How HIV Establishes Its Reservoirs

The vast majority of these updates have described methods for eliminating the primary barrier to a cure: the latent reservoir of HIV that persists in infected individuals despite receiving antiretroviral therapy. Now an international team of researchers reports a major new finding on how this reservoir is actually formed, and what it implies for cure strategies.

Dr. Liang Shan

Dr. Liang Shan

The research was reported in the October issue of the journal Immunity by Dr. Liang Shan, an amfAR Mathilde Krim Fellow working in the laboratory of Dr. Robert Siliciano at Johns Hopkins University in Baltimore, along with colleagues from Yale University in New Haven, CT, Sun Yat-sen and Guangzhou Medical Universities in China, National Taiwan University Hospital in Taipei, North Carolina State University in Raleigh, and Washington University in St. Louis.

Shan and colleagues note that in untreated patients, HIV replicates continuously, avoiding immune responses through rapid evolution in a process known as viral escape. But then why should HIV bother to establish reservoirs, given this ability to evolve and evade? Based on their data, the researchers argue that latency is simply an “unfortunate consequence” of CD4+ T cell infection within a narrow time frame after T cells are activated.

They report that during the natural process of T cell transition from one functional state to another—referred to as EMT, or effector-to-memory transition—T cells temporarily increase the expression of CCR5, a critical receptor for HIV, and decrease the function of certain normal cell genes necessary for HIV growth. So the virus gets into the cells more easily via the abundant CCR5, but then is rendered dormant because of dampened gene activity.

Shan and associates didn’t stop there. They found that this process of viral latency could be interrupted by HIV-specific CD8+ killer T cells and concluded that their finding has “implications for elimination of latent HIV-1 infection by T cell-based vaccines.”

Dr. Laurence is amfAR’s senior scientific consultant.

Scientists Identify HIV’s ‘Hiding Place’

Scientists from the Westmead Institute for Medical Research in Australia have identified the specific immune cells in the body that harbor most of the HIV reservoir, the main barrier to a cure.

Dr. Sarah Palmer

Dr. Sarah Palmer

The study, which was partially funded by amfAR and published in the October 17 issue of Cell Reports, found that genetically intact and presumably replication-competent HIV hides in effector memory T cells, where it avoids detection by the immune system. These are the same white blood cells that “remember” previous infections and provide lifelong immunity to diseases such as chickenpox or measles. Replication-competent HIV DNA produces infectious particles.

“HIV is really very clever,” said amfAR-funded scientist Dr. Sarah Palmer, an associate professor at the University of Sydney and deputy director of the Centre for Virus Research at the Westmead Institute. “Essentially it is hiding in the exact same cells within the immune system that are meant to attack it.”

Palmer and her colleagues developed a next-generation genetic sequencing assay known as FLIPS (Full-Length Individual Proviral Sequencing) to determine where and how much replication-competent virus remained in six HIV-infected individuals on long-term antiretroviral therapy (ART). The assay measures intact HIV proviruses to deduce the amount of replication-competent virus in the body. Using the efficient, high-throughput technology, they discovered that about 70% of presumably replication-competent virus hides in specific subsets of CD4+ T cells.

Interestingly,  the researchers found that only 5% of all HIV DNA present in these participants was genetically intact. (The other 95% was defective, i.e., noninfectious.) However, this small proportion hides in the effector memory T cells and is the likely source of viral rebound after ART cessation.

“This virus inserts its genome into the body's memory cells and sits there quietly avoiding detection by the immune system,” Palmer said. "These infected cells go into a resting state and stop producing HIV, but these latent cells can wake up and start making infectious HIV.”

Palmer said if a person stops taking ART, the virus that is hidden in effector memory T cells can return and start producing more HIV. The virus will spread throughout the body within weeks of stopping ART, she said.

She concluded: “Now that we’ve identified where the replication-competent virus is hiding, we can start work towards targeting these cells with new therapies aimed at fully eliminating HIV from the body.”

See also: Scientists find where HIV 'hides' to evade detection by the immune system

To Reverse HIV Latency, Two Drugs Are Better Than One

Dr. Robert Siliciano

Dr. Robert Siliciano

Use of combinations of antiretroviral drugs in “cocktails” to attack different parts of the HIV life cycle is the reason why most HIV-positive people maintaining undetectable viral loads can anticipate a normal lifespan. But the key obstacle to curing HIV remains the latent reservoir of virus, which is impervious to standard anti-HIV drugs. It has been a target of numerous research teams, many centered on a “kick and kill” approach by which dormant, HIV-infected cells are activated, rendering them susceptible to drug- and immune-based attack.

