Meeting Minutes - April 17, 2008

Office of AIDS Research Advisory Council 
Twenty-Sixth Meeting
April 17, 2008 
National Institutes of Health
U.S. Department of Health and Human Services
5635 Fishers Lane Conference Center
Rockville, MD

Members Present: Dr. James W. Curran (Chair), Dr. Arlene D. Bardeguez, Ms. Dawn A. Bridge, Dr. Coleen K. Cunningham, Dr. Sharon E. Frey, Dr. Betsy C. Herold, Dr. John H. Kempen, Ms. Lynn Paige Nestor, Dr. Kurt Organista, and Dr. Michael F. Summers
Ex Officio Members Present: Dr. Carl W. Dieffenbach, Dr. Kevin Fenton, Dr. Diana M. Lopez, and Dr. Ronald O. Valdiserr
Ad Hoc Members Present: Dr. Richard Anderson and Dr. Jane L. Peterson
Invited Speakers and Guests: Dr. Todd M. Allen, Dr. Abraham L. Brass, Dr. Anthony S. Fauci, Dr. David B. Goldstein, Dr. Michael G. Katze, Dr. David L. Nelson, Dr. Alice K. Pau, Dr. William E. Paul, Dr. Robert Siliciano, and Dr. Hervé Tettelin

Welcome and Meeting Overview

The National Institutes of Health (NIH) Office of AIDS Research Advisory Council (OARAC) convened its twenty-sixth meeting at 9 a.m. at the National Institutes of Health (NIH) in Rockville, Maryland. Dr. James W. Curran, Chair, welcomed the OARAC members, invited speakers, and guests.
The topic of the meeting was “Leveraging Genetic and Genomics Resources for the Study of HIV/AIDS.” During the meeting, invited speakers presented studies and discussed research opportunities related to this topic. The OARAC members and the invited guests discussed these presentations and directions for future research.
The minutes of the October 24, 2007 OARAC meeting were approved as submitted.

Twentieth Anniversary of the Establishment of OAR

Dr. Jack Whitescarver, Director of the Office of AIDS Research (OAR), commemorated the twentieth anniversary of the establishment of the OAR. The OAR was established within the Office of the NIH Director in 1988 to coordinate the scientific, budgetary, legislative, and policy elements of the NIH AIDS research program. The Office was established first by the Assistant Secretary of Health and later codified in the Health Omnibus Programs Extension of 1988 (Public Law 100-607). Dr. Whitescarver recognized the former OAR Directors: Dr. Anthony S. Fauci (1988-1994), Director of the National Institute of Allergy and Infectious Diseases (NIAID); Dr. William E. Paul, (1994-1997), Chief, Laboratory of Immunology, NIAID; and Dr. Neal Nathanson (1998-2000), Professor Emeritus, University of Pennsylvania School of Medicine and presented them each a plaque. Drs. Fauci and Paul were in attendance at the meeting. Dr. Curran recognized Dr. Whitescarver for his service as the current Director of the OAR.

NIAID HIV Vaccine Summit Update

Dr. Fauci, Director, NIAID, presented an update on human immunodeficiency virus (HIV) vaccine research and development and an overview of the March 25, 2008 NIAID HIV Vaccine Research Summit.

Dr. Fauci noted the tremendous burden of HIV and acquired immunodeficiency syndrome (AIDS) on global public health and the need for improved HIV prevention strategies. In 2007, there were 2.5 million new HIV infections worldwide, and for every person started on antiretroviral drug therapy, three become infected.

Dr. Fauci noted that between fiscal year (FY) 1995 and FY 2007, the relative proportion of the NIAID AIDS research budget dedicated to HIV vaccine research increased. In FY 2007, one third of the NIAID AIDS budget was allocated to HIV vaccine research.

Dr. Fauci presented an overview of the necessary components of vaccine research, which include a balance of basic knowledge of the nature of immune responses, product safety, etc. and the empiricism of developing and testing a vaccine candidate. He noted the immune response to some vaccine candidates is predictive of efficacy; such is the case with influenza vaccines. The correlation is much less strong with other effective vaccines, including the measles, mumps, rubella, and hepatitis vaccines.

Dr. Fauci reviewed the types of HIV vaccine candidates that have been developed and tested, including viral subunit vaccines and vector-based vaccines containing HIV genes. He noted that many of the HIV vaccine strategies explored to date produced promising results in animal studies that did not extend to use in humans. This was true, for example, of the recent international Merck STEP study that tested an HIV vaccine candidate consisting of an adenovirus type-5 (Ad5) vector containing three internally conserved HIV genes. This phase IIb concept trial was halted because preliminary results indicated that the vaccine did not protect against infection and did not lower the viral set point. Dr. Fauci stated that there were more HIV infections in vaccinated individuals than in individuals receiving a placebo injection, especially in trial participants who had previously been exposed to the Ad5 virus. The increased risk was observed in uncircumcised men with pre-existing Ad5 immunity. Further studies are investigating the biological mechanisms underlying these unexpected and disappointing results. A second trial of the Ad5 vectored vaccine, the Phambili study in South Africa, also was halted early.

