Report from genomics workshop at CROI
Svilen Konov, HIV i-Base
This years CROI had an intensely broad coverage of studies in the field of genomics and HIV. Indicative of this interest was a well attended special workshop on genomics and HIV, organised on the first day.
The opening broad question posed was how to search the genome for determinants of response to HIV. David Goldstein from the Duke University, US showed how some of the analysis software tools that his team has developed work in practice .
He illustrated their use in a whole genome association study seeking to identifying genes, influencing set point, making use of both samples from the MACS cohort and a new cohort, called EuroChavi, that has been developed as a collaboration between CHAVI (Center for HIV/AIDS Vaccine Immunology) and multiple European cohorts. This will allow associations from different genetic phenotypes to be related to individual clinical response.
Another presentation on genotype technologies by Kevin Scianna also from the Duke University provided insights of how a genome-wide screen using DNA chips that detect up to 650 000 single nucleotide polymorphisms (SNPs) will be performed. Many of those SNPs are tagging SNPs representing other closely associated variations in the genome. The tagging arrays detect deletions and duplications, commonly referred to as copy number variations (CNV). The genome-wide identification of CNV is now possible through the use of high-density SNP-based arrays. The importance of this new analysis and mapping comes from the fact that it is highly probable that some CNV will be associated with certain complex diseases or traits. Hence, the identification of these variants plays a role in genome-wide association studies. This can help for targeting diseases like rheumatoid arthritis and systemic lupus erythematosis.
Amalio Telenti from the University of Lausanne, Switzerland showed several practical applications of genomic analyses. 
Susceptibility to HIV-1 and the rate to disease progression reflect the influence of the genetic diversity of the virus as well as variations in the host factors. Identification of relevant genetic variants provides information of interest for understanding pathogenesis, for diagnostics, and for therapies. Currently, approximately 50 candidate genes are being investigated. Current knowledge, however, can explain only a fraction of the observed variability in the course of HIV-infection. The practical use of the genetic analysis will depend mainly on its cost-effectivenes and on validation through clinical trials.
The recent discoveries of intrinsic restriction mechanisms against HIV have focused attention on how primates bodies defend against retroviral infections. 
It is already known that the strategies often involve a direct interaction between the host encoded antiviral proteins and viral proteins. The single stranded DNA editing enzyme APOBEC3G was discovered as a result of its ability to restrict a vif-deficient HIV-1 virus. APOBEC3G interactions with gag-encoded proteins ensure the packaging of the editing enzyme into the viral capsid, but avoiding interactions with the viral accessory protein vif is also of major importance in order to avoid proteolytic degradation (a process where a targeted protein is recognised for degradation by the ubiquitinating enzyme complex, then a polyubiquitin chain is formed on the target protein, and finally the protein is digested by the proteasome complex).
The cytoplasmic protein TRIM-alpha was also discovered because it conferred restrictive ability against HIV-1 to rhesus cells and TRIM5-alphas viral capsid-binding discriminative domain determines its antiviral specificity. Antagonistic proteins locked in such conflicts are predicted to be subject to rapid evolution. As one protein evolves to avoid interactions while the other evolves to restore them (referred to as the Red Queen hypothesis). We now know that both APOBEC3G as well as TRIM5-alpha have been subject to such rapid evolution. These episodes of rapid evolution date back to (or before) the evolutionary origin of primates (approximately 35 million years ago), much before the origin of lentiviruses like HIV-1.
Thus, in spite of the fact that both APOBEC3G and TRIM5-alpha were discovered because of their anti-HIV effect, the constant evolutionary pressure imposed by endogenous retroviruses mobilising in primate germ lines is likely responsible for their rapid evolution and species-specificity. We have been able to use the signature of rapid evolution to identify a small patch in the TRIM5-alpha protein that is responsible for antiviral specificity, highlighting the power of such evolutionary analyses. Screening human populations for genetic variation in TRIM5-alpha, an impaired allele at an unexpectedly high frequency (~ 50%) in certain ethnic groups was uncovered.
David Haas from the Vanderbilt University in the US had a talk on genetic cohorts and application of the data in pharmacogenetics. 
Even though antiretroviral medications greatly reduce morbidity and mortality in people living with HIV/AIDS, drug toxicity is still a major problem. The field of pharmacogenomics seeks to understand the influence of human genetic variants in response to medications. Investigators worldwide have begun to identify associations among human genetic variants, predisposition to HIV drug toxicities, and likelihood of virologic failure. Pharmacogenomics also holds promise to identify novel targets for drug development. The seminal discovery that a naturally occurring, nonfunctional variant of the HIV receptor gene CCR5 protected against HIV infection fostered the development of CCR5 antagonists. Numerous laboratory methods are now available for rapidly identifying genetic variability, and technological advances of genomic analysis are progressing at a rapid pace. However, deciphering relationships between such variants and clinical outcomes during HIV disease and its therapy remains a difficult task, and often requires large sample sizes. The speaker suggested that investigators must establish and utilize large DNA banks linked to cohorts and clinical trials to allow future unplanned analyses.
Because of the well-recognised risk of false discovery due to multiple comparisons in high-throughput human genomic association studies, such repositories are critical both for the initial identification of potential genotype-phenotype associations, and for validation of initial putative associations. Through continued translational and applied research, pharmacogenomics will ultimately benefit persons living with HIV worldwide by identifying new targets for novel therapeutics, through individualised drug prescribing that is informed by human genetic testing, and by anticipating the likely frequency of adverse treatment events among diverse populations worldwide based on knowledge of genetic architecture, concluded the researcher.
- Goldstein D., Shianna K., et al. Searching the genome for determinants of response to HIV. Workshop 3a.
- Shianna K. Genotyping technologies: small and large scale studies. Workshop 3b.
- Telenti A. Practical applications in HIV disease. Workshop 3c.
- Malik H., Emerman M. Intrinsic immunity against retroviruses in primate genomes: evolutionary retrospectives and prospectives. Workshop 3d.