Such a strategy demands a robust shock to the latent state, but so far no single pharmacologic approach—using classes of drugs known as latency-reversing agents (LRAs)—has come close to the required potency. amfAR-funded scientist Dr. Robert Siliciano and colleagues at Johns Hopkins, Columbia, and Harvard Universities, writing in the May issue of The Journal of Clinical Investigation, have now put numbers on the amount of viral production an LRA needs to induce to be effective. Using the level of T cell activation required for maximum reactivation of dormant HIV in the test tube as the benchmark, the most potent drug tested thus far, bryostatin-1, could only get us 4% of the way.

A possible solution? Returning to lessons learned in designing antiretroviral therapy cocktails, Siliciano and associates explored two-drug combinations of mechanistically distinct LRAs. Using resting CD4+ T cells from HIV-positive individuals as targets, they found that certain LRA combinations acted synergistically to induce HIV growth. Equally important, this occurred without the release of proinflammatory immune hormones or cytokines, which can have deleterious side effects. They also developed a quantitative assay that uses the information gained from their test-tube studies to predict how effective the drug combinations might be in patients.

Dr. Laurence is amfAR’s senior scientific consultant.

Combination Antibody Strategy Shows Promise for HIV Cure

A combination of broadly neutralizing antibodies protected monkeys from infection with an HIV-like virus better than single antibodies in two recent, separate studies.

The results offer further evidence that a combination strategy may be the key to preventing HIV infection. Previous studies have found that individual antibodies do not provide sufficient protection from the virus.

Dr. Rowena Johnston

Dr. Rowena Johnston

“The virus is just so good at mutating away from any single thing we throw at it,” said amfAR Vice President and Director of Research Dr. Rowena Johnston in an interview with HealthDay. “When we treat HIV, you can’t give a single antiretroviral drug. You have to give a combination of at least two and optimally three. They are now also looking at this idea for antibodies.”

In one study, an amfAR-funded research team injected monkeys with a cocktail of two HIV-blocking antibodies and then exposed them to two different strains of SHIV (a combination of HIV and SIV—the simian version of HIV). Each strain was vulnerable to one of the antibodies.

The monkeys that received one of the antibodies individually became infected with the strain that was not sensitive to the one antibody; however, when they received the two-antibody cocktail, they were protected against both.

In the other study, scientists from the National Institutes of Health (NIH) and the Paris-based pharmaceutical company Sanofi created a three-pronged antibody based on three individual antibodies, each of which neutralizes many strains of the virus. The “trispecific” antibody binds to three different vulnerable sites on the virus.

None of the monkeys given the three-pronged antibody became infected after being exposed to two strains of SHIV.

Plans are underway to begin clinical trials of both the trispecific antibody and the two-antibody cocktail in the hope of eventually using the strategies for both HIV prevention and treatment.

However, as Johnston noted to HealthDay, all antibodies die off quickly. That means, “if you were going to use these in clinical practice to prevent HIV infection, you would have to repeatedly administer them,” perhaps as often as every several weeks, she said.

Both studies were published September 20 in the journals Science and Science Translational Medicine.

Read a press release on the NIH study here.

Using Groundbreaking CAR-T Cancer Therapy to Eliminate HIV

On August 30, 2017, the U.S. Food and Drug Administration approved Kymriah as the first gene therapy for patients with a drug-resistant form of acute leukemia. The chimeric antigen receptor (CAR) therapy involves modifying a patient’s own T cells to seek and destroy cancer cells. It is a one-time treatment, and for many people, a lifesaving one. The approval of this therapy received worldwide publicity. But what may come as a surprise to many is the critical role HIV research played in the development of Kymriah, and how this proof-of-concept treatment for cancer relates to progress toward an HIV cure.

Dr. Scott Kitchen

Dr. Scott Kitchen

Writing in the September issue of the journal Translational Research, amfAR-funded scientist Dr. Scott Kitchen and colleagues from the University of California, Los Angeles note that most investigators believe that enhancing a person’s natural immune response will be key in eliminating HIV-infected cells. Indeed, HIV-specific CD8+ killer T cells can be engineered to inhibit HIV growth and reduce the size of the HIV reservoir in the test tube. But this strategy has numerous drawbacks, including the need to alter HIV killer cells based on an individual’s HLA tissue type. CARs are based on engineering CD4+ T cells, which don’t have that requirement. Almost all HIV-infected patients can be treated with the therapy, regardless of genetic makeup.

The researchers explain that the first CAR T cells to be used in clinical trials were actually designed and tested for the treatment of HIV—not cancer. In addition, in order to enable those cells to recognize infected cells, a self-inactivating lentivirus—a modified form of HIV—was used to introduce the necessary genes. However, pilot trials showed less than satisfactory results, as unlike cancer, HIV can attack the very CAR T cells administered to fight the infection. With this in mind, Kitchen and associates discuss several novel approaches to enhance the activity of anti-HIV CAR T cells and to protect them against infection.

