Research Magazine 2009
Decoding Infectious Diseases
This year’s outbreak of the H1N1 virus—formerly known as the swine flu—illustrates how quickly an infectious disease can spread around the world. Since the advent of international jet travel, bacteria and viruses once confined to remote regions have frequently hitched rides with passengers, crossing multiple time zones in a matter of hours. As globalization continues apace, the public health community is redoubling its efforts to contain the spread of infections. Researchers at Boston University are bringing together their expertise in science, engineering, medicine, and health care management, as well as the specialized skills of investigators scheduled to work at BU’s National Emerging Infectious Diseases Laboratories (NEIDL) when the facility is fully functional, to speed up vaccine and drug discovery and to advance innovative health care delivery solutions for some of the world’s most vulnerable populations.
Combating the Deadliest Viruses
The National Emerging Infectious Diseases Laboratories will enable basic tanslational, and clinical research on naturally occurring diseases as well as pathogens likely to be used in bioterrorism.
Possibly transmitted by cave-dwelling African bats and highly sought after for use in bioterrorism, Ebola and Marburg are two viruses that pack a wallop. Inducing severe fevers and internal and external bleeding, these so-called filoviruses kill approximately 90 percent of their victims. While fewer than 4,000 cases have been documented since the first outbreaks of Marburg in 1967 and Ebola in 1976, scientists have observed a rising number of new cases over the years. No prevention or cure has yet emerged, but three leading filovirus researchers at BU’s NEIDL facility are fast gaining ground.
“The host recognized the surface Ebola protein, and built up an immune response. So when the monkey’s immune system encountered live Ebola virus, it fought it off.”
Thomas W. Geisbert, associate director of the NEIDL and director of its Specimen Processing Core Laboratory (SPCL), and Joan Geisbert, associate director of both the SPCL and the NEIDL Training Simulator, have spent several years studying and reengineering the immune response of nonhuman primates to infection by filoviruses. Their work has produced two vaccines—one for Marburg, another for Ebola—that protect monkeys against infection from these viruses.
Thomas W. Geisbert
Portrait Courtesy of Thomas W. Geisbert
To develop the vaccine against Ebola, the Geisberts and colleagues at the National Institute of Allergy and Infectious Diseases’ Rocky Mountain Laboratories in Hamilton, Montana, extracted a protein from the surface of the Ebola virus and inserted the gene for that protein into a particle of vesicular stomatitis virus (VSV), a live virus that commonly strikes horses and cattle but is safe for monkeys. When the scientists injected the Ebola protein–coated VSV particle into a macaque monkey, it traveled to the exact same immune system cells that Ebola would infect, and then replicated.
“The host recognized not only VSV but primarily the surface Ebola protein, and built up an immune response against that protein,” Tom Geisbert explains. “It’s a memory response, so when the monkey’s immune system actually encountered live Ebola virus, it fought it off.” The vaccine even helped monkeys fight off Ebola when it was administered after exposure to the virus.
As the Geisberts continue their efforts to develop human versions of these vaccines, Elke Mühlberger, associate professor of microbiology, investigator at the NEIDL, and associate director of its Biomolecular Production Core Laboratory, is seeking to identify promising targets for antiviral drugs. To begin with, she aims to decipher how Ebola and Marburg viruses replicate and disrupt the immune response.
“These viruses spread very rapidly, so there’s no chance for the host’s immune system to counteract them,” she notes. “Filoviruses also have their own proteins that are needed for replication. If you target one of these proteins and switch it off, the virus can’t replicate anymore.”
Mühlberger has targeted one such protein, VP35, that’s instrumental in enabling filoviruses to replicate. By bombarding VP35 with small compounds called P-PMOs, she has prevented filoviruses from replicating in cells. In a collaborative study, P-PMOs were injected in Ebola-infected mice and 100 percent of the mice survived while those untreated died. VP35 also targets several signaling proteins in the host, ultimately blocking many pathways in its innate immune response—pathways that may enable the host to produce proteins to combat Ebola and Marburg.
Mühlberger next plans to explore how her findings on filovirus replication and immune response disruption in cells may apply to humans.
Hooking the Worm
Along the shores of Lake Victoria in western Kenya, there lurks a hidden danger that threatens anyone who bathes or goes fishing in the lake or uses its water to clean vehicles in one of many nearby carwashes. Snails in the lake host a parasitic worm that causes schistosomiasis, a debilitating disease that brings on fatigue, anemia, stunted growth, and, occasionally, death.
Schistosomiasis has claimed about 207 million victims, primarily in Asia and Africa, and threatens 800 million more who dwell near bodies of water in the tropics. While largely effective, the current treatment is inadequate because it works primarily against the adult worm, leaving young worms and eggs intact to cause additional symptoms or reinfect the host. To help prevent this illness, Lisa Ganley-Leal, an assistant professor of infectious diseases, is seeking to advance the world’s first effective vaccine for a parasitic disease.
