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HIV and Host Genetics: Complexity and Contradiction

By Bob Huff

January/February 2004

I vividly remember the moment I understood how complex the life cycle of HIV must be and how difficult it could become to find a cure. During a press briefing at the 1989 International Conference on AIDS in Montreal, Professor Jay Levy, of the University of California, San Francisco, was asked about the prospects for halting the devastation of AIDS. He said the course of the disease in any one person was due to interactions between the virus, the host and the environment. Host genetics were stable, viral genetics evolved, but the environment within the body could be manipulated with medicine. Science needed only to find some process necessary to HIV's survival and block it -- without upsetting anything the host requires to remain healthy.

The first generation of HIV drugs targeted the virus itself. If they also affected some of the body's systems, that was a side effect. Now, as we learn more about HIV's dependency on the body's own cellular functions, a new generation of therapies that act on host factors may be on the horizon. One potential advantage to using drugs directed to host proteins is that viral resistance might become less problematic. While HIV's genetics are wildly error-prone and produce an abundance of mutations every day (and it only takes one successful mutant to launch a resistant strain), the genetics of the human cell are stable. If you can block a host target once, you should be able to block it again and again. Of course HIV may still find a way to mutate around the impediment. A new class drugs called CCR5 blockers are designed to keep HIV from interacting with a protein on T-cells that the virus must bind to before it can infect a cell. The drugs stick to CCR5 and interfere with HIV binding thereby restricting infection. But laboratory studies have demonstrated that, as with every other treatment tried to date, HIV can eventually produce a mutation that evades the obstacle.

So far, all evidence suggests that CCR5 can be blocked without causing harm to the host, which is great news. But the big challenge to using drugs that disrupt natural mechanisms is to make sure they only inhibit HIV's interactions with the system and leave the normal activities alone.


Everyone Into the Pool

To complicate matters, while any one person's genes are stable, there may be important genetic variations between individuals in a population that influence how well a medicine will work. One drug may not behave the same in every body. This is because human genes evolve in a population the way viral genes do in a body, albeit over a much longer period of time. This means there is diversity in our gene pool. Furthermore, each set of genes has a twin; with one coming from each parent. (This, as Bill Clinton knew, is the real meaning of sex.) The gene pairs are called alleles, but not every pair is identical. For example, most people have two working copies of the gene that makes the CCR5 protein that HIV uses to infect new cells. But some people have only one working copy, and a few have none. Because people without a working copy of the CCR5 gene can't make the protein, very few of them become infected. And those who have contracted HIV typically experience minimal disease progression; a CCR5 blocker would be wasted on them.

Host genetics are increasingly recognized to play a role in everything from one's initial susceptibility to HIV infection, to the strength and durability of the immune defense the body can mount, the pace of viral replication and the seriousness of damage done over time, to the likelihood that drug therapy will be successful. A picture is emerging that shows the virus hijacking natural mechanisms at nearly every stage of its life cycle to do the work of transporting, reproducing and distributing itself. Yet we are only at the threshold of grasping the design and shadings of the system's complexity.

At the 11th Annual Retrovirus Conference, HIV's dependence on its host was the subject of a number of important presentations. Speaking at one of the final sessions of the conference, Amalio Telenti, an HIV researcher from the Institute of Microbiology at the University of Lausanne, Switzerland, offered a qualified vision of how knowledge about host genetics might increasingly affect care and treatment for people with HIV.

Biology used to be simple, said Telenti, describing a time when genetic researchers were content to look for the role of single genes that produced phenotypic traits such as blue eyes or fluffy coats. But the field has rapidly evolved as we increasingly understand that phenotype is the net result of many small contributions from multiple genes that shape the complex traits we see in life.

Many host determinants and environmental factors at many points of interaction cumulatively help determine the clinical course of HIV disease. Although many of these factors are still unnamed, acting in concert they are responsible for the wide variability in disease progression rates seen in populations. The time from infection to a serious state of AIDS can average ten years in an untreated individual, but can range from one year to possibly never for a few people. Telenti has modeled the contribution of alleles of various markers of disease progression on the rate of CD4 decline from 500 to 200 in members of the Swiss HIV Cohort. People with the common alleles progressed on average in 5.1 years; those with bad alleles progressed in 3.1 years and those with protective alleles in 7.7 years.

Since a newly diagnosed person may not need or want to begin antiretroviral therapy right away, Telenti proposes that it would be useful to be able to predict when treatment should be started. By analyzing certain host genetic determinants associated with the course of HIV disease, it may one day be possible to predict the slope of T-cell decline and estimate a date when treatment will become advisable. Some of these determinants of faster or slower progression include genes that affect co-receptor availability, such as CCR5, but there are many others with less dramatic impact, such as various HLA types and genes for immune system messengers such as IL10.

A whole host of other host factors come into play when antiretroviral therapy is thrown into the mix. With multiple, variant transport molecules at the gut, the liver and cell, each person will process and eliminate different drugs at slightly different rates and may have different susceptibilities to toxicity. Genetics can help explain the wide variability in drug concentrations that are observed in population studies, and may explain why, for some people, drugs can never quite control their virus.

