Proteomics

Proteomics looks for patterns among proteins. The term "proteomics" was first coined in 1997 as an analogy with genomics, the study of the genes. The word "proteome" is a blend of "protein" and "genome".

The proteome is the entire complement of proteins, including the modifications made to a particular set of proteins, produced by an organism or system. This will vary with time and distinct requirements, or stresses that a cell or organism undergoes.

Since genes provide the design for producing proteins, proteomics is often considered the next step after genomics in the study of biological systems. However, proteomics is much more complicated than genomics. This is because while an organism's genome is more or less constant, the proteome differs from cell to cell and from minute to minute depending on the activity of specific genes. This makes interpreting a protein measurement difficult.

	Image Courtesy of U.S. Human Genome Project

Whereas genomic studies of cancer usually require tumor tissue, proteomic studies can use blood or urine samples to look at proteins circulating throughout the body.

How Does the Proteome Compare to the Genome?

The biggest conceptual challenge inherent in proteomics lies in the proteome's increased degree of complexity compared to the genome. For example:

• One gene can encode more than one protein. The human genome contains about 21,000 protein-encoding genes, but the total number of proteins in human cells is estimated to be between 250,000 to one million.
• Proteins are continually moving and undergoing changes such as binding to a cell membrane, partnering with other proteins, or breaking into two or more pieces. The genome, on the other hand, is relatively static.
• Cells are continually modifying proteins once they are produced. As a result, the types of proteins measured can vary considerably from one person to another, under different environmental conditions, or even within the same person at different ages or states of health.
• Proteins exist in a wide range of concentrations in the body. For example, the concentration of the protein albumin in blood is more than a billion times greater than that of interleukin-6, making it extremely difficult to find the low- abundance proteins in a mixture.

Implications of Proteomics for Medical Practice

"The world of personalized medicine today is very gene-centric. This is not surprising given that genomic studies are among the most promising strategies to help advance personalized medicine efforts. However, while genomics will always remain a cornerstone of personalized medicine, these studies alone cannot capture the complete view of disease processes.

		While genes are the 'recipes' of the cell, containing all of the instructions for assembly, proteins are the products of these recipes, functioning as the cellular "engines" that drive both normal and disease physiology. So while genomics may provide the likelihood of developing a certain disease, proteins may diagnose what is happening in a patient in real time. Together, these complementary fields (genomics and proteomics) are absolutely necessary for understanding the molecular underpinnings of disease and for enabling personalized medicine." - Quote from National Cancer Institute

What Proteomics Means for People

A breakthrough in future cancer treatment was the discovery that tumors "leak" proteins and other molecules into blood, urine, and other accessible bodily fluids.

This insight has led to the possibility of diagnosing cancer at an early stage simply by collecting such fluids from patients and testing them for the presence of cancer-related molecules, also called "cancer biomarkers/tumor markers". The greatest promise for the early detection and treatment of cancer lies in the ability to find valid molecular indicators, or biomarkers, of the disease.

Progress in cancer genetics has been rapid, but this provides us with only a glimpse of what may occur. We need to measure what is happening inside a patient in real time, and that means finding tell-tale protein biomarkers. This is because genes are only the "recipes" for the cell. The proteins encoded by the genes are ultimately the critical molecular players that drive both normal and disease physiology.

The earlier a patient's cancer is diagnosed the more treatable it is by surgery, radiation or chemotherapy. Biomarkers found in blood and other fluids might also be valuable for monitoring the response of cancer during treatment or detecting the recurrence of tumors after treatment.

Certain blood proteins are already being used as cancer biomarkers.

Here are two examples:

• Prostate specific antigen (PSA): Elevated levels may suggest the presence of prostate cancer.
• Cancer antigen 125 (CA-125): Elevated levels suggest recurrent ovarian cancer.

		Unfortunately, both tests may result in: False negatives - failure to detect cancer in those who have it (poor sensitivity), or False positives - a positive test result for the presence of cancer in people who are actually cancer-free (poor specificity).