SYSTEMS BIOLOGY: A Boon for Analytical Chemists? Opportunities and challenges await those who are willing to take a ride on the But the innovation that really facilitated the birth ollowing on the heels of genomics, prosystems biology of modern systems biology was the development teomics, and metabolomics, systems biolof high-throughput technologies, such as automatogy is the latest buzzword. Instead of bandwagon. ed DNA sequencers for the analysis of entire genomes, spending years focusing on an individual gene, prohe says. Leroy Hood at the Institute for Systems Biology tein, or metabolite, many researchers are now taking a holistic “systems” approach to studying pathways, cells, and even (ISB) agrees: “We really couldn’t do the kind of systems bioloentire organisms. Although everyone has his or her own spe- gy we’re talking about now until the [Human] Genome Project cific definition of systems biology, most researchers in the field [HGP] was finished.” The HGP, he explains, gave researchers integrate results from high-throughput studies to test biologi- “the ultimate definition of all the elements in an organism—that cal models. Proponents of the approach say it could revolu- is, all the genes that encode proteins.” Systems biology also had its roots in MS. Fred Regnier of Purtionize how we study biology and develop medicines. But what does systems biology have to do with analytical due University says that after he co-founded PerSeptive Biosystems chemistry? Analytical techniques have been essential to the with Noubar Afeyan in 1996, they tried to conjure up a vision for growth of systems biology, according to researchers. Genomics, the fledgling mass spectrometer company. “Our idea was, because proteomics, and metabolomics techniques, for example, enable we made analytical measurement devices, that the future was one scientists to identify all or most of an organism’s genes, proteins, where it was becoming possible to measure large numbers of moland metabolites. And once these molecules are known, one can ecules and to understand what cells were doing by simply measurstart fitting the pieces together into a larger systems view of how ing everything—proteins, small molecules, and DNA,” he says. Relating patterns of biomarkers to particular diseases is simply an these molecules work together. Scientists have been attempting to model how cells and or- extension of that idea, Regnier points out. Because systems biology is integrative by nature, ganisms function for decades, according to Trey KATIE COTTINGHAM it demands that biologists work together with engiIdeker at the University of California, San Diego.
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neers, computational scientists, ods, MS is often cited as the most useful tool because of its high mathematicians, and chemists. sensitivity and versatility. But generating all the data in the world does little good if Hans Westerhoff at BioCentrum Amsterdam (The Nether- there’s no way to meaningfully analyze the data sets. According lands) says that no one person can do everything. “That’s why you to Ideker, data sets generated by high-throughput technologies were “all dressed up with nowhere to go” until bench scientists need consortia and collaborations between groups,” he says. But experts disagree on the extent to which analytical chemists and computational scientists found each other in the late 1990s. are currently involved in systems biology projects. Some re- Hood says, “Computational and mathematical tools allow you to searchers say that the rosters of systems and integrative SWI4 biology departments, centers, and institutes include EXG1,MNN1 PCL7,HSC82 CSI2,YGR086C ERG6 large numbers of biologists YDR451C and computer scientists but LYS20,YEL077C PDR12 ISU2,CCP1 few analytical chemists. SNQ2,CPA2 SOK2 TRP4,YIL177C MSN4 YIL056W YER189W,YKL051W Steve Naylor at the Boston YEL076W–C,YHR048W YER190W University School of MediYDR545W HAP4 YGR296W cine says that analytical chemists are often asked to SGA1 QCR2,COX9 YLR465C,YLR467W RPI1 YOR315W ECM13 UTR2 YBL029W YJR078W YNL339C,YLR463C simply provide a service, such as running samples on a mass spectrometer, for YPL283C systems biology projects. CUP9 YLR466W Catherine Fenselau at the University of Maryland, YBL113C,YML133C CLB1 YHL049C,YJL225C YFR006W College Park, has noticed YBL112C,YPR203W YER045C YAP6 ATR1 that scientists in other fields often undervalue analytical RPL19B YPS4,YEL047C chemists’ efforts. “I have a YNR067C YJL2I7W,AAP1 NCE102 YEL045C concern from some of my own interactions with physicians and other life scien- FIGURE 1. A model that was constructed with the program Cytoscape of protein–DNA interactions in yeast. tists that the analytical aspect is viewed by some as a service or a core facility contribution, handle all of this information and create models and formulate itwithout the understanding . . . that the analytical part is a research erative hypotheses that are an integral part of systems biology.” To contribution as well,” she explains. help researchers visualize their data from multiparameter experiOther researchers contend that analytical chemists are partic- ments, Ideker’s group and computational biologists at ISB have ipating in large numbers but that part of the problem is seman- developed a free, open-source program called Cytoscape (Figure tics. “It depends on how you define analytical chemists,” says 1). Different shapes represent proteins, genes, or metabolites. Ruedi Aebersold at the Swiss Federal Institute of Technology, Lines connect interacting molecules, and shading can be used to