Telenti says that at least 40 percent of the variance in infectivity and diversity between individuals with HIV may be due to host factors. But, he cautions, the data on most genetic associations represent modest effects with wide confidence intervals. No single polymorphism likely controls the master switch for progression. Yet some human proteins have the potential to grant virtual immunity to HIV.


So Close ... Yet so Far Away

APOBEC3G is a recently identified host protein with the potential to offer innate protection from HIV by scrambling its genetic code. Unfortunately, a viral protein called Vif readily binds to APOBEC3G and defeats its anti-HIV properties. Immediately upon its discovery scientists began asking, could a drug be designed that blocks Vif or binds to APOBEC3G and stops Vif from shutting it down? Amazingly, there is only one amino acid standing between runaway HIV infection and nearly complete immunity to the virus. Nathaniel Landau, of the Salk Institute for Biological Studies in La Jolla, discovered that if the negatively charged amino acid at position 128 of APOBEC3G changes to a positively charged amino acid, then Vif no longer binds and HIV is rendered harmless. Landau's team now plans to look for that mutation in long-term non-progressors to see if perhaps their natural defenses are impervious to Vif. Others will be looking for variant APOBEC3G in different racial and ethnic groups.

APOBEC3G would normally have a tremendous impact on viral replication rates but it is silent in the presence of HIV. Telenti says there are likely dozens of genes that influence the pace of progression, with the net outcome due to a balance between the influence of rapid and slow factors. Landau agrees. He suspects there may be many factors present in cells in low quantities that, if they were strongly expressed, could protect against the virus. One of these may be a host protein called TRIM5; a potential contributor to innate immunity that may explain why monkeys don't get AIDS. Matthew Stremlau, from the Dana-Farber Cancer Institute in Boston, has discovered a protective factor that prevents human HIV from establishing an infection in the simian host. HIV can attach to and enter a monkey's cells, but gets stuck before it has a chance to replicate its RNA. TRIM5 apparently stops the viral capsid from uncoating and exposing its genetic payload. Humans have a variant of TRIM5, but it is not able to block the virus nearly as efficiently as monkey TRIM5. This new point of interference suggests the possibility of administering a block with a drug or possibly gene therapy. More discoveries like this are almost certainly waiting in the wings.


Budding Genius

Although much recent attention has been given to explaining how HIV binds to and gets into a cell, far less is known about how a newly formed virus leaves a cell. This phase of the viral life cycle is called budding. At the Sunday night plenary that opened the conference, Wesley Sundquist, a virologist at the University of Utah, gave a detailed tour of the mechanism HIV uses to export new virions from an infected cell. First, all of the proteins and RNA that make up a new viral particle must be guided through a briar patch of actin molecules that cluster just below the lipid membrane and give shape and mobility to the cell. Then the premature viral core has to be directed to a site on the membrane that is permissive for virus release. Since HIV is clad in an envelope made up of its host cell's lipid membrane, a new virion has to wrap some of the membrane around itself like a tiny bubble then finally pinch off the last tethering bit before it can go free. Cellular factors are at work in every step of the budding and release process, another example of the body inadvertently helping to send new viruses out into the world.

Sundquist's group identified a host protein associated with HIV budding called TSG101. Fortunately, this protein had already been studied for its role in a cellular housekeeping process that sends unwanted cell-surface proteins to their destruction in the lysosome, a membrane-enclosed bubble inside the cell filled with digestive enzymes. The obsolete proteins are marked for destruction then conveyed from the cell's surface and inserted into the lipid membrane of the lysosome. But before they can be destroyed they need to be brought inside the bubble. This is done by pinching off bits of the membrane holding the doomed proteins and forming tiny vesicles, which are released to the interior of the lysosome. In this regard, vesicles are very similar to HIV particles, and the mechanism that forms these vesicles is probably the same process that HIV hijacks to engineer its release from the cell. TSG101 is kind of routing ticket that directs a protein to the vesicle formation machinery. HIV seems to use TSG101 to send itself to the outside world instead. The details of how this happens are complex and not fully understood, although, Sundquist said, so far we know of at least 20 host proteins involved, with more likely to be found. (Sundquist's fascinating lecture can be viewed as a webcast at: www.retroconference.org.) If HIV inserts itself into this chain of events in some unique way, then a possible treatment might be designed to stop or slow budding without causing havoc to any natural process.


All Over the Map

Variability is not only for genes; it occurs in the scientific literature as well. Telenti took an aside to note the many published discrepancies on the significance of certain host proteins for HIV pathogenesis. P-glycoprotein (P-gp) is a membrane-bound drug transport molecule that protects cells from toxic intruders such as cancer chemotherapies and HIV antiretrovirals by pumping them out of cells. But by lowering the concentrations of protease inhibitors within cells, P-gp can hinder antiviral efficacy. Just as some people produce different amounts of CCR5, some people have different alleles of the MDR1 (for multi-drug resistance) gene that produces P-gp, with different sets of alleles producing greater or lesser amounts of P-gp. A study by Telenti's group published two years ago found an association between different MDR1 alleles and greater rises in CD4 counts within six months of starting an antiretroviral regimen containing nelfinavir or efavirenz. The theory is that people who express less MDR1 have less P-gp, which means that less drug is pumped from their cells and antiviral activity remains higher, longer. (See "The Genetic Edge," GMHC Treatment Issues, January 2002.)

