The Acute HIV Infection Research Program at MGH

 

Mutations in HIV that develop during the first few weeks of infection may play a critical role in undermining a successful early immune response, a finding that reveals the importance of vaccines targeting regions of the virus that are less likely to mutate. A new study in the journal PLoS Pathogens, led by researchers at the Ragon Institute of MGH, MIT and Harvard and the Broad Institute of MIT and Harvard, applied the same next-generation technologies that have revolutionized sequencing of the human genome to study how HIV adapts within the first few weeks after infection.

Ragon and Broad investigators applied an approach called pyrosequencing that allows the simultaneous sequencing of hundreds of viral variants within an individual over the course of infection. These data provided a substantially deeper and more sensitive view of the complexity of mutant strains circulating in a patient following HIV infection and how each of those strains evolves over time. Combining these genetic data with detailed immunological analyses enabled a comprehensive evaluation of viral-host interactions during the critical acute phase of HIV infection.

The study revealed that the majority of early, low-frequency mutations developing during the first few weeks after infection represent rapid adaptations to avoid the response of CD8 'killer' T cells, which play a key role in recognizing and eliminating HIV-infected cells. "These data reveal the ability of HIV to rapidly avoid front-line immune responses attempting to contain the infection," says Todd Allen, Ph.D,  senior author of the study and a Ragon Institute faculty member.

More importantly, Allen notes, their study revealed that rapid viral escape from a few dominant immune responses coincided with the inability of individual patients to maintain early control of HIV. "The ability to sensitively assess early virus evolution across the entire HIV genome revealed that limiting the ability of HIV to become resistant to the earliest immune responses may be a critical component of a successful vaccine," he says. "Therefore, the key to controlling a highly variable pathogen such as HIV may lie in a vaccine's ability to redirect immune responses towards more critical, highly conserved regions of the virus that are unable to successfully mutate."

An important component of the study was development of novel bioinformatics tools to handle the enormous and highly diverse sequence dataset and to assemble the thousands of sequencing reads into complete HIV genomes for analysis and detection of genetic mutations. While next-generation sequencing approaches have helped transform the sequencing of mammalian genomes, the high degree of sequence diversity within and between HIV strains has hindered the routine application of those powerful sequencing approaches to highly variable pathogens such as HIV.  In the current study the researchers were able to apply their approach to successfully sequence the entire HIV genome from dozens of infected individuals.

"The genomic and computational tools developed as part of this study allow researchers to interrogate the complete HIV genome and to identify genetic variants of the virus with unprecedented resolution, allowing us to obtain a novel map of how the virus is changing during the course of an infection.” says Matthew Henn, PhD, the lead author of the study and director of Viral Genomics at the Broad Institute.

Efforts to develop an effective vaccine against HIV have been thwarted in large part because of the virus's ability to rapidly mutate and avoid host immune responses. However, notes Allen – an associate professor of Medicine at Harvard Medical School – "HIV is not able to mutate at will.  Some of these mutations substantially cripple the virus’ ability to replicate, which appears to be critical to enabling a few individuals to uniquely control HIV without the need for therapy."

Understanding more precisely how HIV evolves in an individual and how mutations correlate with the ability to control HIV may provide critical insight into the design of more effective vaccines to contain and possibly prevent infection altogether. Efforts are underway at the Ragon Institute to harness these findings to develop and test novel vaccine approaches against HIV that limit its ability to mutate and escape immune control.

 

Link to Article

 

HIV-specific CD4 cells that control viral levels

Ragon Institute of MGH, MIT and Harvard 

A subpopulation of the immune cells targeted by HIV may play an important role in controlling viral loads after initial infection, potentially helping to determine how quickly infection will progress. In the February 29 issue of Science Translational Medicine, a team of researchers from the Ragon Institute of Massachusetts General Hospital (MGH), MIT and Harvard describe finding a population of HIV-specific CD4 T cells – cells traditionally thought to direct and support activities of other immune cells – that can directly kill HIV-infected cells.

"We observed the emergence of CD4 T cells able to kill HIV-infected cells in those patients who are able to control viral replication soon after acute infection," says Hendrik Streeck, MD, PhD, a Ragon Institute faculty member and senior author of the report. "These cells appear very early in HIV infection, and we believe they may set the stage for the course of the disease."

The primary role of CD4 T cells is to assist other cells of the immune system; and their importance is illustrated by how completely the immune response collapses after the cells, the main cellular targets of HIV, are destroyed. Ironically, CD4 cells that are specifically targeted against HIV are preferentially infected and depleted by the virus.

