Leading the Pack
Maryland's Institute for Genome Sciences

By Jim Swyers, MA

Claire M. Fraser-Liggett, PhD

   There’s an old idiom that says: “If you are ahead of the pack, you have made more progress than your rivals.” Leading the pack in science is often a good position to be in. It not only means you’ve made more discoveries than others in your field but eventually you get more of the glory. However, being too far ahead of the pack can have its drawbacks—especially if the tools or technologies you need to make progress don’t yet exist.

This is a situation faced by researchers of the new University of Maryland School of Medicine Institute for Genome Sciences, or IGS. They not only have to be Jacks and Jills of all trades to keep their research projects running, but others in the field of genomic research look to them for innovation as well.

IGS is headed by Claire M. Fraser-Liggett, PhD, who came to Maryland from The Institute for Genomic Research (TIGR) in Rockville, Md. Fraser-Liggett was the president and director of research for TIGR for almost a decade. Under her leadership, TIGR researchers were intimately involved in a number of high-profile genome projects. Their work provided the first glimpses of the inner workings of some of the worst scourges to have plagued mankind, including cholera, malaria, tuberculosis, pneumonia, syphilis, Lyme disease, and hospital-acquired infections and food-borne illnesses. And, they developed many new experimental and computational approaches for the human genome project

During Fraser-Liggett’s tenure as TIGR’s director, she was the most highly cited scientist in the field of microbiology. Federal funding to the TIGR tripled from $20 million to $60 million per year under her leadership. Because of TIGR’s growing expertise in the genomes of microbes, in 2001, the FBI enlisted some of its top investigators to help hunt down the source of anthrax that was sent through the mail to politicians and journalists. TIGR researchers discovered a unique set of genetic mutations in the anthrax bacterium that were sent through the mail and used that “genetic fingerprint” to identify the master flask at Fort Deitrick, Md., from which the anthrax was taken. Although the FBI’s prime suspect in the case committed suicide before he could be charged, Fraser-Liggett recently told the New York Times, “I’m absolutely convinced the FBI has the right source flask.” She added in that article, however, that she was not prepared to opine as to who the perpetrator might be.

Fraser-Liggett left TIGR in 2007 when it was absorbed into the J. Craig Venter Institute. Fifteen senior TIGR researchers followed her to Maryland to help form IGS, giving it instant world-class expertise and visibility. “IGS is now recognized as one of the leading institutes in the world for microbial genomics,” says Fraser-Liggett.

Identifying Microbes
Microbes, which consist of bacteria, viruses, fungi, protozoa, and a relatively new group known as archaea, are the oldest form of life on earth, dating back approximately 3.8 billion years. By some estimates, microbes make up about 60 percent of the earth’s biomass. However, less than 1 percent of the known microbial species have been identified and studied.

Compared to humans, the genomes of microbes are relatively tiny. The human genome, for example, contains 24 chromosomes and approximately 25,000 genes. In contrast, a bacterial genome typically has only one chromosome and a few hundred to a few thousand genes at most.

IGS moved into its gleaming new offices and laboratories in the University of Maryland BioPark this spring. Its walls are adorned with cover designs of the many high-profile journal articles published by its investigators. The more than 50,000 square feet of space is dotted with cozy little alcoves that are just right for impromptu brain-storming sessions and small, informal meetings. The collective work of the IGS team has identified more than ten times the number of genes found in the human genome. And they now have the capacity to identify many, many more. IGS’ nine DNA sequencers, three of which are the newest and fastest available, can sequence an astounding 565 billion bases per year or more than 10 billion bases per week. That’s equivalent to about three human genomes per week.

One of the major advantages of being part of a medical school is ready access to patient samples. IGS, which currently boasts 80 full-time staff, including 17 senior faculty, has research projects studying the genomes of microbes found in every major organ system in the body.
Fraser-Liggett’s own laboratory is studying the microbial population, or microbiota, naturally present in the human gastrointestinal tract. There’s evidence that the changes in the microbiota of the colon can contribute to at least several intestinal diseases, including colon cancer, inflammatory bowel disease, and even obesity.

“If there are certain bacterial communities in the colon associated with cancer or inflammation or nutrient absorption disorders, we would like to know what happens to those communities as they change from beneficial to damaging. It is possible we may be able to develop a genetic fingerprint for a particular disease,” explains Fraser-Liggett.

The ultimate outcome of such a finding would be a more individualized approach to treatment for gastrointestinal diseases. “By knowing the code for what makes bacteria do what they do, we hope to be able to develop better strategies to control them if they cause disease, or maintain them if they’re important for good health,” adds Fraser-Liggett.

Jacques Ravel, PhD, who followed Fraser-Liggett to Maryland from TIGR, and who was a leading member of the team that decoded the DNA of the anthrax strains for the FBI’s investigation, also studies the microbes inhabiting the gastrointestinal tract and their link to celiac disease. Celiac disease is an autoimmune condition characterized by sensitivity to gluten, a protein found in wheat. His group is collaborating with Alessio Fasano MD, director of the University of Maryland School of Medicine Center for Celiac Research on a project to determine how celiac disease affects the microbiota of the intestine and vice-versa. To do this, they’re collecting and analyzing the stool samples from a group of babies at birth and then comparing those “baseline” microbiota readings to the children as they get older.