NIAID has solicited input from scientists and advocacy groups on future directions of the NIAID HIV vaccine research program since the STEP and the Phambili trials were halted. Dr. Fauci noted that NIAID convened the HIV Vaccine Research and Development Summit in Rockville, MD on March 25, 2008 to review the NIAID HIV vaccine research portfolio and to seek input on the appropriate balance between vaccine discovery and development. During the Summit, panels of experts facilitated the discussion within three broad areas: vaccine-related basic research versus vaccine discovery and development; animal model development and utilization; and clinical research and trials. The meeting co-chairs were Dr. Warner Greene, Professor of Medicine, University of California, San Francisco, a highly respected scientist conducting fundamental studies of HIV pathogenesis; and Dr. Adel Mahmoud, Professor, Princeton University and former President, Merck Vaccines, who has extensive experience in HIV vaccine development. Over 200 people attended the meeting, and the attendees were highly representative of the HIV vaccine research community. Dr. Fauci reported that a clear consensus emerged from the Summit participants that HIV vaccine research should shift in favor of discovery, however must not include a moratorium on clinical research. Participants also expressed a conviction that development of an acquisition-blocking vaccine will require a better understanding of the mechanisms for inducing a broadly reactive, neutralizing antibody response.

Dr. Fauci reported that NIAID is developing an implementation strategy for rebalancing HIV vaccine research that includes the use of targeted initiatives and select paylines to boost HIV vaccine discovery research. He noted that the amount of funds used for such initiatives will depend on the availability and the quality of the science proposed. These funds will result from redirecting resources from ongoing vaccine development activities. Dr. Fauci also noted overwhelming support from non-scientific groups for the adjustments to the NIAID HIV vaccine research program recommended at the March 2008 summit. NIAID will continue to solicit input from the extramural community on how to meet this extraordinary challenge.

Dr. Fauci also commented on the decision-making process for vaccine candidates that were close to entering clinical testing when the STEP study results were released. He stated that NIAID leadership will carefully examine the proposed clinical trials to assess safety criteria and determine whether each trial would add new knowledge to HIV vaccine research. If warranted, a smaller version of some trials may be permitted. Dr. Fauci noted that NIAID is collecting input from international stakeholders regarding the planned PAVE100 phase IIb trial of a recombinant Ad5 HIV vaccine developed by the NIAID Vaccine Research Center. The trial, if conducted as planned, will enroll individuals in Africa who are at increased risk for HIV infection.

Update on OARAC Working Groups for Treatment and Prevention Guidelines

On behalf of Dr. John G. Bartlett, Johns Hopkins University School of Medicine and Co-chair of the Department of Health and Human Services (DHHS) Panel on Antiretroviral Guidelines for Adults and Adolescents Panel, Dr. Alice K. Pau, NIAID and Executive Secretary of the DHHS Panel on Antiretroviral Guidelines for Adults and Adolescents Panel, summarized the recent activities of the five OARAC Working Groups for Treatment and Prevention Guidelines. There are three Antiretroviral Guidelines Working Groups: Adults and Adolescents; Perinatal; and Pediatric. There are two Opportunistic Infection Prevention and Treatment Guidelines Working Groups: Adult and Adolescents; and Pediatrics. The treatment guidelines are available on the HIVinfo website (https://hivinfo.nih.gov/home-page).

The Guidelines for the Use of Antiretroviral Agents in HIV-1-Infected Adults and Adolescents were updated on December 1, 2007 and again on January 29, 2008. The December 2007 revisions addressed the timing of initiation of therapy, drug resistance testing, pre-treatment testing, and management of treatment experienced individuals. The January 2008 revisions addressed drug regimens used when starting treatment to reflect complications associated with some first-line treatment regimens and includes a section on regimens under investigation. The Working Group has advised clinicians to take into account patient characteristics when making therapeutic choices.

Dr. Pau noted that the Perinatal Guidelines Working Group extensively revised and reorganized the Guidelines for Use of Antiretroviral Drugs in Pregnant HIV-Infected Women for Maternal Health and Interventions to Reduce Perinatal HIV Transmission in the United States, which were released in November 2007. Revisions address antepartum management of patients co-infected with hepatitis B virus (HBV), and provide updated information on various antiretroviral (ARV) drugs and on major studies of ARV prophylaxis for preventing mother-to-child transmission (PMTCT) of HIV.

Guidelines for the Use of Antiretroviral Agents in Pediatric HIV Infection were released in February 2008. The revisions included changes in when to initiate recommended therapies and updated appendices with toxicity information. The Pediatric Working Group is currently revising recommendations for management of ART-experienced children

Dr. Pau stated the revised Guidelines for Prevention and Treatment of Opportunistic Infections in HIV-Infected Adults and Adolescents will be released in summer 2008. This revision will combine prevention and treatment guidelines into one document and will re-emphasize the importance of managing opportunistic infections (OIs) for improved patient survival and quality of life. The guidelines focus on patients in the United States. The revisions also will address initiation of ARV therapy; immune reconstitution syndrome; management of pregnant women with OIs; immunizations; management of tuberculosis and HBV; and geographic medicine. Revised Guidelines for Prevention and Treatment of Pediatric Opportunistic Infections among HIV-Exposed and HIV-Infected Children will be available in late summer 2008.

