Caitlin Smith has a B.A. in biology from Reed College, a Ph.D. in neuroscience from Yale University, and completed postdoctoral work at the Vollum Institute.
First genomics mapped the genome. Then came proteomics and the proteome. Now lipidomics is taking a crack at the lipidome.
Lipidomics identifies, classifies, analyzes and quantifies the wide range of lipids found in biological systems—that is, the “lipidome.” A subgroup of metabolomics, lipidomics also examines lipids’ interactions with other types of biological molecules and the metabolites that result from lipid use and production.
Though once regarded largely as cellular junk, material to be eliminated before getting to the more interesting proteins and nucleic acids, lipids are now known to play key roles in nearly every important biological process and structure, including energy metabolism, cell membrane structure, organellar membrane structure, intracellular trafficking and cell-signaling networks.
Given these crucial roles, perhaps it’s not surprising that many researchers are now focusing on lipids’ contributions to disease. When the genetic sequences for enzymes involved in lipid metabolism became available, the lipidomics field “exploded with important discoveries in many aspects of human diseases, such as cancer, cardiovascular diseases, neurological disorders or diabetes,” says Besim Ogretmen, a biochemistry professor at the Medical University of South Carolina (MUSC).
Recent technological advances not only are helping researchers expand their understanding of lipid metabolism, but also may help clinicians develop treatments for challenging diseases.
Mass spectrometry advances for all
It is no coincidence that growth in the field of lipidomics over the past decade has paralleled technological advances in mass spectrometry. Indeed, the two are inextricably linked.
“Advances in mass spectrometry [are] really at the heart of the field of lipidomics, although the use of NMR [nuclear magnetic resonance] and other high-precision instrumentation has also contributed much to recent advances,” says H. Alex Brown, professor of pharmacology at Vanderbilt University School of Medicine. Over the past decade, he says, considerable progress has been made “in the development of methodologies and chemically defined standards that are essential to quantitative analysis.”
One key method is the coupling of soft ionization techniques, such as electrospray ionization, to tandem mass spectrometers, including triple quadrupoles and ion traps. Brown’s lab, for instance, has used a Finnigan (now Thermo Fisher Scientific) TSQ Quantum triple quadrupole mass spectrometer to profile some 250 lipids in human and mouse nonalcoholic fatty liver disease [1]. Other studies from his lab have used an AB SCIEX 4000 QTRAP hybrid triple quadrupole/linear ion trap mass spectrometer, among other instruments.
“A few years ago, only a handful of investigators could conduct this kind of detailed analysis,” Brown says. “In the past, many investigators did not consider lipid or intracellular metabolite changes as part of their studies, because the analysis was too complex or not available.” Today, however, it’s easier for scientists—even those outside lipidomics—to address lipids, because techniques such as mass spectrometry have become more routine.
The importance of mass spectrometry in lipidomics is evidenced by its central role in facilities such as the Lipidomics Core Facility at MUSC, which provides services for researchers worldwide and includes both triple quadrupole and hybrid quadrupole/ion trap mass spectrometers. Ogretmen, who leads the Lipid Signaling in Cancer Program at MUSC’s Hollings Cancer Center, uses the facility for his research today, but remembers when—not so long ago—such tools were unavailable.
“About eight to 10 years ago, we had to measure sphingolipids and other complex lipid molecules using very time-consuming and labor-intensive techniques, which were not very accurate and could not distinguish subspecies of sphingolipids,” Ogretmen says. “Today we can simply send our specimens to the Core Facility and get our quantitative measurements in a very short amount of time.”
One of the most exciting advances in lipidomics is the ability to image the spatial distribution of lipids within tissue sections using imaging mass spectrometry (IMS). IMS is useful for mass profiling experiments or for estimating the relative spatial abundance of lipids in tissue when imaged with higher resolution. “For example, using MALDI [matrix-assisted laser desorption ionization]-imaging coupled with liquid chromatography/mass spectrometry, we are now able to follow lipid-based compounds or their metabolites to identify in which tissues they localize, and how much they accumulate in a given experiment,” says Ogretmen.
Lipidomics vs. disease
Lipidomics researchers are already directing their research at therapies for difficult-to-treat diseases. “We are now able to see how these [lipid metabolism] pathways are involved in challenging problems like treating diabetes, obesity, cancer and infectious diseases,” says Brown. “This is opening up an entirely new set of targets for therapeutic intervention.”
