Designer Genes
Some people appear genetically immune to HIV, but others are particular vulnerable. Why?
By Richard Jefferys & Anne-christine d'Adesky

Over the past few years, researchers have started to unravel one of the central mysteries of HIV: Why do some people remain uninfected despite repeated exposure to the virus? They've also made recent headway with a related question: Why do some people who get infected progress faster to AIDS than others?

By focusing on the frontier issue of genetic immunity to HIV, scientists are looking closely at the role played by HIV genes and their relationship to the immune system. In some people, gene mutations confer resistance to the virus, which is blocked from entering target immune cells because certain cell receptors, or docking points for the virus, appear defective or blocked. In other cases of HIV resistance, changes occur in proteins that bind to these cell receptors, which are also controlled by genes. Similarly, new research shows that gene mutations that affect how HIV enters cells are linked to rapid progression of HIV disease. These gene mutations may also help determine whether an HIV-infected pregnant woman will pass on the virus to her fetus.

Scientists are busy genetically screening selective populations to find out how common these varied HIV gene mutations may be, and how and why the genes are inherited and passed along. Much of this work stems from decade-old studies of long-term non-progressors -- people who've been exposed to the virus but remain healthy, some after 16 years of carrying the virus. This group makes up about five percent of HIV-positive people, but this number is shaky, since many people in the world haven't been tested for HIV. Similarly, a small percentage of people studied to date -- around 15 percent in one large recent study -- carried genes linked to rapid illness and death.

Long-Term Survival
To date, studies of long-term non-progressors with HIV suggest that around 25 percent carry genetic mutations that confer resistance. Several different mutations are prevalent in different racial groups and subpopulations. That leaves the other 75 percent of long-term non-progressors, as well as an unknown number of repeatedly exposed-but-uninfected people, many of them sex workers, who remain healthy, with no active signs of the virus in their bodies (see accompanying story, "The African Connection").

For years, scientists have observed that individuals in both groups often have very specific cellular immune T-cell responses to HIV that keep the virus from taking hold or keep it in check at a very low level. In others, these specific immune responses delay progression of HIV disease. The opposite also appears true: some people have poor HIV-specific immune responses that lead to rapid progression of HIV and here too, genetic makeup is a factor.

Resistance to HIV is associated with a strong cellular immune response, also called the cytotoxic T-lymphocyte or CTL response, that is part of the first arm of the immune system. The second arm involves a humoral immune response carried out by antibodies that are produced by immune B-cells. Right now, the subject of CTL is the hottest issue in AIDS research, with mounting evidence to suggests it is the main key, if not the doorway, to prevention of HIV infection.

The CTL immune response is linked to the activity of subsets of lymphocytes, or white blood cells, called CD4 T-helper cells and CD8 T-suppressor cells. CD4 cells are called T-helper cells because, like a quarterback, they release chemical signals that help coordinate the body's overall immune response to infection. When you get exposed to HIV, CD4 T-cells prompt CD8 T-cells to swing into action and kill any cells that display HIV proteins on their surface. But since CD4 T-cells are a primary target for HIV, many of them also get killed. If the CD4 T-cell response gets screwed up, this affects the CD8 T-cell response -- when the quarterback is down, the team falls apart.

For many years, we've known that long-term non-progressors with HIV have strong HIV-specific CTL responses. Over at the Harvard School of Public Health, Bruce Walker and Spyros Kallams have led the field of CTL studies by showing that people who are exposed to HIV and get treated right away with a strong HIV drug regimen also retain strong HIV-specific CTL responses capable of controlling the virus. By comparison, people with chronic HIV infection start out with strong CTL responses that wane over time as they lose HIV-specific CD4 T-cells. The loss of this immune arsenal makes a person vulnerable to a range of opportunistic infections.

That's why HIV disease is called AIDS: acquired immune deficiency syndrome. The bottom line is, can we reverse that process and acquire immune efficiency or resistance? Can we turn chronically sick individuals into long-term non-progressors? What about the millions at risk for HIV? Can their immune systems be primed, like those of sex workers, to avoid HIV infection?