Dr. Curran commended the members of the Treatment Guidelines Working Groups and other non-NIH government personnel in acting quickly to move published research findings into standard practice.

Director’s Report

Dr. Whitescarver welcomed everyone to the meeting of OARAC. He welcomed Dr. Diana Lopez, who was named the new Ex-Officio member of OARAC from the National Cancer Advisory Board. He noted that Dr. Lopez is a Professor at the Miller School of Medicine; Director of the Microbiology and Immunology undergraduate program at the University of Miami; and Co-leader of the Tumor Immunology and Immunotherapy program at the Sylvester Comprehensive Cancer Center. He stated that her research activities are in the area of breast cancer, cell mediated immunity, and mechanisms of tumor evasion in animal models. He also noted that she is a past president of the International Association for Breast Cancer Research, has served on many NIH study sections, participated in site visits, and has been a member of special NIH panels.

Dr. Whitescarver thanked several members of the Council whose terms will expire in September 2008; thus the April 17, 2008 meeting was their last official Council meeting. He thanked: Dr. Arlene D. Bardeguez of the New Jersey School of Medicine; Dr. John H. Kempen of the University of Pennsylvania; Dr. Kurt Organista of the University of California, Berkeley; and Dr. Michael S. Saag of the University of Alabama at Birmingham. Dr. Whitescarver presented each with a certificate of appreciation from the Secretary, DHHS, and thanked them for their years of service and guidance.

Dr. Whitescarver welcomed two Ad-Hoc members invited to join the discussions of the Council. He recognized Dr. Jane Peterson, the Associate Director for Extramural Research at National Human Genome Research Institute (NHGRI), who directs the NHGRI comparative sequencing program. She has served as scientific administrator for the Human Genome Project since its inception. He also recognized Dr. Richard Anderson, a Program Director in the Developmental and Cellular Processes Branch of the National Institute of General Medical Sciences. He has a broad array of research interests, including the genetic basis of human biology; pharmacogenomics; and ethical, legal, and social issues in genetics. He noted that Drs. Peterson and Anderson represent two Institutes with significant research portfolios and accomplishments in the area of genetics and genomics.

Dr. Whitescarver announced that Dr. Gina M. Brown joined the staff of the OAR as Medical Officer and Coordinator of the NIH Microbicide Research Program. Dr. Brown received her M.D. from Case Western Reserve University Medical School and is board-certified in Obstetrics and Gynecology. In addition, she is an internationally-recognized physician-researcher with extensive experience in the conduct of NIH-supported clinical studies. Dr. Whitescarver noted that Dr. Brown previously served as a member and Chair of OARAC. He commented that she had provided crucial advice to OAR, not only as a member of OARAC, but also as a member of the OAR Microbicides Research Working Group and a member of a number of the Planning Groups that participate in the development of the annual Trans-NIH Plan for HIV-Related Research. Dr. Whitescarver stated that he was delighted to welcome her to the OAR staff to lead a priority area of AIDS prevention research.

Conflict of Interest Statements

Dr. Whitescarver reminded Council members to review and sign the conflict of interest statement provided to them. He stated that NIH policy requires that all individuals appointed to serve as Advisory Council members must complete financial disclosure forms and that he is required to certify that all OARAC members have complied with this requirement.

Microbicide Research Working Group Update

Dr. Whitescarver reported that NIH established the Microbicide Research Working Group (MRWG) as a result of an OARAC recommendation. This independent, non-government panel of experts advises NIH and other government and non-governmental partners that support microbicide research and development. The MRWG held its first face-to-face meeting in conjunction with the International Microbicide Conference in Delhi, India in February 2008. Dr. Whitescarver asked Dr. Gina Brown to present a brief report on the Working Group’s deliberations.

Dr. Gina Brown reported on the February 2008 MRWG meeting that was chaired by Dr. Ashley Haase, University of Minnesota, and attended by the MRWG members, who are experts in many aspects of HIV/AIDS research, including microbicides, basic and clinical science, social and behavioral science, anthropology, and epidemiology. The Working Group also includes individuals involved in HIV/AIDS and microbicides program policy and development. Dr. Brown stated that the Working Group recommended standardization of some aspects of microbicide clinical trial design to enhance the interpretation and inter-study comparability of data, safety measures, and reporting. Dr. Brown reported that the Working Group discussed the need for standardized methodology for prioritizing microbicide candidates for advancement through the development and clinical trials pipeline. She also noted that the MRWG recommended the establishment of a centralized catalog of ongoing, completed, and planned microbicide clinical trials; an increased focus on microbicides containing antiretrovirals; and multi-disciplinary research. In addition, the Working Group suggested including adherence studies in clinical trials, developing biomarkers for adherence, studying the utility of microbicides with a single active compound to improve adherence, and increasing the focus on the basic science of microbicides.

