 |
 |
 |
FDA Home Page | Search FDA Site | FDA A-Z Index | Contact FDA
| Email this Page To a Friend |
 |
By Raymond Formanek Jr.
While the genes that compose the human genome provide the building blocks for who we are, it's the proteins that do the heavy lifting within the body.
"A protein is like a mini-machine in your body that makes it work," says Rick Edmondson, Ph.D., a senior researcher at the Food and Drug Administration's National Center for Toxicological Research (NCTR). "Your muscles are made of protein. If you think that you want to pick up a cup, the proteins are the ones actually doing the work.
"Proteins break down the food you eat so it can be absorbed in a form your body can use. Proteins in your brain store your thoughts. Basically, proteins are what we are made of," says Edmondson, who oversees the NCTR's Center for Proteomics.
The completed human genome published in 2003 contained between 30,000 and 35,000 genes, far fewer than the 100,000 genes predicted by scientists when the project began in earnest in the mid-1990s.
Those genes contain the recipes for between 1 million and 5 million proteins. Many of those proteins are not new proteins. Some proteins become other proteins. Others are modified during metabolism and other body functions.
"When some proteins do their job, they may break down to another protein," says Raj K. Puri, M.D., Ph.D., director of the Division of Cellular and Gene Therapies at the FDA's Center for Biologics Evaluation and Research. "Then they may have another job to do."
All in all, it's the elegant, continuous interaction of your genes, proteins, and other biochemical actions inside your body that make you--you.
Nearly every cell in your body has two complete sets of chromosomes--one from your mother and another from your father. Deoxyribonucleic acid--DNA for short--makes up the core of those chromosomes and serves as the blueprint for another nucleic acid called ribonucleic acid (RNA). The areas of DNA that provide the code for RNA are organized into genes, and most genes contain information for making a specific protein.
The process of building RNA molecules using the DNA sequence code as a guide is called transcription. In turn, RNA molecules direct the building of specific cellular proteins from amino acids in a process called translation. These proteins directly regulate cellular functions including cell growth, responses to activity outside the cell, and cell death.
Put simply, proteomics is the study of the function of all expressed proteins. Initially, the term was used to describe the set of proteins coded for in the genome. But now proteomics is used by many to describe not only all the proteins of any given cell, but also the interactions, modifications, and much of what happens after gene expression.
"You can think of proteomics as profiling changes," says Daniel Casciano, Ph.D., director of the NCTR. "We are using proteomics for pattern recognition. We're taking protein samples--typically blood serum and sometimes urine--and looking for changes between a normal state and a disease state."
Much of the research being done at the NCTR centers on identifying the telltale molecular changes called biomarkers that are characteristic of a disease.
"Finding the protein or proteins associated with a disease or adverse event is going to lead to a much earlier identification of biomarkers," says Edmondson. "Someday, we'll be able to identify proteins in your body signaling that something is occurring long before the symptoms are visible."
For example, prostate-specific antigen (PSA) is a protein produced in a man's prostate gland. A test developed to measure the level of PSA in the blood allows physicians to use this biomarker to help diagnose prostate cancer. PSA levels, alone, do not provide enough information to distinguish between cancer and benign prostate conditions, but high levels of PSA may indicate that further tests for prostate cancer are warranted.
Edmondson's work focuses on pattern recognition--looking for changes in protein expression in blood serum taken from healthy and diseased tissue.
"It's sort of like ‘Sesame Street'--which one is most like the other?" says Edmondson.
Proteomics provides the opportunity for researchers to get a global view of the communications and always-changing events within a cell, instead of focusing on the more static singular gene, says Puri. "Proteins inside the cell talk to each other," he says. "They interact." This nearly constant back-and-forth between cells is called "cell signaling circuitry."
"It's a new way of looking at the biological process," according to Puri. Indeed. The term "proteome" was coined in 1994 by Marc Wilkins, an Australian postdoctoral fellow. Wilkins defined proteome as all the proteins being expressed in a given cell at a given time. He called the study of the proteome, proteomics.
Proteomics, like the other "-omics," is a young science. Many of the tools needed to identify and purify proteins were developed during the 1980s and early 1990s. And, while the progress in mapping the human genome has some thinking about doing the same with the proteome, the technology to do so doesn't exist--at least not yet.
