This computer graphics image shows a colorful depiction of part of an HLA-B protein. The large chain colored orange has a groove at the top, which binds to the epitope, colored red. A smaller chain, colored pink, stabilizes the structure. In the whole protein, the orange chain extends down and crosses the cell membrane at the bottom, attaching the protein to the surface of the cell. Image courtesy of David S. Goodsell, RCSB Protein Data Bank
Their immune systems were able to control the levels of the virus in their body, essentially keeping the disease in check. They were known as HIV controllers and there were about 25 of them when Pereyra joined the lab. She and Walker, an associate member of the Broad, wondered how many individuals elsewhere had this ability. At a conference for HIV providers – people who care for HIV patients – the two asked a room of 300 attendees for a show of hands: how many people had patients like theirs? “Virtually everyone in the room raised a hand,” said Pereyra.
That was the moment the researchers knew they could do it: they could collect samples from 1,000 controllers and find out what gives them the ability to keep the deadly virus under control.
Pereyra and her colleagues at the Ragon Institute teamed up with researchers at the Broad Institute and providers across the United States to tackle the project. Initial funding for the project came through a gift from the Mark and Lisa Schwartz Foundation, with subsequent funding from the Bill and Melinda Gates Foundation. The researchers began recruiting patients, one by one, who control HIV without medications from doctor’s offices around the country, and around the world. In the end, over 300 collaborating physicians and scientists contributed to the project. “There was tremendous enthusiasm among the patients themselves to get involved in this study. Most had been asking their doctors for years why their friends were getting sick and they were not, and they saw this as a chance to get an answer,” said Walker, Director of the Ragon Institute, which coordinated the International HIV Controllers Study.
The researchers looked genome-wide, comparing samples from HIV controllers and samples provided by the AIDS Clinical Trials Group from non-controllers (people with HIV that progresses to AIDS if untreated). They were able to zero in on a protein that plays a key role in immunity. The protein, called HLA-B, acts as an early warning system within cells, where it binds to foreign protein fragments and carries them to the cell surface, thereby signaling the body’s immune system that the cell is infected, and triggering elimination of the infected cell by a class of white blood cells called killer cells. Like a claw crane in a coin-operated arcade game, HLA-B can hold only certain protein pieces (called epitopes) and show them to immune cells. The shape of HLA B varies from person to person. Understanding how genetic differences influence the claw grip of this protein could help scientists understand controllers’ defenses.
“The key motivation for all of this is the fact that AIDS is a huge public health problem and if we’re really going to build a vaccine, we need to better understand the natural mechanisms of protection,” said Paul de Bakker, an associate member of the Broad Institute and, together with Walker, co-senior author of the Science paper detailing their results.
The researchers found five sites lining the protein’s claw grip that frequently differ between people who can control levels of the virus and those who cannot. “What this is telling us is that there’s something special about the nature of the epitope that is being presented in these HIV controllers and causing these people to be protected,” said de Bakker who is also an assistant professor of medicine at the Brigham and Women’s Hospital and Harvard Medical School and director of the Genomics Program of the Harvard University Center for AIDS Research.
It’s estimated that about one out of every 300 people with HIV are such controllers. The researchers began by taking DNA from these people and looking for places where their DNA differed from non-controllers. The most striking differences appeared on chromosome 6 in an area that contains the most diverse genes in the human genome. These genes play a critical role in helping the immune system distinguish “self” (protein pieces that belong in a cell) from “non-self” (protein pieces from invaders). Scientists have hypothesized that these genes vary so much because the pathogens that attack our immune systems are so diverse.
In the past, researchers have described large chunks of genetic sequences called HLA alleles. Some crop up in HIV controllers (protective alleles) and others appear in non-controllers (risk alleles). Many alleles had been found, but no one had pinpointed how they have their effect on the immune system.
“There are lots of HLA alleles, all with different names, that are associated with risk or with protection,” said de Bakker. “This is very intriguing and clearly these signals are real, but what does that tell you?”
To find out, Sherman Jia, a medical student in the combined Harvard-MIT Health Sciences and Technology (HST) program, worked with de Bakker to devise a novel method to get an even more refined look at what was going on. Using data from other large genome-wide association studies and a novel imputation technique, the researchers were able to go from these long stretches of DNA to specific amino acids – the building blocks of protein. Looking across alleles, they noticed five sites in HLA-B where certain flavors of amino acids (for example, valine or asparagine at position 97) matched up with controllers but other flavors (for example, arginine or serine) matched up with non-controllers. When they looked at the HLA-B protein’s structure, they noticed that the five amino acid sites are located within the protein’s claw grip. Thus of the three billion building blocks of the human genome, they were able to determine that only a handful of amino acids make the difference in terms of controlling HIV or not controlling it.
“We’re taking things one step further than previous genome-wide association studies by looking at amino acid positions,” said Paul McLaren, a postdoctoral fellow at the Broad Institute who played a key role in data analysis on the project. “The fact that they all sit right in the HLA pocket, right in the binding cleft – that’s pretty encouraging to see.”
The end goal of this research is to elucidate the mechanisms of natural HIV control to inform vaccine design. “If we can replicate the natural phenomenon seen in HIV controllers (low levels of virus loads without medication) then we can impact the epidemic by decreasing HIV transmission and disease progression,” said McLaren. “There are a lot of steps between now and then, but that’s the ultimate goal.”
The International HIV Controllers Study began about five years ago and has spawned additional projects and collaborations throughout MIT and Harvard. With the help of doctors and patients from across the country, Pereyra and her colleagues at the Ragon Institute have collected over 1,500 patient samples, and have used the platforms at the Broad for sequencing and analysis. In addition to looking at host genetics, Ragon researchers led by Todd Allen are also working with research scientist Matt Henn and the Broad’s Viral Genomics Initiative to look at the genetics of viral populations in people with HIV.
“This is the kind of project that wouldn’t have been possible without collaboration,” said Pereyra. “We’ve been able to leverage the cohort [of HIV controllers], the collaboration, and the funding that we got together with the people at the Broad to do additional projects, all of them related to HIV control.”