Bridging the divide between non-human primate and human research —

AIDS Vaccine Research Lab 5-year Update

Dec. 1, 2010, World AIDS Day
By Marianne English

When the UW-Madison AIDS Vaccine Research Laboratory (AVRL) moved to Science Drive on Sept. 16, 2005, one student remembers how expansive the 20,000 square foot facility seemed at the time. Five years and 67 publications later, the WNPRC-supported facility doesn't seem so empty after all.

Shelby O'Connor prepares SIV sample.

Shelby O'Connor, Ph.D., prepares SIV samples for DNA sequencing at the UW-Madison AIDS Vaccine Research Laboratory. (Photo by M. English)

"We're actually getting to the point where it's full," said Ben Burwitz, a post-doctorate in cellular and molecular pathology who studies at the AVRL. "But the amount of data being generated by the building is also greater."

Burwitz, who has contributed to the AVRL since his years as a technician, has witnessed its growth firsthand, crediting the facility's success to its close-knit community of students and scientists. Despite students and principal investigators working on different projects, the AVRL provides an environment in which people can walk across the hallway to ask a colleague about something rather than across campus, he said.

Burwitz was previously a graduate student at the AVRL under David O'Connor, Ph.D., an associate professor of pathology and laboratory medicine. O'Connor's lab tends to focus on virus and host genetics, whereas the labs of Thomas Friedrich, Ph.D., an assistant professor of pathobiological sciences, and AVRL Director David Watkins, Ph.D., a professor of pathology and laboratory medicine, specialize in immune responses and vaccine development, respectively.

With more than 50 people under one roof, the teams often share equipment and collaborate with one another.

"There's no space that isn't broken down by function -- it facilitates a lot of interaction," Friedrich said. "We're very fortunate to have the cutting-edge equipment to do analyses that others haven't had the chance to do."

Since their first efforts in 1991, researchers at the university have made significant progress in understanding host immune responses and the associated evolution of immunodeficiency viruses. HIV still affects 33 million people worldwide, according to the most recent UNAIDS report. So far, the AVRL has taken a holistic approach on the issue, committing itself to research, outreach and education.

In 2005, the group helped create a unique course dedicated to HIV and AIDS to educate UW-Madison students about HIV. The offering -- called "HIV: Sex, Society and Science" -- was first taught by Watkins, and today both Friedrich and O'Connor co-direct the course. In addition to teaching undergraduates about the basics of HIV infection and immune responses, the two researchers also discuss social, economic and political influences that affect people living with HIV.

Over the years, the research community has dealt with many disappointments and shortcomings in developing an effective AIDS vaccine, Friedrich said. Findings over the past five years have spurred researchers to reconsider how to tackle this rapidly mutating virus.

"A big summit at the NIH a few years ago aimed at finding out what to do about HIV," Friedrich said. "We started going back to the drawing board because we really need to understand more of the basic mechanisms on how HIV causes AIDS and how the immune system can effectively get rid of it. That's going to require a new commitment to the animal model."

Back to the Drawing Board

Since 2005, the AVRL has developed several new approaches to studying HIV and Simian Immunodeficiency Virus (SIV) in efforts to strengthen vaccine designs. SIV, a virus with highly similar genetics to HIV, has been used as a comparative model since the late 1980s.

It is difficult to study the first few weeks of HIV infection in humans because many individuals first arrive at the clinic once overt signs of disease begin to develop, Burwitz said. By studying SIV infection of nonhuman primates, researchers can better understand early immune responses and the ways in which immunodeficiency viruses evade host immunity. In particular, scientists at the AVRL have honed in on responses associated with the Major Histocompatibility Complex (MHC) -- a set of molecules that spur immune responses when a cell is invaded by pathogens such as bacteria, viruses and other microorganisms.

Researchers in the O'Connor lab have furthered the research community's knowledge of SIV, base pair by base pair. Gone are the days when the Sanger sequencing technique represented the norm in DNA sequencing. Now, new next-generation sequencing techniques are highlighting the intricacies of viral evolution by representing individual viruses in a given viral population.

These advances allow a large number of viral genomes to be randomly sampled simultaneously, which provides a nuanced view of what occurs within the blood of people infected with HIV, Burwitz said. However, large increases in data acquisition require novel solutions for data analysis.