However, although HIV-specific CD4 cells have not been a major focus of vaccine research, these cells may have an important role in controlling HIV infection. "Every successful licensed vaccine induces CD4 T cell responses to some extent," Streeck explains, "and we know from many other viral infections that the success of the immune system in gaining control is best achieved in the presence of strong CD4 T cell responses."

To investigate whether CD4 T cell responses are important in the early control of HIV infection, the Ragon Institute team enrolled a group of 11 volunteers who were in the earliest stages of HIV infection, a time when viral levels are exceedingly high. A year into the study, participants were divided into two groups based on the level of HIV in their bodies – one group was able to keep HIV at low levels while the other group apparently had no immune control over HIV replication. Retrospective analysis of samples taken throughout the year showed striking differences in the CD4 T cell responses in both groups. While the HIV-specific CD4 responses in the group that did not control HIV replication quickly dropped and stayed low, the same response increased significantly in participants able to effectively control the virus, suggesting a role for HIV-specific CD4 cells in viral control.

Additional experiments revealed that the HIV-specific CD4 T cell responses showed activity associated with cell-killing and could even destroy HIV-infected macrophages – an unusual function for CD4 T cells, which have traditionally been seen as helper cells. In addition, the researchers determined that the presence of a specific cell-death protein called granzyme A prominently distinguished HIV-specific CD4 cells of participants maintaining a lower "viral set point" from those less able to control viral levels.

To validate these findings, the researchers examined a larger group of HIV-infected individuals and found that those with higher levels of granzyme A in their HIV-specific CD4 T cell response immediately after infection progressed more slowly to AIDS and did not require antiretroviral therapy as quickly as did those with lower levels of the protein. "The key baseline difference between these two groups has to do with the quality, not the quantity, of the HIV-specific CD4 T cell response," explains Streeck, an assistant professor of Medicine at Harvard Medical School. "In those who progressed to a lower viral set point, the early CD4 response was dominated by granzyme A expression, which was highly predictive of the rate of disease progression."

Associating a particular CD4 T cell activity with more successful suppression of viral levels suggests that inducing such responses with a vaccine may be beneficial, Streeck notes. In addition, the association of granzyme A expression with a more effective HIV-specific CD4 cell response suggests that measuring levels of the protein may allow prediction of disease outcome at the earliest stages of infection, something which is not currently possible. Future studies will need to explore the mechanisms underlying the cell-killing activities of the CD4 cell response and the functional and prognostic role of granzyme A.

The lead author of the Science Translational Medicine report is Damien Soghoian of the Ragon Institute. Additional co-authors are Michael Flanders, Kailan Sierra-Davidson, Sam Butler, Thomas Pertel, PhD, Srinika Ranasinghe, PhD, Madelene Lindqvist, Isaiah Davis, Kimberly Lane, Alicja Piechocka-Trocha, Abraham Brass, MD, PhD, and Bruce Walker, MD, Ragon Institute of MGH, MIT and Harvard; Heiko Jessen, MD, Practice Jessen-Jesse-Stein, Berlin, Germany; Jenna Rychert, MD, and Eric Rosenberg, MD, MGH Infectious Disease Unit; and Jason Brenchley, PhD, National Institutes of Health. The study was funded by the National Institute for Allergy and Infectious Diseases of the National Institutes of Health.  

   The Early Capture HIV Cohort Study (ECHO)

The identification of individuals with very acute HIV-1 infection, just days after exposure to HIV-1, is critical for a better understanding of the earliest events that occur following HIV-1 acquisition. The MHRP RV217 protocol, Early Capture HIV Cohort (ECHO), implemented a unique approach for acute HIV-1 infection diagnosis.  This study is based in populations in Thailand, Uganda, Kenya and Tanzania with the hope to study HIV-1 prevalence, incidence, host genetics and viral diversity in acute HIV-1 infection. The goal is to enroll 150 individuals with acute infection within the 3-5 days of exposure to HIV-1 (Fiebig stages I-III).

The study population is followed for two years and consists of individuals who are thought to be at high risk for HIV-1 infection. Throughout the study, these high risk individuals provide blood samples by finger stick twice a week in microvette vials. Using the very sensitive technique of Gen-Probe’s HIV RNA Assay, the blood samples are then used to test for the presence of HIV-1 RNA. The ability to obtain samples during the antibody negative stage provides the opportunity to study the early viral evolution and its relation to innate immunity.

Several studies have suggested that events occurring in very early acute HIV-1 infection influence the ultimate control of viremia and the prognosis of the disease. ECHO provides the opportunity for classification of the founding virus and the understanding of host control among these high risk individuals. This cohort will be followed up for two years which will provide data on the level of viral replication and decline of CD4+ T cell numbers. It also gives researchers the opportunity to determine the relationship between early immunological and virological events, viral load set point and clinical outcome throughout the acute and early phase of the infection. These data will be very relevant for vaccine design.