Frontline scientists think the first goal is possible, based on Walker's studies of acutely infected individuals, among others. Whether these cellular immune responses are sufficient to control the virus if these people go off their HIV drug regimens is hotly debated, but it's the main idea behind the new goal of achieving HIV remission. Frontline treatment strategies are testing powerful three-, four- and five-drug antiretroviral regimens to stop active infections, and adding experimental immune therapies aimed at boosting or restoring CTL immune responses to the virus. For example, in November, researchers at the National Institute of Allergy and Infectious Diseases reported that 14 people taking a three-drug HIV antiretroviral combination or more plus interleukin-2 (IL-2), an immune booster, showed no signs of virus in their blood or lymph nodes.

Resistance to HIV: Putting Up the No Entry Sign
Although HIV was officially discovered in 1982, scientists have traced the virus to a blood sample taken in 1959 from a man living in Belgian Congo who, they speculate, was probably infected a decade after the virus crossed over from primates into humans. HIV's primate viral ancestors have been evolving for much longer, scientists suspect, mutating as they infect new hosts. So, too, has our human immune system and its complex genetic blueprint. Today, the inner workings of the virus remain mysterious, involving a dynamic interplay with the immune system.

We've known for a long time that the virus directly targets and hijacks cells of the immune system to reproduce itself, eventually causing immune dysfuction. But only in 1998 did we get the first close-up 3-D crystal pictures of how the virus does this, which only underscores how much we don't understand about this clever virus. To appreciate its complexity, it helps to start with the basics. First of all, HIV is a retrovirus, which means it must integrate its RNA (ribonucleic acid) genes into the DNA (deoxyribonucleic acid) genes of a host cell in order to reproduce. It does this through a series of complicated steps that involve interactions between viral and cell enzymes or proteins. For example, protease inhibitors block the action of the protease enzyme involved in viral exit from cells.

To initially get inside the cell, the virus must latch onto the cell wall. It does so by targeting several chemokine "co-receptors" (also called beta chemokines) that act like doorways, allowing the virus to bind with a molecule called CD4. Imagine the mythical Loch Ness monster crossing the English Channel, its body snaking into and out of the water. That's the image scientists have offered of a chemokine receptor that is like a molecular snake traversing in and out of the cell's membrane. Everywhere a loop sticks out, the virus can grab onto. Metaphors aside, chemokines are molecules released by immune system cells that act like chemical messengers and allow immune cells to communicate. When a chemokine latches onto a specific receptor on a cell surface, it sends a message to that cell.

Several years ago, scientists identified two chemokine co -- receptors on cells that appear to play a crucial role in HIV infection. The list has since been expanded as new co-receptors have been discovered. The main co-receptors are named CCR-5, found mainly on macrophage cells, and CXCR4, found on T-lymphocytes, or T-cells. Some cell types carry both co-receptors. Viruses that use CCR-5 are called macrophagetropic (or M-tropic), while those using CXCR4 are called T-tropic.

Studies of sexual transmission of HIV show that the virus may initially target macrophages and other immune cells cells that express the CCR-5 co-receptor, and later switch over to infect T-cells expressing CXCR4. This switch -- from M-tropic viruses to T-tropic viruses using CXCR4 -- is associated with an increased rate of CD4 T-cell loss and more rapid disease progression. In 1997, researcher Hyeryun Choe, along with Richard Wyatt and Joseph Sodroski of the Dana-Farber Cancer Institute, fingered a variable loop or section called V3 of the HIV envelope protein gp120 as the culprit responsible for determining which cell co-receptor is used by a given virus.

So far, it isn't clear whether the switch from macrophage infection to T-cells is caused by mutations of the virus or by a decrease in the number of cells with CCR-5 receptors that force the virus to seek new cell targets, namely T-cells. Scientists are asking how we might prevent this switch from happening and are testing co-receptor blocking drugs in test-tube studies that might delay HIV's spread and rate of progression.