Hönggerberg (Switzerland). According to Douglas Kell at the indicate their abundances. Gene, metabolite, or protein networks University of Manchester (U.K.), “What it says on the doorplate can be superimposed, creating a complex web of interactions. doesn’t matter much to me. If you are analyzing complex sysWhen Naylor worked at BG Medicine (formerly called Beyond tems and developing methods for doing it, you’re an analytical Genomics), he and his colleagues attempted to fully characterize chemist whether you’re doing it in a molecular biology depart- the differences between a mouse model for atherosclerosis and ment or a chemistry department.” Kell points out that in the fall control mice; this was the first published systems biology study on of 2005 his laboratory will move to the Manchester Interdisci- a mammalian organism. “We were able to find at the gene-tranplinary Biocentre, which has been specifically designed to blur script, protein, and metabolite levels, many thousands of changes the lines between disciplines. that had occurred for a single gene insertion,” says Naylor. “It was staggering! But what was interesting was it was almost impossible to make any sense of it from a biological point of view.” Tools of systems biology The thought of undertaking a systems biology project can be Most of the methods used in systems biology are the same ones used in genomics, proteomics, and metabolomics: LC/MS/MS, daunting, but according to Aebersold, it doesn’t have to be. “I GC/MS, CE/MS, NMR, FTIR, Raman spectroscopy, protein think it is a misconception that systems biology always tries to microarrays, DNA sequencing, and DNA microarrays. Some re- study whole cells or organisms,” he says. “I think the same prinsearchers also add imaging techniques to the list. Of these meth- ciples are easily applicable to very well defined questions, such as
a particular signaling system in a cell or how a particular metabolic process is controlled.” In fact, Daniel Figeys at the Ottawa Institute for Systems Biology (Canada) says that it is extremely difficult to measure everything in a cell or an organism and that researchers are starting to study much smaller pathways. “I think it would be a bit naive to think that we will understand what nature has learned over billions of years. I don’t think that is the way to approach it,” he says. “I think if you’re looking at very focused systems, they will be able to provide answers.”
place still exists for classical reductionist projects in which single molecules are studied. The two approaches are complementary, according to Aebersold. “There might be a lot of excitement right now in systems biology, but clearly what’s coming out is the need to go back and do very detailed analyses of specific molecules discovered by high-throughput analytical methods. The more one knows about a molecule, the better the understanding of the network,” he explains.
More than the sum of its parts According to experts, studying systems is important because the whole can have different properties than could be predicted from knowing only the features of the individual molecules that comprise it. “The analogy that’s commonly used is if you have a piece of a bicycle or an airplane, it would be difficult to figure out what that piece actually did until you saw the [fully] assembled unit in operation,” says Dick Smith at the Pacific Northwest National Laboratory. Proteins, genes, and metabolites don’t function in isolation of one another. “There [are] all these levels of interaction and complexity between the individual genes and the proteins they make,” explains Ideker. Interactions are extremely important to consider when one is trying to understand how a system works. For example, Westerhoff cites the example of adenosine triphosphate (ATP) synthases. When these enzymes are removed from a cell, they hydrolyze ATP instead of making it. “So many things work the wrong way [in vitro] because they are not organized together with other molecules,” he says. Systems biology is still in its infancy, and only a few proof-ofprinciple papers have been published. Ideker, Hood, Aebersold, and colleagues coauthored one of the first papers that integrated results from proteomics and genomics experiments to fully describe a molecular network. In this study, the researchers used DNA microarrays and quantitative MS to find mRNAs and proteins that were differentially regulated in the yeast Saccharomyces cerevisiae when galactose was added to the growth medium. As the researchers collected data, they used the new information to tweak their model of galactose utilization. The systems approach enabled the team to uncover new levels of regulation that years of experiments on single molecules had failed to detect. In another example of the systems approach, Hood and Nitin Baliga, also at ISB, have studied the unicellular organism halobacteria. “We have delineated perhaps the most complete understanding of the functioning of interrelated biological networks of an individual organism,” says Hood. Researchers cite many potential applications of the systems biology conceptual framework. In addition to gaining insight into how pathways function in model organisms, they are using this approach to understand how some microbes produce hydrogen, to elucidate prostate cancer mechanisms, and to provide a virtual alternative to testing cosmetics on animals. Many scientists are excited about applying systems biology tactics to the development of more effective drugs with fewer side effects. Although systems approaches may eventually provide a treasure trove of valuable information, most researchers say that a