But other reports have suggested that P-gp, even in the absence of therapy, might play a role in how permissive cells are to becoming infected with HIV. A few laboratory-based experiments have shown a dramatic decrease in viral replication in cells that produced P-gp abundantly; protection that was lost when P-gp blockers were added. One theory holds that P-gp may be interfering with various lipid molecules on the cell's surface that are needed to assist with HIV fusion and entry. But these reports have been controversial, partly because some of the cells studied expressed over 1,000 times as much P-gp as T-cells do. A new report from Telenti's lab casts doubt on these previous findings with results from an experiment using T-cells with normal levels of P-gp.

T-cells were collected from 128 HIV-negative persons (representing the variety of MDR1 alleles in that population). The cells were infected with a laboratory strain of HIV and then characterized for permissiveness to infection. When the MDR1 alleles of the donors were correlated with the results of the permissiveness assay, no association was evident between P-gp levels and a cell's susceptibility to HIV infection. But given that such contributory associations are typically small, will these negative results settle the matter? Or does the fact that multiple reports have come up with multiple conclusions signal that something about the field is not ready for prime time? The stakes are likely to be high.


Genes, Drugs and Money

One day, perhaps, before a person steps across the threshold to initiating antiretroviral therapy, the pharmacogenetic likelihood of their response to various medications may be evaluated. The genes for factors that influence exposure to drugs, such as the cytochrome metabolic proteins, P-gp and other transporters will no doubt be analyzed. Next, the toxicogenetic markers for trouble will be examined to prevent toxic catastrophes. An HLA type associated with abacavir hypersensitivity has been located and soon a simple screening test might simplify the use of this drug. And recently an allele in the cystic fibrosis gene has been associated with susceptibility to pancreatitis, a well-known serious side effect of ddI toxicity.

But even mild toxicity can impact efficacy if intolerability leads to discontinuation or missed doses. It would be helpful to know before a drug is prescribed, who is at risk for having unpleasant reactions and who can be predicted to have only benign side effects. One talk at the conference showed that African-Americans may have higher blood levels of efavirenz than European-Americans. But does that translate into better virologic response or does it mean more dropouts due to CNS toxicity? Additional study is required. Ritonavir-boosted protease inhibitors have become standard-of-care, yet ritonavir elevates triglycerides and cholesterol for too many who take it. Individuals with the apoE gene, found in 27 percent of the population, are likely to have elevated lipids at baseline or a higher risk for developing them. It may become useful to screen for that underlying propensity before initiating treatment.

All of this has caught the attention of the U.S. Food and Drug Administration (FDA), the body responsible for ensuring the safety of drugs in the U.S. In attempting to understand the potential for genetic screenings to make medicines safer, the FDA has asked the pharmaceutical industry to voluntarily provide information on the pharmacogenetics of their drugs and has promised not to be prejudiced by what they learn when it comes to regulatory decisions affecting the companies. Many in the industry are skeptical and worry that this new body of knowledge will slow drug approvals. Yet others see opportunity. By selecting out individuals likely to have adverse events or fail to benefit, clinical trials could become more focused and produce results sooner and with more information on the safe use of the drugs.

Before this can happen, Telenti says, more -- and better quality -- research must be done. In reviewing published reports of genetic associations, Telenti found that contradictions and equivocal findings are the rule; only 30 percent of them can be considered true. Since the strength of association of individual genes with complex traits tend to be weak, larger study samples, stronger statistical methods and more rigorous study designs are needed. He recommends building larger cohorts and research consortiums, including cohorts in the developing world, with appropriate ethical safeguards. Finally, laboratory scientists need to continue to uncover the biological secrets of genetic determinants so that clinical medicine can make the most of them.


References

  1. Telenti A. Host genetics and pharmacogenetics: implications for clinical practice. Program and abstracts of the 11th Conference on Retroviruses and Opportunistic Infections (CROI); February 8-11, 2004; San Francisco, California, Abstract 161.

  2. Landau N. HIV Vif: Deactivation of a deadly deaminase. 11th CROI, 2004, Abstract 103.

  3. Stremlau M, et al. The cytoplasmic body component TRIM5 restricts HIV-1 infection in Old World Monkeys. Nature 427, 848-853.

  4. Sundquist W. Cellular factors and HIV budding. 11th CROI, 2004, Abstract 6.

  5. Bleiber G, May M, Suarez C, et al. MDR1 genetic polymorphism does not modify either cell permissiveness or disease progression before treatment. JID, 15 February, 2004:189;583-586.


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