Hervé Tettelin, PhD

“We’re com-paring the microbiota of children on a gluten-free diet versus a gluten-added diet to see what happens to the GI microbes as a result of the autoimmune reaction to gluten,” says Ravel, whose laboratory also is investigating the microbial communities associated with the female reproductive tract.

In addition to microbes that coexist with but normally do not harm people, IGS researchers have a dual focus on those microbes that people don’t often come in contact with and that can put them at risk for serious disease and even death when they do. For example, Hervé Tettelin, PhD, another transplant from TIGR, is leading a group studying the genomes of microbes that cause bacterial meningitis. An infection of the lining of the brain or the spinal cord, bacterial meningitis can result in brain damage and even death if not quickly diagnosed and treated with the correct antibiotic. It is most commonly caused by one of three types of bacteria: Haemophilus influenzae type b, Neisseria meningitidis, and Streptococcus pneumoniae bacteria.

To develop a preventive vaccine against bacterial meningitis, Tettelin and his group are interested in which of the hundreds of proteins that protrude from the surface of these three types bacteria elicit the greatest immune response. Using genomics and what he describes as some “heavy duty” bioinformatics, Tettelin’s group was able to whittle down that list to only a handful of highly immune-stimulating, or antigenic, candidates. A new vaccine again based on those surface proteins is now in Phase III clinical trials to prevent bacterial meningitis caused by Neisseria meningitidis.

For another of its projects, Tettelin’s group is designing a novel database to house and compare the genomes of very closely related microbes. With the cost of sequencing DNA becoming increasingly less expensive, it is possible to rapidly sequence the genomes of many microbes. The idea behind Tettelin’s database is to study how slight genetic differences can lead to significant outward changes.
“We’re loading all these genomes from very similar microbes into this database to look at the small genomic differences between them that might tell us why one is benign and the other, which is very similar, causes disease or is resistant to certain drugs,” says Tettelin.
In addition to sequencing entire genomes of microbes, with its newer generation sequencing machines, IGS has the capability to look at what those genomes are up to. Only a fraction of genes are switched on, or activated, at any given time in an organism. By sequencing an organism’s entire genome, researchers find out what a microbe has the potential to do.

Sequencing the messages (i.e., messenger RNA) being sent out by the genome, gives researchers a much better look at which genes are active and which are not, according to Luke Tallon, PhD, another TIGR transplant who co-directs IGS’s genomics resource center. “If we can analyze the pattern of genes being actively expressed, we get significantly more and better information about what a microbe is up to at any given time in its life cycle,” says Tallon.

This “expression analysis” approach to studying genomes is still relatively new. It is a powerful tool, however, that several investigators at IGS are applying not only to studying microbes but also to a number of clinical problems in people. In one project, Tallon and Lisa Sadzewicz, PhD, of IGS, are collaborating with researchers at the VA Maryland Health Care System in Baltimore to apply expression analysis to the study of individual differences in HDL cholesterol levels. HDL cholesterol, which has been dubbed the “good” cholesterol, has been shown to scour the walls of blood vessels, cleaning out excess bad cholesterol (LDL cholesterol) and keeping a person’s cardiovascular system healthy. The goal of this study is to pinpoint subtle gene variations that influence whether an individual has high levels of this heart-protective molecule versus those who have lower levels.

By knowing the code for what makes bacteria do what it does, we hope to be able to develop better strategies to control them if they cause disease, or maintain them if they’re important for good health.
Genome diversity map of group B Strep based on microarrays. Courtesy of Hervé Tettelin, PhD.	Evolution of IncA/C antibiotic resistance plasmids. Courtesy of W. Florian Fricke, PhD

Managing Oceans of Data
Sequencing a genome or the messages being sent by the genome are extremely important scientific achievements. But, a genomic sequence is of little use without extensive post-production work. Just as a film editor adds special effects and music to a movie, genomic researchers add a great deal of information to the DNA sequence data. It is only through this “annotation” that these DNA sequences become truly valuable. The ultimate goal of sequence annotation is to arrive at a complete functional description of all genes of an organism.
Unfortunately, annotating sequencing data generates what Tallon refers to as an “ocean” of data, creating a monumental challenge and many sleepless nights for anyone trying to store, analyze, and make available for others to access.

At IGS, that task falls to Owen White, PhD, director of bioinformatics. White also ran the bioinformatics group at TIGR and is the author of many of the first complete genomics maps of many important microbes. He faces a daily challenge of not only managing the vast quantities of annotated sequencing data being generated by IGS researchers, but he also is overseeing an almost $10 million grant from the National Institutes of Health for IGS to serve as the data analysis and coordination center for the Human Microbiome Project (HMP). This federally funded project is a consortium of five sequencing centers studying the microbes that live in the various environments of the human body.
To handle the massive amount of data being generated by all these sequencing centers, White is overseeing the development of a state-of-the art data management center that will not only handle IGS current needs but its needs into the foreseeable future. “The infrastructure to handle the massive amounts of data we and other sequencing centers in our consortium are generating didn’t exist when we came here. It doesn’t exist in many other places in the world either. So, we’re basically building a data center from scratch,” explains White.

Just about everyone at IGS agrees that data management is the rate-limiting step for all of their many research projects. However, all are philosophical about it as well. They realize that it comes with the territory.

“We came here to be leaders, not followers,” says Ravel. “We’re used to making do with what we have until the technology catches up with us; so we’re never too bothered by any challenge that comes along.”

Owen White, PhD, at data collection center