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Nearly Half of HIV Patients Have HIV DNA in CSF
Link Seen to Poorer Neurocognitive Performance

Article In Brief

Thirty percent of those with detectable HIV fragments had poorer-than-average performance on neurocognitive tests, compared with just 11 percent of those without detectable HIV in their CSF, a new study found.

Cell-associated DNA fragments of HIV in the cerebrospinal fluid (CSF) were found in nearly half of patients on long-term antiretroviral therapy (ART)—many of whom perform worse on neurocognitive tests than do people without traces of the HIV DNA.

While almost all patients remained within the normal range of neurocognitive function, 30 percent of those with detectable HIV fragments had poorer-than-average performance on the neurocognitive tests, compared with just 11 percent of those without detectable HIV in their CSF, investigators reported in the July 15 online issue of Journal of Clinical Investigation.

Previous studies looking for free-floating HIV in either serum or CSF have rarely found HIV in people on long-term ART, although pathology studies had found it in brain tissue samples.

Whether the cell-associated HIV directly causes the neurocognitive effects, or is merely associated with it, remains unclear, according to the study. But the findings demonstrate the need for future studies of HIV's presence in the brain, the study's first author said.

“People have looked for a long time for evidence of HIV in the nervous system in patients on treatment,” said Serena S. Spudich, MD, Zimmerman/Spinelli professor of neurology and chief of neuroinfectious diseases and global neurology at Yale University School of Medicine. “Now we know it's there. But this doesn't tell us what it's doing there or what it could cause. The benefit of this study is that it should focus some attention of the field and people living with HIV on the nervous system. If we're thinking about how to rid HIV from the body permanently and cure HIV, we have to be thinking about the brain and the nervous system.”

She emphasized, however, that the increased risk of neurocognitive deficits seen in people whose CSF had HIV DNA should not be exaggerated.

“They have slightly worse performance on formal neurocognitive tests,” Dr. Spudich said. “Most are not having symptoms, they're not missing work or demented. There were some who, based on their scores, fell into what we would call an impaired performance range. But none of them were coming into our clinic because of dementia. Most were in the normal range of performance. These people were really quite healthy.”

While progressive dementia was a common consequence of HIV infection prior to the advent of combination ART over two decades ago, patients today still routinely experience milder neurocognitive dysfunction, according to a commentary accompanying the study.

“The surprising prevalence of viral DNA in cells in the CSF revealed by Spudich et al. justifies continued investigation into how HIV might directly impact brain function in treated HIV patients and begs discovery of practical ways to eliminate the virus from this reservoir,” stated the commentary by David B. Clifford, MD, FAAN, professor of medicine and neurology in the division of infectious diseases at Washington University School of Medicine.

Study Details, Results

The study involved 69 participants (97 percent male, median age 50) enrolled in the AIDS Clinical Trials Group HIV Reservoirs Cohort Study, all of whom agreed to undergo lumbar puncture, phlebotomy, and neurocognitive assessment. They had been receiving ART for a median of 8.6 years at the time of study.

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“I think the paper was fascinating. But for me, the question is: What is this HIV DNA? Is this DNA junk that can never express again? If it can express, can it make a copy? Do we need to get rid of it for a cure? And where does it come from? Perhaps HIV-infected cells in the blood have an increase capacity to transmigrate across the choroid plexus. I personally have no doubt that theres HIV in the brain itself, but this study doesnt prove that one way or another.”—DR. HOWARD S. FOX

Dr. Spudich's group used a quantitative PCR method shown in previous studies to detect as few as three copies of HIV DNA or RNA in 80 to 100 percent of PCR reactions, and even a single copy in 40 to 70 percent of tests. The neuropsychological assessment consisted of 15 tests in seven domains including language, fine motor, verbal memory, speed of functioning, etc.

They tested for both DNA and RNA strands of HIV, in both cell-free and cell-associated samples of CSF. (After spinning in a centrifuge, the cell-free portion is the clear fluid that rises to the top; the cell-associated portion is the heavier mass of cells and cellular debris at the bottom.)

They found HIV DNA in 48 percent of cell samples, but far lower levels of RNA in either cell-associated or cell-free samples. Median levels of detectable cell-associated DNA in the CSF were 2.1 copies per 1,000 CSF cells.

