Proteomics

A recent proteomic discovery in inflammatory breast cancer (IBC) is already in a phase 1 clinical trial. Through the collaborative work of Chip Petricoin & Lance Liotta at George Mason University and Fredika Robertson at M.D. Anderson, ALK (a protein called anaplastic lymphoma kinase) a key driver in human IBC samples was identified. As stated, this is still early stage research but it is already in the clinic in a phase 1 trial because there is a compound targeting ALK currently approved for use in lung cancer. While this won't be a treatment option for all patients, it is another step in personalized medicine to aid those with this deadly form of breast cancer. It is hoped that continued proteomic exploration will identify additional therapeutic targets.
http://www.eurekalert.org/pub_releases/2011-11/gmu-gmu111411.php Proteomics is currently not used in a clinical setting to treat cancer patients. Rather proteomics is at the interface of basic science and clinical research. This type of research is termed “translational research”. For example biomarkers discovered by proteomics will need to go through several rounds of independent and rigorous validations. Markers that are validated and shown to provide clinical applicability (i.e. improved diagnosis, prognosis or treatment stratification) could then be integrated into a clinical setting. Based on results obtain by a proteomics experiment sensitive yet simple assays need to be developed to be applicable in a routine clinical setting.

Proteomics is a modern version of protein biochemistry. It combines methods and approaches from classic protein biochemistry with analytical chemistry and computer science to study the “proteome”. The proteome is defined as the entirety of proteins expressed by an organism, tissue, cell or organelle at any given time. In contrast to the genome, the proteome is highly dynamic, therefore reflecting changes throughout development, external influences (i.e. environment) and/or disease. Proteomics is a specific scientific discipline to study the proteome. This new type of science termed “systems biology” has the goal to study an organism at the systems level (i.e. obtaining information on all proteins present in a cell, rather than studying a single protein and/or pathway). In terms of cancer research, proteomics has several main applications. First, model organisms such as cell culture models or animal models are used to study basic mechanisms of cancer research. These could be identification of changes in the cellular proteome in cancer cell lines in response to a treatment, identification of protein targets of a given drug, etc. Similar approaches are also applied using banked human tissues from biopsies or surgery. A second application of proteomics in cancer research is for the discovery of biomarkers. A biomarker is a biological substance (i.e., protein, lipid, post-translational modification, etc.) that is used to evaluate the presence, progression, or treatment-response of a disease. To be clinically useful, a biomarker should be readily accessible (i.e. from body fluids) and provide sufficient sensitivity and specificity by minimizing false negatives and false positives. Since proteomics is a powerful tool to identify and quantify hundreds to thousands of proteins in a single sample intense research has been focused on proteomics-based biomarker discovery. The main analytical platform that is used to study these questions is mass spectrometry, a powerful tool for the identification and quantification of proteins in complex systems. Proteomics is a modern version of protein biochemistry. It combines methods and approaches from classic protein biochemistry with analytical chemistry and computer science to study the “proteome”. The proteome is defined as the entirety of proteins expressed by an organism, tissue, cell or organelle at any given time. In contrast to the genome, the proteome is highly dynamic, therefore reflecting changes throughout development, external influences (i.e. environment) and/or disease. Proteomics is a specific scientific discipline to study the proteome. This new type of science termed “systems biology” has the goal to study an organism at the systems level (i.e. obtaining information on all proteins present in a cell, rather than studying a single protein and/or pathway). In terms of cancer research, proteomics has several main applications. First, model organisms such as cell culture models or animal models are used to study basic mechanisms of cancer research. These could be identification of changes in the cellular proteome in cancer cell lines in response to a treatment, identification of protein targets of a given drug, etc. Similar approaches are also applied using banked human tissues from biopsies or surgery. A second application of proteomics in cancer research is for the discovery of biomarkers. A biomarker is a biological substance (i.e., protein, lipid, post-translational modification, etc.) that is used to evaluate the presence, progression, or treatment-response of a disease. To be clinically useful, a biomarker should be readily accessible (i.e. from body fluids) and provide sufficient sensitivity and specificity by minimizing false negatives and false positives. Since proteomics is a powerful tool to identify and quantify hundreds to thousands of proteins in a single sample intense research has been focused on proteomics-based biomarker discovery. The main analytical platform that is used to study these questions is mass spectrometry, a powerful tool for the identification and quantification of proteins in complex systems.