These strategies include removing, through genetic engineering, the primary HIV co-receptor CCR5. (The “Berlin patient” became the first person to be cured of HIV after receiving a stem cell transplant from a donor with a CCR5 mutation.) The scientists also propose a combination approach to kill infected cells and eliminate latent HIV reservoirs.

The authors conclude: “CAR-based therapy for HIV infection is becoming a promising approach to provide lifelong immune surveillance and viral suppression without the use of antiretroviral therapy … a closer step toward a functional cure for HIV.”

Dr. Laurence is amfAR’s senior scientific consultant. 

Injection of Specific Antibodies May Reduce HIV Viral Load

While the role of antibodies in preventing infection is clear, a growing number of researchers are enlisting antibodies to help cure HIV. One of the most promising avenues to achieve this is passive immunization, in which antibodies are injected directly into the patient.

Dr. Dan Barouch

Dr. Dan Barouch

In the August issue of the Journal of Virology, amfAR-funded scientist Dr. Dan Barouch of the Center for Virology and Vaccine Research at Beth Israel Deaconess Medical Center in Boston, with colleagues from the Ragon Institute of MGH, MIT, and Harvard in Cambridge, MA, the National Institutes of Health in Bethesda, MD, and Leidos Biomedical Research and Frederick National Laboratory Center for Cancer Research in Frederick, MD, uses a passive immunization approach to explore the potential role of antibodies in curing HIV infection.

Barouch and associates tested two antibodies, PGT121 and N6, in 18 monkeys infected with SHIV, a combination of HIV and SIV (the simian form of the virus). Both PGT121 and N6 are known to be active against HIV. The monkeys were treated with either PGT121 or N6, a combination of both, or a placebo. The antibodies reduced the viral load in the monkeys.

The researchers then measured SHIV DNA in the blood and lymph nodes to see if the antibodies had any effect on infected cells. They found significantly reduced levels of SHIV DNA in the blood two weeks after the antibodies were administered; in the lymph nodes, SHIV DNA dropped markedly after 10 weeks. The authors note that the monkeys’ naturally occurring antibodies and immune responses to SHIV were not enhanced as a result of the PGT121 or N6 infusions, arguing against their contribution to the observed viral effects.

These results suggest that passive immunization using these antibodies might, under the right conditions, kill cells of the persistent viral reservoir and thus play a role in curing HIV.

Understanding Exactly How the ‘Berlin Patient’ Was Cured

Understanding Exactly How the ‘Berlin Patient’ Was Cured

The strongest proof that HIV can be cured comes from the case of Timothy Brown, the “Berlin patient.” That triumph was predicated on physicians taking advantage of nature’s own experiment: the existence of a genetic mutation in a normal cell protein, CCR5, the main co-receptor that HIV uses to gain entry into a cell.

Innovation Grants 2017

Innovation Grants: July 2017

PI: Andrew Badley, MD
Mayo Clinic College of Medicine, Rochester, MN
$200,000 (#109593)
Ixazomib to reduce HIV reservoir size: Cells have a recycling mechanism that disposes of or reuses old proteins—the proteasome. If the proteasome is disrupted, these damaged proteins persist, clogging up the cell and eventually leading to cell death. Ixazomib is a drug that is currently used in multiple myeloma, a form of blood cancer. Dr. Andrew Badley proposes to conduct a clinical study to test the ability of the drug to reduce the viral reservoir, the main barrier to a cure. 

PI: Benjamin Burwitz, PhD
Oregon Health and Science University, Portland, OR
$199,948 (#109596)
Creation of CCR5 knockout Mauritian cynomolgus macaques for stem cell transplants:
The Berlin patient, the first and only patient so far to have been cured of HIV, received a stem cell transplant from a donor who was genetically resistant to HIV because the donor lacked a key HIV receptor, the protein CCR5.  The Berlin patient’s difficult medical history and complications have made it difficult to determine exactly what led to his cure: was it the stem cell transplant, the complications presented by his new immune system attacking HIV-infected cells as part of a transplant complication known as graft vs. host disease, the chemotherapy and radiation used in the transplant, or some combination of these? Dr. Benjamin Burwitz proposes to answer these questions by generating a monkey model lacking CCR5, enabling him to test the multiple hypotheses concerning the Berlin patient’s cure.

PI: Andrew Henderson, PhD
Boston University School of Medicine, Boston, MA
$200,000 (#109603)
Disabling HIV provirus by promoting chromatinization: CRISPR/Cas9, a protein complex recently discovered in bacteria, has revolutionized biology because of the flexibility and ease with which scientists can use it to target and edit DNA, cutting out unwanted pieces, including the DNA form of HIV. Dr. Andrew Henderson is proposing to use this protein complex to silence the HIV DNA in a so-called “Block & Lock” approach. Unlike “Shock & Kill”, which requires the cell to wake up from latency- a formidable challenge - “Block & Lock” would permanently silence HIV and prevent the emergence of virus when ART is stopped.

