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Feature Articles : Mar 15, 2010 (Vol. 30, No. 6)

Systems Biology Transforms Vaccine Design

Novel Approach Gives Investigators an Edge in Targeting More Tenacious Pathogens
  • Gail Dutton

Systems biology is bringing a new, more robust approach to vaccine design that is based upon understanding the molecular network and re-engineering the immune system. With this approach, it is within the realm of possibility to develop vaccines against some of the most tenacious pathogens like HIV, TB, and malaria.

Recently, the NSF, the University of California, Berkeley, and Stanford University collaborated to create BIOFAB: the International Open Facility Advancing Biotechnology. BIOFAB combines systems biology with synthetic biology to produce a DNA parts-lab of thousands of standardized control elements that are critical to engineering microbes. Researchers expect the results will provide the tools to make microbial engineering both easier and less expensive.

That approach is just beginning, but researchers throughout the world are already making notable inroads as they apply systems biology to vaccine design. The goal is to measure, understand, and then leverage the relationships among various components of an immune response to  design vaccines that initiate a more robust response and, particularly, to develop vaccines against pathogens for which there is, as of yet, no effective vaccine.

Typically, the response of the innate immune system is sufficient to control many common infections. In more resistant cases, however, the adaptive immune system must also be triggered. The latter launches a highly specific response and, more importantly, remembers the trigger. That memory is the foundation for the success of vaccinations in preventing specific infections.

Vaccines based upon that understanding aren’t protective against pathogens that hide inside macrophages, hepatocytes, or other cells, however. To eradicate such pathogens, a T cell-mediated response is also needed. To generate that response, several researchers are focusing upon the interactions of dendritic cells.

Systems Vaccinology

“We are specifically interested in understanding how the immune system senses pathogens and how it translates that information to launch an immune response that can last a lifetime,” says Bali Pulendran, Ph.D., systems vaccinology, Emory University Vaccine Center. Dendritic cells play a key role in sensing pathogens and tuning immune response. His work focuses on understanding dendritic cells’ molecular mechanisms and genomic networks, and the various microbial stimuli that can modulate their functions.

Dendritic cells express such innate immune receptors as Toll-like receptor 4 (TLR4), which senses molecular components of pathogens and initiates a cascade of events that culminates in the induction of a protective immune response, Dr. Pulendran explains.

“We’re using synthetic ligands to bind to and activate these receptors to stimulate adaptive immunity.” Therefore, this strategy can be used as a vaccine adjuvant. For example, he points out that GlaxoSmithKline  recently received a license to use MPL, a ligand for TLR4, in the U.S. as an adjuvant for HPV.

“However, not all pathogens require the same type of response. For HIV, we have some idea, but need to understand more.” Some pathogens may require multiple types of responses, “therefore, we need to define the correlates of immunity.”

Dr. Pulendran’s lab determined that stimulation of multiple TLRs is essential to elicit an immune response from the yellow fever vaccine, one of the most successful vaccines ever developed. Based on this result, his laboratory is designing synthetic vaccines against a variety of diseases. They contain multiple TLRs to recapitulate the efficacy of the yellow fever vaccine.

“We’re finding that, if we immunize mice with the nanoparticles that contain antigens and a combination of TLRs, we evoke an immune response that lasts the lifetime of the mice,” he says. Therefore, vaccines based upon synthetic nanoparticles containing multiple TLRs can be as effective as empirically made vaccines. “The benefit is that we are no longer tied to attenuating a pathogen. That is very important in developing vaccines against deadly diseases.”

Most recently, Dr. Pulendran’s lab predicted vaccine efficacy with 90% accuracy using a systems biology approach. Dr. Pulendran and collaborators used an interdisciplinary approach including immunology, genomics, and bioinformatics to predict a vaccine’s immunity without exposing individuals to infection—a long-standing challenge in the development of vaccines. The team used several lines of study to identify distinct gene signatures that were correlated to the antibody response induced by the vaccine.