The presence of the cell-associated DNA was associated with worse neurocognitive outcomes, including a global deficit score (p=0.005), even after adjusting for age and nadir CD4 count prior to the patient's initiation of ART. Although the study did employ clinical measures of HIV-Associated Neurocognitive Disorders (HAND), the findings imply an increased risk of HAND in those with detectable cell-associated HIV DNA in their CSF, the study concluded.

The study also measured inflammatory biomarkers by enzyme immunoassay, but in contrast to some earlier studies, did not find any association between such measures and the risk of neurocognitive impairment.

Also of note, the study found no significant association between the detection of CSF HIV DNA and pre-ART CD4 count, pre-ART plasma HIV RNA level, and years of ART at time of lumbar puncture.

In an interview with Neurology Today, Dr. Spudich pointed out that an earlier study, published in 2018 in PLoS Pathogens, found cell-associated HIV DNA in seven of 16 people with HIV. But the small size of that study left open the question of how representative the findings were. The new study confirms that a substantial portion of patients have HIV DNA circulating in their CSF even after years on ART, she said.

It remains unknown, however, whether the entire HIV genome is present, or just certain genes that the PCR was able to detect, Dr. Spudich said.

“Whether it's just a fragment of the DNA hanging out in the cell, or that has inserted itself into the host genome, is unknown,” she said. “If it's not in the genome, then it's not going to be able to replicate.”

Dr. Clifford said that Dr. Spudich's finding of HIV DNA in her population of well-controlled patients was “eye popping.”

“What's surprising is that these people are the very best patients,” he said, “yet almost half have recoverable virus in their spinal fluid. Even more surprising is that it was correlated to a change in their neurocognitive function.”

But, he added, “It might not be causal. It could be a legacy effect of their infection before beginning ART.”

While the degree of neurocognitive effect was very modest, he said, “We would be concerned if this leads to deterioration in the future. At this point we don't know if this is progressive, but we need to follow people over time to see if those with HIV DNA have a different trajectory.”

Expert Commentary

Justin McArthur, MBBS, MPH, FAAN, agreed with Dr. Clifford's view that finding HIV DNA in nearly half of the patients on ART was unexpected, particularly because the patients were so well controlled with therapy.

“It's very surprising,” said Dr. McArthur, director of the Johns Hopkins department of neurology and founding director of the Johns Hopkins/National Institute of Mental Health Research Center for Novel Therapeutics of HIV-Associated Cognitive Disorders.

“It's been suspected for a while that the brain might act as a sanctuary for HIV, even in virologically suppressed people. This is the first definitive proof that there is latent virus or HIV RNA in the CSF in a large proportion of HIV-positive individuals. I think it's potentially very relevant biologically, as we consider how we're going to deploy strategies to eradicate HIV. We will need to consider the persistence of HIV in the brain and CSF compartment as we seek a cure.”

But other researchers said they doubted the biological relevancy of the DNA fragments found in the CSF, even questioning whether they came from the brain.

“I think the paper was fascinating,” said Howard S. Fox, MD, PhD, professor of pharmacology and experimental neuroscience at the University of Nebraska Medical Center and leader of the Steering Committee of the National NeuroAIDS Tissue Consortium.

“But for me, the question is: What is this HIV DNA? Is this DNA junk that can never express again? If it can express, can it make a copy? Do we need to get rid of it for a cure? And where does it come from? Perhaps HIV-infected cells in the blood have an increase capacity to transmigrate across the choroid plexus. I personally have no doubt that there's HIV in the brain itself, but this study doesn't prove that one way or another.”

Even so, he added, “It's an important paper. It opens up a lot of questions and will generate interesting hypotheses.”

Not all neurologists familiar with the paper said they found the results surprising.

“It is not a surprise to me that integrated HIV DNA can be found in mononuclear cells from CSF in a fair number of individuals on long-term ART,” said Susan Morgello, MD, professor of neurology, neuroscience and pathology at Mount Sinai Medical Center in New York. But, she said, it seems unlikely that the DNA fragments found in the CSF can replicate.