Council of Councils

Dr. Whitescarver explained that the NIH Reform Act of 2006 provided new authorities to the NIH that are envisioned to enhance trans-NIH research activities. This Act included the establishment of the Division of Program Coordination, Planning, and Strategic Initiatives (DPCPSI), within the Office of the Director of NIH. The purpose of DPCPSI is to identify and report on research focused on novel scientific opportunities, emerging public health challenges, and/or knowledge gaps that deserve special emphasis and would benefit from the conduct of additional multi-Institute research or otherwise benefit from strategic coordination and planning. 
Dr. Whitescarver noted that the NIH Reform Act also established the “Council of Councils,” a body of approximately 30 members selected from NIH Institutes, Centers, and Offices (ICOs) Advisory Councils, representatives nominated by the NIH Office of the Director program offices, and public representatives. The Council of Councils’ role is to advise the NIH Director on matters related to the policies and activities of DPCPSI and to advise on research proposals that would be funded by the new Common Fund. The Council of Councils is currently administered by the Office of Portfolio Analysis and Strategic Initiatives. Dr. Whitescarver reported that the OARAC representative on the Council of Councils is Dr. Coleen K. Cunningham of Duke University Medical Center and asked her to summarize the group’s first meeting. Dr. Cunningham reported on her attendance at the first meeting of the Council of Councils. She noted that members of the Council of Councils are expected to think broadly and be bold in their role.

Budget Update

Dr. Whitescarver reported that NIH has had an essentially flat budget for the past five years that has led to an approximate 25 percent loss in buying power. In FY 2006, the total for NIH AIDS research funding increased by $11million. He noted that utilizing OAR’s unique budget authority to shift funds to higher priority research, he was able to increase funding for HIV vaccine research by $100 million. He noted that in subsequent fiscal years of budgetary constraints, he has identified additional resources for prevention, specifically microbicides and behavioral research by decreasing funding for therapeutics and natural history and epidemiology research. Since the tight budget era for NIH is projected to last beyond FY 2009, any new research must be funded with resources from shutting down or restricting other projects.

Meeting Overview

Dr. Whitescarver reported that he had spoken with Dr. Zerhouni about a year ago about the need to refocus AIDS research on “back to basics” and his interest in bringing together and coordinating NIH genetics and genomics resources that can be applied to AIDS research. Dr. Whitescarver noted that since his discussion with Dr. Zerhouni, he spoke with Dr. Francis Collins, Director, NHGRI, and Dr. Anthony Fauci, Director, NIAID, about the importance of such an initiative. He also noted that the recent HIV Vaccine Summit hosted by NIAID further underscored the need for such a “back to basics” effort. Dr. Whitescarver stated that for these reasons, the topic of genomic studies of HIV and the host immune response was chosen for the OARAC meeting.

Dr. Whitescarver stated that the application of genomics, proteomics, systems biology, and other approaches promises to increase the understanding of virus-host interactions, knowledge that may eventually lead to improved strategies for prevention of HIV infection and treatment for HIV disease. Dr. Whitescarver explained that the OARAC agenda was designed as a scientific workshop to highlight the need to examine, in depth, ways to fill knowledge gaps that have been revealed by recent disappointing clinical trial results. He was especially pleased that the OARAC meeting speakers included several young investigators, who are making innovative contributions to the field. Dr. Whitescarver stated that he looked forward to a lively discussion of possible avenues for discovery research, including the application of genomics and genomics-related tools to the study of HIV and the host response. He said that such studies may ultimately lead to the development of innovative treatment and prevention strategies that can be used to combat the AIDS pandemic.

Dr. Whitescarver asked Dr. Karin Lohman, who now serves as the OAR Strategic Planning and Evaluation Officer, to take the lead in planning the OARAC agenda and to set the stage for the discussions at the meeting.
Dr. Lohman outlined the OARAC meeting agenda. She noted that over the past 25 years, the NIH and other federal agencies have invested billions of dollars in genomics research. She stated that the returns on this investment have been enormous and dividends will be realized for many years to come. Dr. Lohman explained that the OARAC meeting had evolved into a scientific workshop that would include reports on bacterial and primate genomics studies, the use of genomics and genomics-related technologies to study HIV etiology and pathogenesis, and genomic insights into mechanisms of pharmacological control of HIV replication. She highlighted the need for cross-disciplinary research and collaboration to link the large amounts of data generated from the application of high throughput genomics and genomics-related technologies to biological function. Dr. Lohman stated that the meeting would provide a forum to discuss opportunities to apply genomics methodologies to studies of HIV disease and the host immune response. 
Dr. Curran asked OARAC members to develop recommendations to NIH and OAR on the role of genomics in HIV research and the need to provide resources for this important area of research based on the presentations that followed.

Use of Genomics to Understand Bacterial Diversity and Virulence, Study Host-Pathogen Interactions, and Identify Vaccine Candidates and Drug Targets

Dr. Hervé Tettelin, University of Maryland School of Medicine and the Institute for Genome Sciences discussed his research on bacterial diversity and reverse vaccinology. He also discussed the use of powerful new sequencing technologies to generate high quality genomic sequence data. He discussed the concept of the “pan-genome” and investigations of multiple strains of Neisseria meningitis, Group B streptococcus (GBS), Group A streptococcus(GAS), and Bacillus anthracis. He also discussed the development of GBS vaccine candidates using “reverse vaccinology”.