Another receptor called US28, which is remotely related to the human co-receptors CCR-5 and CXCR4, was identified last year by French reseachers who said it allows HIV to infect human cells, possibly mediating how the virus binds to the CXCR4 co-receptor. Interestingly, another human virus, cytomegalovirus (CMV), also uses US28.

The Language of Genes
Enter genes into the picture. The discovery of chemokine co-receptors has highlighted how genes, and especially genetic muations, can affect the structure and function of chemokine receptors (cell doorways). Certain genetic mutations may cause these chemokine receptors to be absent from the cell's surface or to be present in some altered form so that the virus can't easily latch onto the cell and sneak inside. In a remarkable piece of molecular detective work, scientists led by Stephen O'Brien of the National Cancer Institute have tracked down pieces of the genetic code relevant to the chemokine receptors CCR-5 and CXCR4. O'Brien's group has also found a CCR-5 gene mutation linked to rapid progression of HIV.

In earlier studies of exposed-but-uninfected individuals by Richard Koup and Bill Paxton of the Aaron Diamond AIDS Research Center, among others, researchers found that people who had a mutation in the gene affecting the CCR-5 receptor were partially or completely resistant to HIV infection. They called this mutation Delta 32, based on its location on the genome. The effect of this mutation, like that of other genetic changes, depends on whether it's inherited from one parent or both.

Remember that a gene, or DNA strand, comes in two copies, one in each pair of chromosomes (see sidebar). A person with a genetic mutation inherited from both parents is said to be homozygous for that mutation. A person with a mutation inherited from only one parent is heterozygous for that mutation. It appears very hard for M-tropic viruses that use CCR-5 to infect cells that don't have these receptors. That's why people with the double mutation (homozygous) for Delta 32 are highly resistant to HIV infection; in these people, there is no CCR-5 receptor for HIV to grab onto. Those with only a single Delta 32 mutation are partly resistant to HIV because the CCR-5 receptor is present on the surface of the cell, but its structure has been altered.

Additional mutations have been found in the CCR-5 gene that take place at other points in the genetic alphabet and could influence disease progression. The 59029 mutation takes place in what's called CCR-5's promoter region, which could affect what the CCR-5 receptor will look like. What's usually found at position 59029 is the nucleotide adenine, or letter A. But in some people the letter G, guanine, has been substituted, and this tiny difference affects the function of the CCR-5 receptor, a change that's linked to a slower rate of progression to HIV. If you inherited a letter G from both your parents, you'd be given the clumsy name homozygous CCR-5 59029 G/G. Studies suggest that people with this double G/G guanine pair have an even slower rate of progression to HIV than those with the standard double A/A adenine or those with the heterozygous A/G pair.

In January 1998, a French team reported a mutation at position 303 on the CCR-5 genome that also confers resistance when it occurs along with Delta 32.

Another gene mutation goes by the catchy name of CCR-2 (actually CCR-2-641). This mutation is thought to affect the CCR-5 receptor in some way, although exactly how isn't yet understood. The CCR-2 mutation doesn't seem to affect one's susceptibility to HIV infection, but those with a double mutation also have a delayed progression to disease. Those who are heterozygous for CCR-2, with only a single inherited mutation, also have a slowed rate of progression similar to that seen in people with a single Delta 32 CCR-5 mutation.

T-cell Infection
What about CXCR4? Here, another genetic mutation has been discovered that has an indirect effect on how HIV viruses enter T-cells. The gene is involved in the production of a protein called SDF-1 that binds to the CXCR4 receptor and may block attachment of HIV. Its actual name is a tongue-twister: SDF-1-3'UTR-8016-A, known to aficionados as simply SDF-1. On the genetic highway of DNA, this mutation shows up at position 801, where the letter A, adenine, has been subsituted for G, guanine. In a study of 2,800 people, O'Brien's group found that 5 percent carried two copies of the double mutation required for full protection against HIV. People who have this genetic mutation, along with the Delta 32 or CCR-2 deletions, have even better prospects for survival.