Opportunities and challenges Researchers say that the emergence of systems biology will help analytical chemistry and vice versa. “Analytical chemistry has been something of a Cinderella subject because a lot of it has been concerned with somewhat routine and unexciting measurements,” says Kell. But with the realization that systems biology needs innovative quantitative methods, Westerhoff says that analytical chemistry is becoming more attractive and is winning more advocates. According to Smith, systems biology “has provided an enormous incentive and justification for improving the analytical techniques that we have. The needs are almost openended . . . so there’s a strong driver for those who are involved in the development of analytical technology to make better and higher-throughput tools.” Analytical chemists are uniquely poised to address many of the limitations that systems biology approaches now face. Most researchers say that better separations techniques are necessary for the analysis of complex mixtures, such as plasma. More sensitive instruments would allow scientists to measure low-abundance molecules. Kell says that typical proteins and metabolites have a dynamic range of 6–12 orders of magnitude, which is difficult for current instruments to detect. Ideally, systems biology researchers would like to have instruments capable of even higher throughput than what they can handle today. “Once you take very sophisticated instruments and you measure the things that are changing as a function of a stimulus . . . you would like to do it with 100 patients or 1000 patients to make sure you’re right,” says Regnier. “We just don’t have the throughput with mass spec instrumentation and things like that to completely look at 1000 patient samples to study one stimulus. That is what’s necessary to fully enjoy all the fruits that the various systems biology approaches have to offer.” According to Smith, analytical chemists are developing faster approaches. For example, combining gas-phase ion mobility separations with conventional separations could reduce analysis time from hours to minutes, he says. Researchers also say that imaging techniques should be improved. Smith predicts: “One of the biggest things will be the development of better microscopies that will simultaneously follow many metabolites and individual proteins at very high spatial resolutions so that their localization within cells, and thus their function, can be better understood.” But analytical chemists are not the only ones who need to don their thinking caps. Mathematicians must develop new calculations to account for thousands of variables at once, says WesterM A Y 1 , 2 0 0 5 / A N A LY T I C A L C H E M I S T R Y
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hoff. Better computational tools to manage large data sets are also necessary, according to Ideker. Although technological challenges abound, some researchers say that the greatest hurdles for systems biology are more intangible. In fact, Hood says that one obstacle is “how to create groups that really have these critical masses of biology, technology, computation, and mathematics [and] that can effectively and coherently work together.” When Naylor recently organized a systems biology conference, for example, he noted that experts tended to socialize only with researchers in their own area of specialization. He says it is very difficult to break down barriers and to get researchers from diverse fields to converse with and understand each other. But other experts have a different perspective. Bringing together scientists from diverse areas is becoming easier, says Smith, particularly because U.S. funding agencies are beginning to recognize the benefits of these collaborations. Although Westerhoff also says that he has not experienced difficulties establishing interdisciplinary teams, he adds that European funding agencies have not been as progressive as those in the United States in encouraging large collaborations, particularly international ones. “In a small country like The Netherlands, when you want to do something and some [resources] that you need are just not pres-
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ent in the country . . . you can’t [easily] get funding to collaborate with other countries,” he says. Another issue is how to train the systems biologists of the future. Westerhoff wonders: Do you require students to study multiple disciplines, or do you train people to be experts in one field but also teach them communication skills? Also, academic institutions bestow tenure on researchers on the basis of their individual contributions. Hood says that the integration and collaboration that are so necessary for the success of systems biology projects are antithetical to the traditional tenure system. Clearly, many challenges remain for researchers interested in systems biology, but those challenges translate into opportunities for analytical chemists. Because of their unique skills, analytical chemists are well positioned to accelerate the development of systems biology and broaden its applicability. In fact, Hood predicts that systems approaches to disease will transform medicine during the next 10–20 years. As Regnier says, “I think we are in the era of discovering relationships and understanding things by looking at large numbers of patterns of chemical features, as opposed to looking at one substance at a time. The really exciting thing is that analytical chemistry can enable this.” Katie Cottingham is an associate editor of Analytical Chemistry.
