophoresis may evaluate whole-cell or tissue protein extracts. The use of narrow, immobilized pH gradients for the first dimension increases resolving power and can help detect low-abundance proteins. Radioactive or fluorescent labeling and silver staining allow visualization of hundreds of proteins in a single gel. Differences between the samples can be compared and relative quantities determined by quantifying the ratios of spot intensities in independent two-dimensional gels. Matrix-assisted desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) allows the analysis and identification of very small amounts of protein isolated from the gel. These advances have combined to make two-dimensional electrophoresis a more attractive option for the analysis of complex protein mixtures. A brief overview of complementary and other rapidly evolving proteomic technologies is provided below.

Source: Pother R. Srinivas, Mukesh Verma, Yinming Zhao, Sudhir Srivastava