Michel Lagarde, professor in the Multidisciplinary Institute of Biochemistry and Lipids at the Université de Lyon, France, focuses on functional lipidomics of fatty acids and metabolites. He says it is not enough to study lipids and their metabolites in a snapshot of time and advocates a more holistic view. “We are interested in the metabolism of polyunsaturated fatty acids, especially of the omega-3 family, in vascular diseases such as metabolic syndrome, diabetes and stroke,” he says. “The challenge for the future is ‘fluxomics’ of lipids, meaning quantitative measuring of lipid precursors and metabolites in function of time in various compartments.” He calls this approach fluxolipidomics—studying the flux of lipids and their metabolites as part of a living biological system.
Ogretmen’s lab studies the role of sphingolipids in the regulation and treatment of cancer, using lipidomics methods to measure changes in levels of bioactive sphingolipid molecules such as ceramide, whose diverse functions suggest different strategies for combating cancers of the lung, breast and head and neck.
“We use a lipidomics approach to measure sphingolipid molecules in a global way using mass spectrometry in various specimens and conditions, such as in tumor vs. normal tissues, or in cancer cells with or without treatment with anti-cancer agents,” Ogretmen says. “Then we follow these lipidomics measurements with molecular and pharmacological approaches to dissect the roles and mechanisms of sphingolipid molecules in the regulation of cancer growth, proliferation, and resistance to anti-cancer therapy.”
The work isn’t easy. One of the main challenges lipidomics researchers encounter is in extracting and solubilizing the lipids. There aren’t universal protocols for the procedure, as every type of tissue is unique in its composition, structure, and lipid contents. Also, some lipids exist in complexes with other types of molecules, such as glycolipids or lipoproteins. These lipids can usually be released using an acid treatment that breaks bonds holding the complexes together. Then the lipids are extracted from the remaining material using an organic solvent. Complications can arise, however, in removing nonlipid contaminants from the sample, inactivating lipolytic enzymes and protecting lipids from hydrolysis or oxidation.
Overall, says Ogretmen, it’s a process that’s overdue for a makeover. “New and innovative techniques for the extraction and measurement of specific lipid molecules ... and for defining lipid-protein interactions that regulate various biological processes are needed to take the lipidomics field to the next level,” he says.
Capturing lipids of interest
Lipids aren’t interesting only from the perspective of disease, of course; they’re interesting in their own right. For instance, by comparing the human lipidome to that of worms, flies, yeast and bacteria, researchers can gain insight into evolutionary biochemistry.
Markus Wenk, associate professor of biochemistry at the National University of Singapore, studies variations among lipidomes, both over time and with changes in physiological conditions such as diet. His lab also is working on new methods to capture and extract lipids according to their different chemistries.
“Selective recognition of lipids is evident for a few select cases where cell-surface receptors are known,” he says. “However, several recent developments suggest that the chemical diversity of other lipids found in nature might have to do with much more selective interactions with lipid and protein counterparts. Some of the principles underlying these interactions might allow us to develop new and more specific capture devices for lipids.”
Wenk’s group also relies on chromatography and mass spectrometry to characterize and measure lipids. Because of the increasing interest in lipidomics, Wenk is seeing higher demand for education and training in these techniques—which is one reason he organizes and hosts the workshop-style International Singapore Lipid Symposium (ISLS) for ongoing education and communication about lipid research. Another reason Wenk organizes ISLS is that the nascent field of lipidomics is not yet structured into the groups and societies found in other research communities (such as genomics and proteomics, for example). “We are supporting such community-building with ISLS,” Wenk explains.
The fast progress in lipidomics over the past decade may be only a foreshadowing of what’s to come in the next. “I believe that the lipid metabolism and signaling field has been under-represented in the scientific community,” says Ogretmen. “I expect that there will be an explosion of new and exciting discoveries that uncover the roles and mechanisms of lipid molecules for the regulation of various important biological processes during the next decade.”
Reference
[1] Gorden, DL, et al., “Increased Diacylglycerols Characterize Hepatic Lipid Changes in Progression of Human Nonalcoholic Fatty Liver Disease; Comparison to a Murine Model,” PLOS ONE, 6(8):e22775, 2011.
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