But that hasn't slowed researchers armed with high-throughput systems capable of mining mountains of data in search of the defective proteins responsible for diabetes, arthritis, Alzheimer's, cancer and a host of other maladies.
"It's a different way of looking at things," says Puri. "If you can correlate gene expression with protein expression, you have a very powerful technology."
Besides disease, proteomics holds the promise of identifying early markers in blood and other body fluids of drug-induced damage to the heart and other body organs. Proteomics also may be used to develop tools to evaluate the purity, potency, and consistency of drug and biological products such as cellular therapies.
For the last 25 years, the mainstay in proteomics research has been two-dimensional gel electrophoresis (2DE), a process that separates large mixtures of proteins by their size and by their electrical charge.
The advantage of 2DE is that many proteins--3,000 to 10,000--can be separated visually. A disadvantage to using 2DE is that very large or very small proteins, proteins present in minute amounts, or certain kinds of proteins such as membrane proteins, are difficult or impossible to visualize using 2DE.
Since the mid-1990s, mass spectrometry has been used more and more to analyze complex protein samples. The technique itself is complex and involves the measurement of two properties--the mass-to-charge ratio of a mixture of particles with an electric charge (ions) and the number of ions present at each mass-to-charge ratio in a protein sample.
Mass spectrometry has an advantage over other technologies. It has the ability to detect and rapidly measure thousands of elements in several drops of blood quickly and cheaply using powerful computers.
The end product, called a mass spectrum, is a chart with a series of peaks, which each represent the ion present in a sample. The height of the peak is related to the amount of the protein in the sample. The size of the peaks and the distance between them provide hints on which proteins are present.
"Proteomics has provided an opportunity to look at the characteristics of cells," says Puri. "We now have a global view. Using biomarkers, you can compare medicine A and medicine B and how they work in a person."
Regulating the proteomics revolution won't be easy. Competition is fierce. Hundreds of new companies staffed by thousands of researchers have sprung up in recent years, drawn by the potential of identifying biomarkers or by the potential of developing treatments for defective proteins.
"It's an evolving field," says Puri. "The FDA has a major role to play as a regulatory agency."
Part of the challenge for the agency, according to Puri, is the variety of proteomics technology platforms used by scientists and the lack of standards. "There are different systems, even homemade systems in some labs," he says. "The FDA needs to stay current in these technologies in order to evaluate the products and their safety. We are interested in working to establish the standards that will allow us to validate data across different platforms."
The FDA is collaborating with technical experts, companies, and academic representatives who will help develop future guidance documents for proteomics and related rapidly growing technologies.
"There are many ways to look at the proteome," says Puri. "We have to understand the different platforms and set a standard."
The Human Genome Project and technical advances in computers during the 1990s set the stage for the proteomics revolution and the accompanying race among drug developers to find protein drug "targets."
Some are focusing their efforts on how proteins relate, how they change, what they do, and which are present in healthy tissue and which are evident in disease.
"When you are looking at millions of proteins at a time, you need bioinformatics, the organization and use of computers to analyze data and databases, to analyze the results," says Puri. "Are they meaningful or not?"
Researchers are learning that analyzing patterns of proteins, rather than identifying every protein active in a disease, may be sufficient to diagnose diseases such as cancer.
For example, National Cancer Institute and FDA scientists collected blood samples from a group of patients with diagnosed ovarian cancer and used mass spectrometry to obtain the protein profiles in the serum samples. While there was some variation from patient to patient, clinicians were able to determine what subset of proteins consistently was a biomarker to cervical cancer by pooling samples of those with confirmed ovarian cancer.
"The typical way to diagnose cancer is by having a pathologist looking at a slide containing cells," says Edmondson. "However, looking isn't always enough. Many times, there is a disease within a disease."
New technologies such as laser capture microdissection (LCM) allow scientists to capture single cells out of a section of tissue and to collect all the proteins contained in the selected cells. The protein patterns, if any, are then stored in a computer database.
LCM allows researchers to collect sets of cells from normal, cancerous, and precancerous tissue from the same biopsy sample.
"This new technology will allow us to design better drugs to better treat cancer and other diseases," says Edmondson.
From the Genome to the Proteome
U.S. Department of Energy Office of Science
http://www.ornl.gov/sci/techresources/Human_Genome/project/info.shtml