H. Alex Brown, Ph.D. is leading one of six national centers to identify every lipid species in the cell.
Counting fats: new consortium to map cellular lipids
Though fats are well-recognized contributors to the expanding waistlines of America, their roles in individual cells have been largely overlooked. Until now. Lipids –– cellular fats and oils –– are taking center stage as the focus of a new collaborative effort, supported by a $35 million grant from the National Institute of General Medical Sciences.
The Lipid MAPS (metabolism and pathways strategy) Consortium will identify and measure all the lipids within a cell and how they change during cellular signaling. This information is expected to shed light on a range of diseases including heart disease, cancer, arthritis and diabetes.
“The major killers in American society all have abnormalities in either lipid metabolism or lipid content,” said H. Alex Brown, Ph.D., Ingram Associate Professor of Cancer Research and Pharmacology. Brown is leading one of six national “lipidomics” centers, the consortium sites that will sift through and identify all of the lipids in the cell.
“The basic function of each of these lipidomics cores is to take on what’s never been attempted before in biology, and that’s to comprehensively identify every lipid species in a certain type of cell,” Brown said.
“These studies will provide unprecedented and important background, achieved more thoroughly because of the global effort, for the next phase of discovery concerning bioactive lipids,” said Lee E. Limbird, Ph.D., associate vice chancellor for Research.
Lipids come in many varieties and perform a wide range of cellular functions. They form the cell membrane, putting them in a prime position to participate in cellular signaling processes. That potential is only beginning to be fully appreciated, Brown said.
“Most scientists think of lipids as the gluey stuff in the membrane that holds the proteins in place,” he said. “Proteins and nucleic acids have always been considered the more important molecules.”
Lipid MAPS is the latest of five “glue grants” –– so named because they enable large-scale biomedical research projects by bringing together diverse groups of scientists. Brown’s group, then at Cornell University, was the lipidomics laboratory for the Alliance for Cellular Signaling (www.signaling-gateway.org), the first “glue grant” consortium. The Lipid MAPS initiative grew out of an appreciation that there were multiple classes of lipids that needed to be characterized and measured, Brown said.
“Traditionally, very few lipids could be measured at one time,” he said. “What we’ve developed is a technology called lipid arrays, where 300 distinct species of phospholipids can be simultaneously analyzed and their relative concentrations determined.”
Phospholipids are the focus of Brown’s lipidomics center; they are especially important to cell signaling and account for a large portion of the cell’s lipid pool. “We’re either blessed or cursed, depending on how you want to look at it, since our core alone will be responsible for identifying at least half of the lipid species in the cell,” Brown said.
Brown continues to participate in the Alliance for Cellular Signaling; his group is one of only two that are involved in multiple glue grants. “Alex is very unique in that he represents the intersection between Lipid MAPS and the Alliance for Cellular Signaling,” said Lawrence J. Marnett, Ph.D., Mary Geddes Stahlman Professor of Cancer Research, Biochemistry and Chemistry. “He’s an important bridge between these two huge initiatives.”
All of the Lipid MAPS Consortium lipidomics centers will be taking advantage of the techniques pioneered by Brown and his team since they came to Vanderbilt just one year ago. Brown, who was recruited by the department of Pharmacology and the Vanderbilt Institute of Chemical Biology, had the goal of developing high throughput technology for measuring cellular lipids. The work has advanced with “surprising speed,” says Heidi E. Hamm, Ph.D., Earl W. Sutherland Jr. Professor and Chair of Pharmacology.
“Alex and his team have, in recent breakthroughs, shown that they can detect even the extremely rare lipid species that are most likely to be involved in key cellular processes such as cell signaling and vesicle trafficking,” she said.
“It makes eminent sense that metabolites that arise out of the membrane pool of lipids will be signaling mediators,” Marnett said. “They’re right there when an extracellular signaling molecule hits the cell surface. Lipids are at the center of all biological communication now.”
The cell of choice for the Lipid MAPS effort is the macrophage, a white blood cell involved in the primary immune response. The macrophage has a rich history in terms of cell signaling research, Brown said, and it is amenable to genetic manipulation methods like RNA interference –– a powerful tool for defining signaling networks.
The Lipid MAPS lipidomics centers will identify all of the lipids in the macrophage not only at rest, but also under various stimulated conditions. “We’re especially interested in the new species of lipids that get created in conjunction with biologically relevant signaling processes,” Brown said.
“The ability of lipidomics to uncover completely novel lipids may well lead to the discovery of new synthetic and breakdown pathways,” Hamm said. “The enzymes making up those pathways may serve as drug targets for diseases as disparate as atherosclerosis, rheumatoid arthritis, cardiovascular disease and cancer.”
Even lipids themselves –– not just the enzymes that make them or take them apart –– are becoming important new drug targets, Brown said.
Another aspect of lipidomics that excites Brown is the idea of using “lipid profiles” as a way to further refine the molecular understanding of disease. He expects lipid profiles to add to the knowledge base being accumulated by gene arrays and proteomics efforts. Lipid changes may in some ways be a better measure of damage to a cell than proteins, Brown said, because they usually stick around longer.
Vanderbilt is one of very few institutions in the country with investigators pursuing all three technologies –– gene arrays, proteomics, lipidomics –– Brown said.
“We believe that by combining these technologies and cluster analyzing them against each other, we’re in a unique position to actually be able to molecularly dissect human diseases and develop improved prognostic and diagnostic indicators,” he said. Brown’s own interests focus on breast cancer, cardiovascular disease and neurodegenerative disorders.
It is advances in mass spectrometry that have made lipidomics possible, Brown said. Brown and colleagues have used refinements of electrospray ionization mass spectrometry (ESI-MS) and computational mathematical algorithms written by members of his team to directly identify the lipids in a complex mixture from a cell sample. The same approach will be applied to disease tissue samples. Vanderbilt’s investment in mass spectrometry –– along with its historical strengths in analytical and patient-oriented lipid biochemistry –– were factors in the NIH awarding the Lipid MAPS Consortium grant, Brown said. The new lipidomics center will be developed as part of the Mass Spectrometry Research Center.
“I’m excited about lipidomics being part of the center,” said MSRC director Richard Caprioli, Ph.D., Stanley Cohen Professor of Biochemistry. “It is the daily elbow-to-elbow interaction of investigators with great ideas and enthusiasm that moves research forward in giant leaps.”
Marnett, director of the Vanderbilt Institute of Chemical Biology, and Dr. L. Jackson Roberts II, professor of Pharmacology and Medicine, are also participants in the Lipid MAPS Consortium. Marnett will work with the lipidomics center based at the University of California at San Diego that is focusing on a category of lipids called eicosanoids –– products of the cyclooxgenase enzymes. Roberts will lend his expertise in the area of lipid oxidation.
Brown earned his Ph.D. in Neurobiology and Pharmacology from The University of North Carolina at Chapel Hill and completed postdoctoral training with Paul C. Sternweis, Ph.D., at the University of Texas-Southwestern Medical Center. During his tenure on the faculty at Cornell University, he was a Sidney Kimmel Foundation for Cancer Research Scholar.
The Lipid MAPS Consortium is under the leadership of principal investigator Edward Dennis, Ph.D., professor of Chemistry and Biochemistry at the University of California at San Diego. The consortium will involve more than 30 researchers at 16 universities and two corporations and will maintain a Web site to share its progress: www.lipidmaps.org.