PI: Brad Jones, PhD
The George Washington University, Washington, DC
$199,998 (#109606)
HLA-E specific TCR-like Antibodies for the Universal Targeting of Persistent HIV Reservoirs: Broadly neutralizing antibodies that target the viral protein Env—the only viral protein expressed on the surface of infected cells - must circumvent the high mutation rate of Env in order to be effective. On the other hand, viral proteins present inside the cell are much less subject to mutation but are poorly accessible to our body’s antibody making machinery. Because of a newly discovered immune mechanism, scientists have now found that the internal viral proteins may be digested and displayed on the surface of cells in a molecule called HLA-E. Dr. Brad Jones proposes to engineer antibodies that will recognize the digested protein/HLA-E complex and make the cell susceptible to death by Natural Killer cells.

PI: Fabio Romerio, PhD
University of Maryland, Baltimore, MD
$199,999 (#109612)
Permanent Silencing of HIV-1 Expression through the Polycomb Repressor Complex 2 epigenetic pathway: Dr. Fabio Romerio has uncovered a unique mechanism through which HIV drives its own latency, namely by making a molecule called Ast. He proposes that Ast participates in actively preventing the viral DNA from making virus. Dr. Romerio aims to determine how Ast asserts its effect and whether it can be delivered to all HIV infected cells to permanently and specifically block viral DNA. In contrast to the curative approach “Shock & Kill”, this “Block & Lock” approach aims to silence HIV and prevent the emergence of virus when ART is stopped.

PI: Joshua Schiffer, MD
Fred Hutchinson Cancer Research Center, Seattle, WA
$200,000 (#109614)
Anti-proliferative therapy for eradication of the HIV reservoir: Antiretroviral therapy (ART) controls viral load because the virus is prevented from infecting new cells. However, the reservoir persists even under ART through mechanisms that are still being uncovered. One possibility is that normal cell division of latent HIV infected cells maintains the reservoir even in the absence of viral replication. Dr. Joshua Schiffer aims to determine if CellCept, a drug that reduces cell replication – normally used to prevent organ transplant rejection - can also eliminate the persistence of the reservoir. His clinical trial will span 2 years, after which participants will discontinue their ART and determine whether the curative intervention worked.

Shocking Latent HIV, Enhancing Immune Defense with a Single Drug

Last month we highlighted the work of scientists from the amfAR Institute for HIV Cure Research at the University of California, San Francisco, and their identification of a new pathway to induce HIV out of its latent state. Such activation renders the virus vulnerable to attack by the immune system. Unfortunately, many of the drugs currently being studied as such latency reversing agents work much better in the test tube than in patients.

Dr. Ole Søgaard

Dr. Ole Søgaard

Writing in the June issue of the journal Clinical Infectious Diseases, amfAR-funded scientist Dr. Ole Søgaard of Aarhus University in Denmark, with colleagues from there and the University of Copenhagen, joining an international team from Barcelona, Berlin, Belgium, Boston, San Francisco, and Philadelphia, report on an experimental drug with the capacity not only to activate latent HIV, but also to enhance the patient’s innate immune defenses against the activated virus.

Lefitolimod, also known as MGN1703, activates a protein known as TLR9, found on the surface of many types of immune cells. It belongs to a class of agents known as “immune surveillance reactivators,” which induce production of immune hormones, such as interferon-alpha, and enhance the function of dendritic cells, B cells, and natural killer cells. All of these cell types form part of our innate defense against HIV. Lefitolimod is currently in advanced stages of testing in colon cancer patients.

Based on promising studies in the test tube with cells from HIV-infected patients, Søgaard and associates sought to test the drug’s effects in patients themselves.

Fifteen adults taking effective antiretroviral therapy (ART) for at least one year were enrolled in the study. Lefitolimod was injected under the skin twice a week for four weeks. In 40% of the participants, HIV levels dramatically increased, from undetectable (less than 20 copies) to over 1500 copies, consistent with the role of a latency reversing agent. In addition, the researchers observed an enhancement of all immune responses evaluated.

The authors noted that the use of another drug to enhance TLR7, a related immune surveillance reactivator, in monkeys infected with the simian form of HIV also showed promising results, but only when combined with a therapeutic vaccine.

They concluded that their research is “the first clinical trial using a single drug in HIV-1-infected individuals on ART with the aim of both enhancing innate immunity and activating the HIV-1 reservoir.”

Further studies are underway in this promising area of cure research.

Dr. Laurence is amfAR’s senior scientific consultant.