Researchers says the vast majority with this genetic profile will remain healthy for at least 10 years after HIV infection. On average, 50 percent of HIV-infected people normally progress to disease within this period. In 1997, Richard Ferri and colleagues screened over 3,000 people for CCR-5 and CCR-2 mutations. Nearly 29 percent of those with either of the mutations were long term non-progressors who had avoided AIDS for 16 years or more.

How long this protection will last is uncertain. In December, French re-searcher Jean-Francois Zagury and colleagues found that the CCR-5, CCR-2 and SDF-1 genes lose their protective benefit after about eight years, based on a study of 200 slow or non-progressors and 90 rapid progressors. The protective effect also occurs earlier in HIV infection.

Role for Outside Factors?
Interestingly, the evidence to date suggests that outside factors may influence HIV gene mutations. While 10 to 15 percent of Caucasians are estimated to carry the CCR-5 gene muation, it is rarely found among African-Americans, Asians, or Latinos. They are more likely to carry the mutations for CCR-2 and SDF-1, as do Africans. In another Texan study of 235 African commercial sex workers, CCR-2 gene mutations were found in 23 percent, while CCR-5 and SDF-1 mutations were completely absent. Because of this variety, the Texas group speculates that "an extinct or presently unidentified microbe or other environmental pressure may have modified the human genome, causing selection for the gene variants."

That backs a theory put forth by Stephen O'Brien, who's reached all the way back to the 14th century to suggest that survivors of the Black Death, a bubonic plague that wiped out two-thirds of the population of Europe, may be responsible for passing on HIV resistance to us today. Using evolutionary backtracking, O'Brien found signs that a major outside factor, possibly a microbe or great plague, caused the Delta 32 mutation in the CCR-5 human gene around 688 years ago that is linked to HIV resistance today. Black Death, says O'Brien, neatly fits the niche. That might partly explain why Europeans and their American descendants carry this gene mutation, and why it's absent among other groups.

The discovery that different genetic differences arise in different populations tends to reinforce the popular, but false, idea that there are significant genetic differences between races: there aren't. We all have a million differences in our genetic makeup from that of another person. There are far greater genetic differences between two individual African-Americans or two individual Caucasians than there are between African-Americans as a group and Caucasians as a group. The reason scientists like O'Brien study differences in the presence of these genes in racial groups is simply to look for clues as to where, when, and why specific mutations arise.

Genetic Vulnerability to HIV
Over the years, O'Brien has also been looking for a gene connection in people who seem to get sick faster than others. He's now found it: the CCR-5 promoter gene. In a recently published NCI study of 700 people with HIV, of whom 15 percent had progressed rapidly to HIV illness and death, O'Brien's team found that 10 to 17 percent had that genetic mutation. Looking futher, his team found that there are up to 10 genetic sites within the CCR-5 promoter region that varied from person to person, and four were common. O'Brien thinks that one in ten people carries this mutated gene.

According to gene hunter Francis Plummer who works in Kenya, studies of rapid progressors suggest that they also have an immune response to the virus that isn't as strong as other people, something that may be influenced by genes (see "The African Connection"). Others are hotly studying how genes might be manipulated to control or alter the immune response to HIV.

Given daily progress in this field, hopes are high that the insights we've already gained will produce new weapons, including a desperately needed vaccine. With dozens of vaccines and new agents in the pipeline, there's reason to be encouraged. Speaking from the epicenter of the epidemic, Plummer says he, for one, is hopeful. "A lot of the pieces of the picture are coming together. We just need to build on that."

Richard Jefferys wrote about simpler HIV regimens in the September issue of HIV Plus. Anne-Christine d'Adesky is Editor-In-Chief of the magazine.