"Sequencing itself is getting easier with the technology," he added, "but now the biggest bottleneck is actually analyzing all the data. We've gotten to the point where sequencing itself is the easy part; it used to be the hardest part."

In fact, members of the O'Connor lab were the first to apply next-generation sequencing to genotyping the MHC Class 1 of nonhuman primates in 2009.

Several other discoveries have stemmed from the AVRL, including the knowledge that CD4+ T cells, or "helper" T cells, cannot recognize other SIV infected CD4+ T cells.

Many students and scientists focus on CD8+ T cells, which identify and kill SIV infected host cells. Burwitz said that CD8+ T cells apply immune pressure on HIV, which encouraged researchers to explore vaccines that elicit CD8+ T cell responses. In addition to these developments, Friedrich said he was excited about preliminary research from other labs that test the ability of antiretroviral microbicide gels to prevent the spread of HIV in women.

The Daily Grind

On a daily basis, the AVRL supplies valuable services to researchers at UW-Madison and around the world. In addition to housing cutting-edge research, the lab supports four service cores: Immunology, led by Eva Rakasz, Ph.D.; Protein, headed by Nancy Wilson, Ph.D.; Molecular, managed by Richard Rudersdorf, B.S.; and Virology, led by Friedrich. In addition, O'Connor leads the Genetics Services for the WNPRC.

Of the Primate Center's Research Services channeled through the AVRL in 2009, the Virology Services Unit performed more than 1,700 SIV viral load determinations and produced more than 4,000 vials of high-titer SIVmac239 stock and three custom mutants for the Primate Center's investigators, according to the WNPRC's Annual Progress Report.

Genetics Services supported more than 24 labs worldwide in 2009 through providing high resolution MHC genotyping of several nonhuman primate species. O'Connor is also creating an electronic health records system, which would expand the number of scientists who can access data from the center.

Controlling the Future

Looking forward, researchers at the AVRL will continue to study SIV in nonhuman primates, especially in animals called "Elite Controllers" (ECs) that can effectively manage levels of the virus without expressing typical signs of infection. A small percentage of humans living with HIV are also ECs who limit replication of the virus. Determining the mechanism responsible in managing viruses will point researchers in the right direction in designing more effective vaccines.

Friedrich said that MHC genes are involved in this control in the majority of monkeys, crediting specific alleles to this type of immunity. Notably, the lack of genetic diversity of one monkey species called Mauritian cynomolgus macaques has strengthened research in the lab.

These primates share very similar genes in the MHC region, which allows the AVRL to possess greater experimental control when analyzing the monkeys' responses after being challenged with viruses. Studying immune responses against SIV in Mauritian cynomolgus macaques is comparable to looking at immune responses in identical twins, Burwitz said.

The lab's approach, one that draws from both human and nonhuman primate models, has been the goal all along, O'Connor added. The AVRL's work in nonhuman primates complements continuing partnerships with other researchers around the world.

"From the time I started my lab, I hoped to bridge the divide between nonhuman primate and human research," O'Connor said. "…I believe that there is a huge value in prototyping new ideas in nonhuman primates where we have exquisite control over the virus that is used before trying to extend this research into humans."

Previously working with infectious disease doctors at UW Hospital and Clinics, O'Connor said he has experience analyzing HIV-infected samples and adhering to regulatory details inherent to conducting human research studies. Because HIV samples are not as common in Madison, Wis., O'Connor began to collaborate with longtime colleague Esper Kallas, Ph.D., in São Paulo, Brazil.

In the following years, the two developed a partnership to extend observations originally made in SIV-infected macaques at the AVRL to Kallas's HIV patient samples in Brazil.

Last summer, O'Connor and Kallas co-authored a manuscript published in the Journal of Virology that described a new way to sequence HIV and SIV genomes. The team first used the technique in SIV, where the genetic homogeneity of the virus made assay development simple; then, they applied the method to sequence viruses from Kallas's patients.

In the future, the team plans to gain funding to use similar technology to identify HIV antiretroviral drug resistance variants, O'Connor said.

Overall, despite the AVRL's location off campus, researchers still work closely with Animal Services staff at the WNPRC to closely monitor experiments and ensure the quality of care for the animals involved in research.

Both O'Connor and Friedrich have publicly commented on the importance of animal models in their field while answering critical questions about biomedical research with nonhuman primates at county public hearings and through the local news media, most recently.