“While this is certainly a very interesting cell population in regard to its relationship with cognitive impairment, it may be not be relevant to the reservoir capable of re-seeding tissues once ART is stopped,” she said. “Which of course raises the question: if the association is not somehow related to the full life cycle of HIV, what accounts for the association of these cells with cognitive abnormality?”

Benjamin B. Gelman, MD, PhD, director of the Texas NeuroAIDS Research Center at the University of Texas Medical Branch in Galveston, said he, too, was not surprised by the findings. And, like Dr. Morgello, he questioned whether the DNA fragments are biologically active.

“It doesn't make biological sense, based on the neuropsychological mechanisms we're familiar with, for this DNA to be causing the dysfunction,” he said. “These are likely transcriptionally silent, indolent pieces of DNA.”

Dr. Gelman said he does not, however, subscribe to the theory that the effects are a legacy of the period before patients went on ART. Rather, he sees it as a result of the brain's sensitivity to the body's infection with the virus.

Elyse J. Singer, MD, professor of neurology at the David Geffen School of Medicine at UCLA, also said she was not surprised by the finding of HIV DNA in the new paper, given her own 2016 paper showing that HIV DNA could be found in postmortem tissue from the brain and other organs.

“The most important thing about this paper, which is a very good paper, is that it correlates the presence of detective HIV DNA with the patients' neuropsychological profile, which we couldn't do. It will upset the apple cart for researchers who don't want to deal with treating the brain. It's expensive and it's hard to study. There are a lot of people who will want to minimize the importance of this, but I think it's very, very important. It shows that it will take something more than long-term ART to really cure these patients.”

Seen in context, Dr. McArthur said, the paper demonstrates that neurocognitive impairment associated with HIV remains a challenge for clinicians to treat.

“The problem of cognitive dysfunction in HIV is less severe than it was 20 or even 10 years ago, when patients would develop frank dementia,” he said. “That's fortunately a fairly rare event today, especially in people with good virological control. Nonetheless, somewhere between 15 and 40 percent of people will still have some level of cognitive impairment.”

For now, he said, in addition to antiretroviral therapy, the best treatment that neurologists can provide to offset the neurocognitive effects is to recommend lifestyle changes.

Figure

“This is the first definitive proof that there is latent virus or HIV RNA in the CSF in a large proportion of HIV-positive individuals. I think its potentially very relevant biologically, as we consider how were going to deploy strategies to eradicate HIV. We will need to consider the persistence of HIV in the brain and CSF compartment as we seek a cure.”—DR. JUSTIN MCARTHUR

“The importance of exercise, diet, and controlling vascular risk factors are, I believe, as important in a 40-year-old with HIV as they are in a 70-year-old with mild cognitive impairment,” Dr. McArthur said.

Disclosures

Drs. Spudich, Gelman, McArthur, Fox, and Clifford had no disclosures.

Link Up for More Information

• Spudich S, Robertson KR, Bosch RJ, et al. Persistent HIV-infected cells in cerebrospinal fluid are associated with poorer neurocognitive performance https://www.jci.org/articles/view/127413. J Clin Invest 2019; 129(8):3329–3346.
    • Clifford DB. Is successful HIV therapy a pyrrhic victory for the brain? https://www.jci.org/articles/view/127831J Clin Invest 2019; 129(8):3052–3053.
      • Oliveira MF, Chaillon A, Nakazawa M, et al. Early antiretroviral therapy is associated with lower HIV DNA molecular diversity and lower inflammation in cerebrospinal fluid but does not prevent the establishment of Compartmentalized HIV DNA populations https://journals.plos.org/plospathogens/article?id=10.1371/journal.ppat.1006112. PLoS Pathog 2017;13(1):e1006112.
      • Lamers SL, Rose R, Maidji E, et al. HIV DNA is frequently present within pathologic tissues evaluated at autopsy from combined antiretroviral therapy-treated patients with undetectable viral loads https://jvi.asm.org/content/90/20/8968. J Virol 2016;90(20):8968–8983.
      • Singer EJ, Thames AD. Neurobehavioral manifestations of human immunodeficiency virus/AIDS: Diagnosis and treatment https://www.sciencedirect.com/science/article/pii/S073386191500078X?via%3Dihub. Neurol Clin 2016;34(1):33–53.
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