Dr. Tettelin discussed the power of combining different sequencing technologies, which can virtually eliminate the gaps in genome sequence inherent in the use of the technologies individually, yielding very accurate sequence data. These new systems also can aid in the discovery of single nuclear polymorphisms (SNP).
Dr. Tettelin and his colleagues combined DNA sequencing with the use of microarray technology to examine bacterial diversity between different strains of bacteria. They discovered that a surprising amount of genomic diversity can exist between different strains of the same species. This discovery led to the development of the concept of a “pan-genome.” He explained that the pan-genome encompasses the core bacterial genome consisting of all the genes shared across multiple strains within a species, as well as the genes present in some, but not all, strains. Dr. Tettelin introduced the terms “closed pan-genome species” and “open pan-genome species.” Species with no genes except the sets of shared essential and nonessential genes are termed “closed pan-genome species.” Bacteria in this category, such as Bacillus anthracis, require genome sequencing of only a few strains to identify all genes in the pan-genome. Open pan-genome species, such as group B streptococcus (GBS), have a “strain-specific genomic halo,” or genes that are present in only one strain of a species. For open pan-genome species, it is not clear how many genomes must be sequenced to find all possible trace genes. 
Dr. Tettelin reviewed his laboratory’s development of a Web-based bioinformatics tool for comparative genome analysis of bacterial sequences. They are designing a set of databases that integrates data from multiple “omics” (genomics, proteomics, etc.) approaches and presents it in a format that can be readily queried, e.g. to determine regions of biologically relevant genetic diversity.

Dr. Tettelin reviewed his work using “reverse vaccinology,” a process that applies high throughput genomics and bioinformatics to the discovery of vaccine candidates. Dr. Tettelin and colleagues worked with Dr. Rino Rappuoli, Novartis Vaccines and Diagnostics, to apply reverse vaccinology in the search for a vaccine against N. meningitis. A vaccine candidate containing a cocktail of four antigenic peptides currently is in phase III clinical testing. 
Dr. Tettelin and his colleagues now are applying reverse vaccinology within the context of a pan-genome approach to develop vaccine candidates against GBS. They have discovered an optimally antigenic cocktail containing four GBS proteins, only one of which is coded for by a gene in the core genome. The other three proteins in the antigenic cocktail are coded for by genes in the “dispensable genome” (e.g., genomic sequence not present in all strains). These results highlight the benefit of considering the pan-genome in vaccine development.

Dr. Tettelin commented on ongoing high throughput projects to crystallize and study the structure of all families of HIV surface proteins, including those of unknown function. The hope is to develop a model structure for each HIV surface protein and to combine comparisons of protein structures with evolutionary studies based on the genome sequence. He also noted that after obtaining the pan-genome sequence for GBS and N. meningitis, it took about 18 months to identify the antigen cocktail that elicits the maximum immunogenic response in animal models.

Primate Genome Sequencing: A Status Report

Dr. David L. Nelson, Baylor College of Medicine, spoke about primate genome sequencing, the Human Genome Project, improved genomics technologies, non-human primate genomics, the Rhesus Macaque Project, and future research directions.

Since accomplishing the sequencing of the human genome in 2003, researchers have been filling sequencing gaps, improving the accuracy of the sequence, acquiring additional sequences to understand human variation, and building resource tools. For example, researchers have developed haplotype maps (HapMaps), or maps of human SNPs from many related individuals to aid in the discovery of disease-associated variants common throughout the human population. Researchers also have discovered that humans vary in the copy number of their genes. For example, copy number of the CCL3 gene affects susceptibility to HIV infection. Dr. Nelson mentioned the collaborative “1,000 Genomes Project” aimed at sequencing additional human genomes. Another new technology, exon capture, uses oligonucleotide arrays to isolate exons of specific genes for sequencing.
Dr. Nelson reported that the chimpanzee genome was published in Nature in 2005 and the macaque genome was published in Science in April 2007. Investigators are working on sequencing genomes of other nonhuman primates, including the bonobo, gorilla, orangutan, gibbon, and baboon. Dr. Nelson noted the usefulness of comparative genomics to better understand the function of human genes.

The recently published macaque sequence is allowing investigation of orthology relationships and the “humanness” of genes. Orthologic investigation revealed that genomes are much more dynamic than originally appreciated. In the human, macaque, and chimpanzee, different genome sequences have been duplicated and dispersed throughout the genome. The selective constraints that have driven this duplication and dispersion of genetic material are not known. Dr. Nelson and colleagues are investigating possible explanations for the benign presence of gene mutations in macaques that cause diseases in humans.

Dr. Nelson suggested that development of SNP maps, HapMap-like resources, and exon capture experiments are the next step in primate genome research. Studies of genes and gene families may be applicable to infectious disease research. Other areas of interest include characterization of large-scale evolutionary genomic rearrangements, and complementary DNA (cDNA) sequencing to support expression analysis. Dr. Nelson proposed that the rhesus and chimpanzee genome sequencing projects be completed to levels approaching that achieved for the human genome project. He noted that this work will require additional primate genome sequencing tools and other resources that are increasingly difficult to acquire, such as chimpanzee and some other non-human primate animal tissue samples.