With Pauline Mwinzi, director of the schistosomiasis lab at the Kenya Medical Research Institute, Ganley-Leal is studying how the human immune system responds to schistosome infection. In particular, they’re focused on why some victims are reinfected upon subsequent exposure to the worm, while others are not. Learning more about the immune response of individuals in both categories could enable scientists to pinpoint how to boost the human immune system’s defenses against the disease.
Ganley-Leal’s investigation centers on antigen-specific IgE, a type of antibody in the immune system that, at sufficiently high levels in the blood, correlates with protection against schistosome reinfection. “Scientists have known about IgE’s protective effect for 60 years, but nobody’s understood the mechanism behind it,” says Ganley-Leal. “We’re trying to determine the mechanism and also what the parasite does to IgE and its receptors to block the immune response.”
Funded by a National Institutes of Health grant and supported by multiple residents, students, and fellows within the School of Medicine, Ganley-Leal ultimately hopes to identify whatever parasite protein is responsible for subverting the immune response and engineer it for use in a vaccine.
Freshwater snails serve as intermediate hosts of the parasite that causes schistosomiasis, the world’s second most socioeconomically devastating disease, after malaria.
Culturing human cells with parasites extracted from infected snails, she is now investigating how the worm changes the IgE receptors on the cells. So far she’s found that the parasites employ multiple strategies to target a particular IgE receptor associated with resistance to the disease—including lopping off the IgE receptor from the cell like a paper cutter.
“We’re trying to find the protein the parasite is using to cleave that IgE receptor protein from the cell, and we think we’ve identified it,” says Ganley-Leal, who is collaborating with a Tufts University Veterinary School scientist, Patrick Skelly, to silence parasite genes suspected of cutting off the IgE receptor. “After validating the responsible protein, we’ll clone it and see if people who are resistant have antibodies to that protein. That would be one way to identify a vaccine candidate.”
Blueprint for Better Drugs
One of humanity’s top four killers, tuberculosis (TB) causes up to three million deaths each year, primarily in developing countries. Combating the disease with today’s commercially available treatments entails administering three to four drugs for up to nine months—a difficult feat to achieve in places that lack a robust public health infrastructure. To sharply reduce TB’s death toll in the foreseeable future with simpler, faster treatments, scientists will need to come up with a new blueprint for drug development.
So argues James Galagan, assistant professor of biomedical engineering and microbiology, and associate director of the Systems Biology Core in Boston University’s NEIDL. In preliminary studies he plans to validate at the high-containment facility, Galagan is now probing the interactions of the gene and protein networks within the tuberculosis bacterium. By mapping out these interactions, he hopes to arrive at a better understanding of how TB functions—and to identify prime targets for more effective drugs.
Driving this research is the fast-growing discipline of computational systems biology. Unlike traditional microbiology, which often relies on knocking out one gene or protein at a time and studying the effect on the behavior of an organism, systems biology empowers scientists to measure all of the organism’s gene and protein interactions at once. The process affords a holistic view that accelerates drug discovery.
“We have the unique opportunity to put together a systems-level view of the metabolic and regulatory networks of TB and other infectious diseases,” says Galagan, whose work is supported by two grants from the Massachusetts Life Sciences Center and students in engineering, math, computer science, and molecular and microbiology. “Our goal is to come up with the functional blueprint of these diseases—how the parts work together and the rules by which they operate.”
To build a functional blueprint of TB, Galagan is applying new techniques from systems biology to what’s known about the TB genome—primarily the sequence and identity of its approximately 4,000 genes. Using a technique called genome profiling, he’ll attempt to determine when each component of the genome is active. For example, when TB is infecting a macrophage (an immune system cell that operates as a first line of defense against infectious agents), genome profiling pinpoints which proteins and metabolites (small molecules that produce energy for TB) are turned on or off.
“If we see certain genes on or off together, then they may be part of the same sub-circuit,” Galagan explains. “And this gives us a systematic way to identify where to disrupt the circuitry of TB.” By knocking out selected sub-circuits of the metabolic and regulatory networks of TB in simulation and determining the effect on TB behavior, Galagan aims to identify new drug targets and evaluate the impact of potential drug compounds.
Reducing HIV Risk
In Springfield’s Latino community, heroin is cheaper than a pack of cigarettes. Unfortunately, HIV is often included in the price. So reads the opening line of the brochure for La Voz, an HIV prevention and substance abuse reduction program based in Springfield, Massachusetts. In the last decade, the disease has affected a disproportionate number of the city’s Latino community, primarily due to an alarming rise in heroin and other intravenous drug use.
“We go beyond research and use our backgrounds as program planners and developers and clinicians to provide these organizations with the knowledge they need when they need it.”
Traditionally underserved by culturally sensitive HIV prevention and substance abuse treatment providers, Latino-Americans often do not seek out or complete detoxification and treatment services. Not only does this predicament perpetuate a state of poverty for many in the nation’s Latino community, it also drives up emergency room costs and threatens to widen the spread of HIV.