To determine whether the gene could predict immune response, “we vaccinated a second group of individuals and were able to predict with up to 90% accuracy which of the vaccinated individuals would develop immunity to yellow fever,” Dr. Pulendran explains. Such an approach is likely to be highly valuable in predicting the immunogenicity of a range of vaccines, and in identifying individuals who launch sub-optimal immunity such as the elderly, infants, or the immune compromised. By determining why the yellow fever vaccine was so effective, equally effective new vaccines against global pandemics and emerging infections can be designed.

T Cells

Traditionally, biologists have interrogated narrow avenues of information, learning, for example, what a T cell does without the ability to measure its interactions. “Systems biology lets you measure everything,” says Rafik-Pierre Sekaly, Ph.D., scientific director at the Vaccine and Gene Institute. By taking such a systems approach, “you find novel things you never thought to ask.”

That approach led him to the understanding that, in HIV, T cells are dysfunctional. Based on this understanding, Argos Therapeutics has invented and developed an HIV vaccine that is in Phase II trials now, and Dr. Sekaly’s lab is participating in and analyzing immuno-monitoring data from this trial.

Basically, Argos’ therapy re-educates a patient’s immune system. The therapy is designed by extracting dendritic cells from a patient, introducing them to that patient’s own HIV virus, and then reintroducing these dendritic cells back into the patient, enabling the immune system to respond more robustly.

Phase II trials of the Argos vaccine are showing a viral load reduction that is so significant that some of the patients have stopped their drug regimen for up to six months without increasing the viral load, Dr. Sekaly says.

The next step, he adds, is to introduce the knowledge of systems biology to develop better adjuvants.

Variations

Paul de Bakker, Ph.D., assistant professor, Brigham and Women’s Hospital and Harvard Medical School, and associate member at The Broad Institute, is studying the host genetic basis of spontaneous control of HIV. Specifically, he is looking for genetic variations between HIV elite controllers and HIV progressors to determine why the disease does not advance substantially in elite controllers or viremic controllers (those whose HIV viral loads are, respectively, below 50 virus particles or between 50 and 2,000 virus particles, per milliliter of blood). To put that in perspective, the viral load for untreated patients averages more than one million particles at the time of acute infection.

This work is being done in collaboration with Bruce Walker, M.D., professor of medicine at Harvard Medical School and director of the Ragon Institute of Massachusetts General Hospital, MIT, and Harvard, under a grant from the Bill and Melinda Gates Foundation. As a result of this work, “we are now able to explain associations of HLA alleles that have been documented for many years,” Dr. de Bakker says.

“We have developed a novel computational approach to look at specific amino acids in molecules of the immune system. Something is happening on chromosome 6. There’s a lot of variation, so it is difficult to read the genome in terms of what is important for elite controllers and what is not. Evolution has left a wicked mark on this part of the genome.”

Dr. de Bakker’s lab is looking closely at HLA genes, which are important in determining how the immune system reacts to nonself entities it encounters. “We are looking at proteins encoded by these genes to pinpoint specific amino acids that can at least partially explain why some are controlling the virus and why others are not.”

His lab uses Illumina microarrays installed at the Broad Institute to interrogate up to one million SNPs. The limitation to that approach is the number of samples needed to unequivocally determine which genes are causal factors in the replication of a specific, complex viruses like HIV. That is exacerbated by the relatively small population of elite controllers. To date, this project has included approximately 1,000 controllers and 3,000 noncontrollers. “These numbers pale in comparison to the numbers of patients investigated in other diseases,” Dr. de Bakker says.     

“We’re getting some pretty exciting results so far. The next question is how to use this information to build a more complete picture of how viral peptides are presented to the immune system.”

These and other concepts in systems biology will be explored more fully at the the Institute for Systems Biology’s “Systems Biology and Global Health” conference next month in Seattle.