Dr. Nelson answered OARAC members’ questions on the feasibility of sequencing particular sections of the human genome in large numbers of people to learn more about the function of SNPs that affect susceptibility to HIV infection. He referred to Dr. Goldstein’s approach, presented later in the meeting, of searching genome wide for genetic loci that associate with susceptibility to HIV infection, disease progression, etc. Another low cost approach would be to investigate candidate genes using exon capture methods to study coding sequence variations.

Host Genetic Determinants of Response to HIV-1

Dr. David B. Goldstein, Duke University Medical Center, presented on the Center for HIV/AIDS Vaccine Immunology (CHAVI) program that is focused on identifying host gene variants that influence the early responses to HIV infection and disease progression. Dr. Goldstein noted that CHAVI research may help determine the role of immune mechanisms of HIV control observed in the general population. These studies also may provide insights that inform the development of an AIDS vaccine.

Dr. Goldstein reported that new technologies, such as the HumanHap550 BeadChip, allow researchers to represent virtually all of the approximately 10 million common genetic variations in the human genome. However, the technology cannot probe rare genetic variants. BeadChip technology is based on the premise that certain variants tend to associate together in sets. Therefore, detection of a subset of associated variants implies the presence of the larger set of variants. The BeadChip works well in analyzing samples from individuals not of African ancestry, but less well in samples from individuals who have a primary African ancestor in their genetic makeup. This phenomenon appears to be caused by a lower degree of association among common genetic variants in individuals of African ancestry.

Dr. Goldstein and colleagues used the HumanHap550 BeadChip to study viral load set point, or the level of viral load maintained during the asymptomatic period of HIV infection. Dr. Goldstein and his collaborators from Europe and Australia assembled a cohort of patients with proven recent infection, high quality longitudinal viremia data, and who had given informed consent for genetic studies. They conducted a genome-wide association study using the cohort to identify variants associated with disease progression. Their analysis revealed two previously unidentified genetic variants associated with HIV control: one in the human leukocyte antigen C (HLA-C) gene and the second in the zinc ribbon domain-containing 1 (ZNRD1) gene. They also identified a third variant that had previously been shown to be a controlling allele for HIV. Dr. Goldstein and colleagues estimate that about 14 percent of variation in HIV progression in the studied population is explained by the combined effect of these two newly identified variants. Interestingly, these variants appear to be associated with disease progression in individuals of European ancestry, but not in individuals of African ancestry.

Dr. Goldstein presented findings showing a strong association between beneficial immune variants and HIV control. They found that for individuals who have no known beneficial variants for alleles involved in HIV control, CD4+ cell counts drop below 350 cells/μL within an average of two years of HIV infection. In individuals with multiple beneficial alleles, it takes an average of 8 years for CD4+ cell counts to drop to this level. Dr. Goldstein noted that these findings highlight the promise of research on the genetics of HIV control.

Dr. Goldstein and colleagues were not able to identify a role for HLA-C or ZNRD1 variants in HIV control in individuals of African ancestry. They would like to expand their studies to identify the role of genomic variants in HIV control in this population. Other plans for future research include systematic screening for the effects of genetic interactions on HIV control and further research on the genetic determinants of acquisition of HIV infection. Dr. Goldstein is studying previously unknown genetic variants that influence resistance to HIV infection, including important rare variants.

Finding Host Proteins Required for HIV Replication

Dr. Abraham L. Brass, Harvard Medical School, described his collaborative work with Dr. Judith Lieberman of Children’s Hospital Boston on the identification of host proteins for HIV replication. He reviewed the complicated HIV lifecycle and the genes and proteins known to be essential for its replication. Dr. Brass noted that every protein that is necessary for viral replication is a potential weakness that could be exploited by host-directed therapies.

Dr. Brass reviewed the use of RNA interference (RNAi) technology to identify HIV-dependency factors (HDFs). This technology uses non-coding, small RNAs (micro-RNA) to interact with cellular machinery to regulate gene expression. This technology can be harnessed to deplete cellular proteins, one by one and in an unbiased fashion, to observe the effect of that depletion on phenotype.

Dr. Brass and colleagues worked with two different micro-RNA screening techniques: small-interfering RNAs (siRNAs) and short hairpin RNAs (shRNAs). siRNAs are a class of double-stranded RNAmolecules that transiently interfere with the expression of certain genes when transfected into a population of cells. Short hairpin RNA (shRNA) technology works similarly, but can be used to create pools of stably infected cells and allows long term interference with specific genes.

Dr. Brass and colleagues used a combination of shRNA and siRNA technologies to identify 273 proteins associated with HIV replication, from an original screen of about 21,000 human genes. These proteins included several that are known to affect HIV replication, including CD4 and CXCR4. The 273 proteins also included several enzymes known to be important for HIV replication: e.g., DDX3 helicase, and ZNRD1.

Bioinformatics analysis confirmed that many of the identified proteins were indeed involved in the HIV life cycle. Dr. Brass and colleagues are investigating several proteins identified in their screen, including transportin-3, which may transport HIV into the host nucleus. Preliminary results indicate that proviral formation is blocked when this protein is depleted. Dr. Brass and colleagues are investigating the mechanism of this effect.