Since 2002, Lena Lundgren, professor of social welfare policy and director of the Boston University Center for Addictions Research & Services (CARS)—together with colleagues Maryann Amodeo, Melvin Delgado, Sally Bachman, Luz Lopez, center staff, and students—has sought to reverse this trend through hands-on partnerships with two community-based Latino organizations: La Voz, a program of Tapestry Health Services that offers substance abuse, HIV prevention, and mental health services in neighborhood drop-in centers and other non-clinical settings; and Casa Esperanza, a statewide residential program in Roxbury for Latino adults seeking to end their drug addiction.
Supported by nine federal grants totaling more than $14 million for health services, evaluation, and research since 2002, the center has provided research, training, and consultation to both organizations. “More than 30 mental health counselors and substance abuse workers, and 20 social work and public health masters and doctoral students have been trained, resulting in more than 1,800 members of the Latino community receiving HIV prevention and substance abuse services,” says Lundgren. “We go beyond research and use our backgrounds as program planners and developers and clinicians to provide these organizations with the knowledge they need when they need it.”
As described in the journal Evaluation and Program Planning (volume 31.1), Lundren’s efforts—with other Social Work faculty and graduate students—have enabled Casa Esperanza and La Voz to reduce HIV risk and substance abuse rates. Separate CARS outcome evaluations have shown, for instance, a 56 percent increase in abstinence from alcohol and illegal drugs in Casa Esperanza clients interviewed between intake and a six-month follow-up, and a 40 percent reduction of injection drug use among La Voz clients surveyed for a similar period.
Photo courtesy of Patrick Geryk/Tapestry Health Services
Key to these success stories is Lundgren and her colleagues’ translation of research findings into helping organizations select a customized suite of services, such as teaching relapse prevention techniques in order to reduce alcohol and drug abuse, and the provision of mobile vans that offer HIV outreach, testing, and counseling services in at-risk neighborhoods.
“Through consultation and training with leaders and frontline staff, we have helped them provide evidence-based services that we know are linked to reduced HIV risk and substance abuse rates, and we have seen these rates reduced through their services,” Lundgren maintains. “Community-based treatment and prevention organizations often don’t have access to the resources we have as a university, and that’s why it’s so important that we work with them.”
Probing Periodontal Disease
Caused by oral bacteria and the body’s immune response to them, the world’s second most common disease, periodontitis, inflames the tissues that buttress the teeth and can lead to tooth loss. Of the 700 bacterial species present in dental plaques, only 10 to 15 have been characterized, a knowledge gap that has undoubtedly affected the accuracy of diagnosis and treatment for this disease. Better knowledge of the plaque agents and their impact on the host would translate into a more focused approach likely to improve treatment outcomes.
Salomon Amar (l) & Daniel Segrè (r)
Portrait of Daniel Segrè courtesy of Daniel Segrè
One such agent that’s particularly virulent in the most destructive forms of periodontal disease is a bacterium called Porphyromonas gingivalis. Recognizing the importance of P. gingivalis, Salomon Amar, professor of dental medicine, and Daniel Segrè, assistant professor of bioinformatics, have embarked on a collaborative study to improve our understanding of this bacterium and its role in periodontal disease.
“Our idea is to examine the metabolic pathway associated with this periodontal pathogen and begin to understand what possible interference we could engineer to destroy or reduce the virulence factors of this microorganism or prevent its growth without destroying it completely,” says Amar. “If the virulence factors of this microorganism can be reduced, we can begin to have a more sustainable therapeutic approach and prevent disease recurrence.”
In pursuit of such an approach, Amar, an expert in periodontal disease, and Segrè, a seasoned modeler of microbial metabolism, have developed a genome-scale model of the metabolic network of P. gingivalis. Using the model, they hope to predict where they can intervene in this network and thus pinpoint what genes they can mutate—and ultimately target with drug compounds—to reduce the microorganism’s virulence and prevent its proliferation. Eventually they’ll test the mutated microorganisms in animal models to see if they produce less periodontal disease.
The metabolic network of Porphyromonas gingivalis, one of the microbes responsible for periodontal disease, is projected onto a mannequin head. A computational model of this network developed by Salomon Amar and Daniel Segrè can be used to produce testable predictions of the bacterium’s metabolic fluxes under different environmental conditions and genetic perturbations.
Image reprodued by permission of the publisher from Journal of Bacteriology 191.1 (January 2009), cover. © 2009 American Society for Microbiology
The collaboration between Amar and Segrè represents the first major research project that brings together oral microbiology and systems biology to predict which genes to target in a pathogenic microorganism. By uniting these disciplines, the scientists hope to accelerate the pace of drug discovery.
Toward that end, Amar and Segrè’s computational model is designed to predict all the flows of compounds between any two nodes in the metabolic network, and show the impact of removing each gene, one by one, on the virulence and growth of the organism. “This would be very laborious experimentally,” says Segrè. “But with our model, in less than an hour you can obtain a prediction of how the cell would respond to the perturbation of each metabolic enzyme gene. Some gene deletions won’t affect the organism, others will kill the bacterium, and others will reduce the amount of virulence factors that are produced.”
The project is described in a paper by Amar, Segrè, and bioinformatics postgraduate students Varun Mazumdar and Evan S. Snitkin in the January 2009 issue of the Journal of Bacteriology. Results of this ongoing research can be found at http://ohmics.bu.edu/.