AIDS Vaccine Conference 2011

Features Oral and Poster Presentations from Ragon Institute's Acute P01 Investigators

The 2011 AIDS Vaccine conference, held in Bangkok, Thailand, was organized by the Global HIV Vaccine Enterprise, a collaboration in an effort to advance HIV vaccine research. This conference is the largest scientific meeting, which focuses exclusively on HIV vaccine research and annually brings together scientists from across the world engaged in AIDS vaccine research and development. The conference featured oral and poster presentations by a number of investigators from the Ragon Institute who participate in the effort to develop a protective HIV-1 vaccine. These included several presentations by investigators involved in the Acute HIV-1 Infection research efforts at the Ragon Institute that are directly supported by an NIH Program Project Grant.  Below we have listed these oral and poster presentations: 

Symposia:

Antiviral Activity of NK Cells in HIV-1 Infection
Marcus Altfeld

Oral Abstracts

Identification of Escape-Refractory Subdominant CD8 Epitopes for Common HLA Alleles CL Boutwell, C Oniangue-Ndza, A Schneidewind, H Streeck, A Seese, E Mellors, K Murthy, K Power, M Kemper, T Dudek, BD Walker, M Altfeld, TM Allen

HIV-Specific Cytolytic CD4+ T-Cell Responses During Acute HIV-1 Infection Predict Disease Outcome DZ Soghoian, H Jessen, S Cutler, M Flanders, S Ranasinghe, M Lindqvist, I Davis, K Lane, J Rychert, ES Rosenberg, BD Walker, H Streeck

Important Contribution of Subdominant HIV-Specific CD8 T Cell Responses to Early Control of HIV Replication  Streeck, D Kwon, M Addo, M Flanders, I Davis, S Cutler, J Rychert, K Lane, B Yassine-Diab, J Routy, S Little, H Jessen, A Kelleher, F Hecht, R Sekaly, E Rosenberg, B Walker, T Allen, M Altfeld

Frequent and Strong NK Responses to HIV-1 Env Peptides in Individuals with Acute and Chronic HIV-1 Infection CF Thobakgale, L. Fadda, K. Lane, F. Pereyra, B.D. Walker, T. Allen, M. Altfeld

Poster Sessions:

Differential Regulation of Various TLR Pathways in Acute and Chronic HIV-1 Infection J Chang, A Lacas, RJ Lindsay, E Doyle, K Axten, BD Walker, F Pereyra, T Allen, M Altfeld

Different Cytokine Profiles Induced by HIV-1 and HIV-1-Derived TLR Ligands in Monocytes and mDCs RP Simmons, E Groden, JJ Chang, R Lindsay, L Fadda, JD Lifson, K Lane, K Axten, E Rosenberg, T Allen, M Altfeld

Dysregulation of Tim-3 Expression on NK Cells in Chronic HIV-1 Infection S Jost, UY Moreno-Nieves, J Reardon, I Toth, A Piechocka-Trocha, G Alter, M Altfeld, MM Addo

Increased Plasma Levels of Hemoxygenase-1 (HO-1) and Presence of HO-1-Specific Regulatory T Cells in Acute HIV-1 Infection M Angin, A Fathi, M King, MM Addo

Preexposure Prophylaxis Reduces HIV Acquisition

A recent study has found that the use of preexposure antiviral treatment (termed preexposure prophylaxis or "PrEp") can be highly successful in preventing HIV infection in men-who-have-sex-with-men (MSM). Dr. Ken Mayer, Medical Research Director and Co-chair of the Fenway Institute, is one of the Principal Investigators on the iPrEx study, which included nearly 2,500 participants from the United States as well as Peru, Ecuador, Brazil, Thailand, and South Africa. The iPrEx study consented HIV- uninfected men who reported having sex with men as well as engaging in risky sexual behaviors. The study participants were randomized to either oral doses of a combination pill containing tenofovir (TDF) and emtricitabine (FTC) or a placebo pill. The results of this study indicated that subjects provided with preexposure antiviral treatments or "PrEp" had 44% reduction in HIV acquisition. Furthermore, the study showed that among those participants who took the drug at least 90% of the time, HIV acquisition was further reduced by 73%. Those who took the drug less than 90% of the time had a 21% reduction in HIV acquisition. Both the placebo pill and the PrEp groups showed similar rates of serious adverse events, suggesting that the use of FTC-TDF was well tolerated, although nausea was reported more frequently during the first four weeks of the PrEp group. These promising results suggest that combining PrEp with behavioral interventions has the potential to maximize the reduction of HIV incidence in MSM.

More About iPrEx       Link to Abstract       Fenway Institute Press Release