Dr. Brass’ future plans include the development of a systems-level understanding of HIV and host cell interactions. He and colleagues would like to screen additional siRNA and shRNA libraries to identify and validate HDFs not identified in their previous investigations. They also plan to investigate the mechanistic role of HDFs and HDF pathways and to begin performing small molecule screening for compounds that may inhibit HIV infection and/or replication. Dr. Brass anticipates this work may advance the knowledge needed to define better HIV therapies and therapeutic targets.

OARAC members discussed the importance of studying both immune-mediated mechanisms and non-immune-mediated mechanisms of HIV control. They affirmed the need for interaction between genetic discovery and biological studies to identify important HIV-associated factors and to elucidate their function. Attendees also discussed the need for a better animal model for HIV disease and the potential value of a repository of T-cell lines that could be used for siRNA and shRNA studies.

Impact of Immune Pressures on HIV Evolution

Dr. Todd M. Allen, Harvard Medical School, presented his research on the impact of immune pressures on HIV evolution. Dr. Allen’s talk focused on HIV and viral genomics and the interplay between the immune response and viral diversity. Dr. Allen noted the large collection of evidence suggesting that CD8+ T cell responses are a driving force of the evolution of HIV in an infected individual and also at the population level.

Dr. Allen reviewed the biology of the immune response to HIV infection. In general, HIV infected cells express HLA class I alleles that present viral peptides on the cell surface to permit recognition and elimination by the adaptive CD8+ T cell response. There are numerous genetic variants of HLA class I alleles, only some of which are present in each individual. Therefore, each individual infected with HIV will mount a tailor-made immune response against very specific regions of the virus. One difficulty in HIV vaccine research is in defining which immune responses are correlated with effective immunity. However, evidence from elite controllers of HIV infection suggests that the most effective responses may be characterized more by the attack against specific vulnerable viral targets than by the broadness of immune response.

Dr. Allen and colleagues seek to identify correlates of immunity by studying HIV sequence evolution. They examined viral diversity and the adaptation of the virus to specific host immune responses. They identified HIV mutations that allow the virus to escape immune control, but impair viral replication. These mutations, which usually occur in highly conserved regions of the HIV genome, often revert to the more common variant upon transfer to a new host. Dr. Allen and colleagues also identified an HIV variant that mutated to escape from immune responses against its gag epitope that had impaired viral replication. They observed that compensatory mutations in other regions of this variant’s genome partially restored the rate of viral replication, thus allowing escape from immune control. Dr. Allen and colleagues, as well as other researchers, found similar results when examining other documented HIV escape variants. Dr. Allen’s research suggests that the protective HLA alleles drive mutations at highly conserved regions of the virus. Dr. Allen currently is working with the Broad Institute to generate a large database of full-length HIV genome sequences that can be used to study the relationship between viral diversity, HLA alleles, and immune control

Exploring the Limits of HAART: New Insights into Residual Viremia, Eradication, and the Fundamental Mechanism of Pharmacologic Control of HIV Replication

Dr. Robert R. Siliciano, of the Howard Hughes Medical Institute and Johns Hopkins School of Medicine, discussed three elements necessary to cure HIV infection: 1) prevention of viral replication with antiretroviral therapy; 2) identification of all stable reservoirs in which the virus can persist; and 3) elimination of all viral reservoirs.
Dr. Siliciano hypothesized that highly active anti-retroviral therapy (HAART) stops all HIV replication and that the residual viremia in individuals with HIV on therapy is caused by the occasional reactivation of dormant cells from reservoirs containing latent virus, such as a small pool of memory CD4+ T cells.

Dr. Siliciano outlined four testable predictions related to his hypothesis: 1) HIV in the plasma should resemble the HIV present in the latent reservoir; 2) it should be possible to have viremia without viral evolution; 3) intensification of therapy should not produce a decrease in residual viremia; and 4) it should be possible to explain pharmacologically how ARV therapy can control all viral replication. He presented data in support of all four concepts.

Dr. Siliciano presented detailed mathematical modeling data to support his fourth prediction. He reported that ARV drugs exhibit a phenomenon similar to cooperativity of ligand binding. Dr. Siliciano and colleagues used this model to compare drug concentration to drug efficacy as measured by percent of uninfected cells.
Dr. Siliciano reported that their results showed that different ARV drugs exhibit different levels of ligand binding cooperativity. For example, AZT-like drugs and integrase inhibitors showed no cooperativity. Non-nucleoside reverse transcriptase inhibitors, protease inhibitors, and fusion inhibitors generally show some level of cooperativity. Dr. Siliciano suggested that drugs that show this cooperative effect typically target cellular complexes that are present in multiple copies in one cell, which creates a form of intermolecular cooperativity.
Dr. Siliciano noted that traditional measures of ARV drug effectiveness do not consider a possible cooperative effect between dosage and efficacy. He and colleagues developed a new index of antiviral activity, the “instantaneous inhibitory potential,” that considers the impact of cooperativity. Dr. Siliciano suggested that inhibitory potential may provide a means to help predict the antiviral activity of ARV drugs, although ultimate clinical outcomes will depend on many factors.

Dr. Siliciano reported that experimental results from his laboratory are consistent with his hypothesis that there is no ongoing viral replication in individuals with HIV who are on HAART; and therefore there is no viral evolution or development of new drug resistant mutations. He postulated that free virus in the plasma represents virus released from latent reservoirs without additional cycles of replication. He also proposed that not all stable viral reservoirs have been identified. He stated that his laboratory will to continue to work to identify additional reservoirs and to develop strategies for eliminating latent viral reservoirs.

Can Systems Biology and Functional Genomics Reveal the Secrets of AIDS Pathogenesis and Vaccine Efficacy? 
Dr. Michael G. Katze, University of Washington, discussed functional genomics and systems biology approaches for studying AIDS pathogenesis. Dr. Katze defined microarrays as a mechanism or technique to examine global gene expression in cells and tissue at the RNA level. He defined proteomics as a high-throughput technique to examine global gene expression at the protein level. Dr. Katze noted that bioinformatics platforms include sophisticated computational infrastructure, hardware, and software to compile, store, and analyze the enormous amount of data generated by high throughput technologies. He stipulated that systems biology requires investigators to embrace new approaches, take advantage of “-omics” technology, and work together with mathematicians and biostatisticians.

Dr. Katze stated that a systems biology approach is essential to HIV research because of the incredible complexity of the virus. Systems biology can help elucidate the global impact of viral infection on host gene expression, discover cellular regulatory pathways targeted by viruses, identify new cellular targets for antiviral therapy, inform vaccine development, and inform basic research.

Dr. Katze reported that he and his colleagues are collaborating to apply systems biology approaches to HIV research. He described one project that used in vitro microarray technology to identify 600 host proteins in CEMx174 cells that underwent change after they were infected with HIV. By contrast, two dimensional gel electrophoresis and other traditional protein detection techniques typically identify 20 to 40 proteins under similar conditions. Dr. Katze also reported that, in collaboration with Dr. Michael McCune of the University of California at San Francisco, his laboratory also applied systems biology to explore the differing pathogenicity of simian immunodeficiency virus (SIV) infection in several non-human primates. He stated that pilot project data suggest that a critical distinction between pathogenic and non-pathogenic infections may lie in the balance of pro-inflammatory versus anti-inflammatory innate and adaptive responses to acute infection. Dr. Katze stated that his laboratory, in collaboration with Dr. Marjorie Guroff of NCI, is developing RNA profiling techniques to compare differential regulation of genes during a successful vaccination compared to unsuccessful or no vaccination in non-human primates.

Dr. Katze proposed that the availability of high throughput technologies, coupled with interdisciplinary research and systems biology approaches, may lead to the development of improved antiretroviral drugs and an effective HIV vaccine. He envisions the integration of functional genomics into main stream basic research; improved understanding of host-pathogen interactions and the power of computational biology; and elucidation of host responses to viral pathogens as an integrated whole. Dr. Katze noted that his laboratory is planning to refine RNA profiling techniques to study immune responses to vaccination.

General Discussion

The OARAC members’ discussions underscored the importance of genomics, systems biology, and transdisciplinary studies to HIV research. Dr. Whitescarver noted that the NHGRI and NIAID are interested in conducting additional research in these areas if sufficient funds are available. Dr. Whitescarver stated there is a need to attract experts to the field of HIV research who are familiar with high throughput/systems biology tools. 
Dr. Curran asked for input on how OAR or NIH might facilitate the marriage of the technologies discussed at this meeting with HIV research. OARAC members discussed the need for increasing the number of investigator-initiated grants in this area of research. Dr. Curran noted the challenge to increase research activities in the area in an era of budgetary constraints.

Public Comments

Ms. Patricia Nalls, the founder and Executive Director of the Women’s Collective, a woman focused, peer-based, and family-centered HIV/AIDS organization based in Washington D.C., stated that she was appreciative of OARAC’s commitment to making microbicides research a priority. Ms. Nalls noted that HIV disease is a vitally important issue for women, especially women of color.

Ms. Nalls urged the Council to commit to the inclusion of women living with HIV/AIDS, especially women of color, in clinical trials of microbicides. She also noted the importance of determining the effects of microbicides on HIV-infected women and understanding the interactions between microbicides containing ARVs and ARV drugs. Ms. Nalls requested that women living with HIV/AIDS be included on the OARAC and that OARAC promote greater involvement of community-based organizations and AIDS service organizations in policy discussions.

Adjournment

Drs. Curran and Whitescarver thanked the OARAC members, speakers, and discussants for their participation in the Council meeting. Dr. Whitescarver commented that genomics research will generate additional enthusiasm for AIDS research, attract new researchers to the field, and yield scientific advances that may lead to new prevention and treatment strategies. Dr. Whitescarver again thanked Drs. Bardeguez, Organista, Kempen, and Saag for their years of service on OARAC. 
The meeting adjourned at 5:00 p.m. on April 17, 2008.
Signed:
/Jack Whitescarver, Ph.D./
Jack Whitescarver, Ph.D., Executive Secretary
/James W. Curran, M.D., M.P.H./
James W. Curran, M.D., M.P.H., Chair