Elite controllers may self-vaccinate against
active HIV infection, gene study suggests
Authors say one of their subjects has probably
'cured herself' of HIV
A study published in Nature on Wednesday has
used novel gene-sequencing probes to investigate
exactly how the one in 200 people with HIV
who are so-called “elite controllers”
manage the feat.
The study is by Chenyang Jiang and colleagues
from the Ragon Institute, a research consortium
dedicated to finding vaccines and cures for
HIV and other infectious diseases. It suggests
that a dynamic process happens whereby a strong
anti-HIV response by the CD8 cells of the
immune system preferentially kills off cells
that are more likely to produce active HIV.
The low-level stimulus from the cells that
are left – and which contain HIV genes that
are much less likely to spring into action
– is nonetheless enough to keep the anti-HIV
CD8 response attuned to HIV.
In one individual among the 64 elite controllers
studied, the investigators were unable to
find any replication-competent HIV genetic
material in over a billion T-cells, and were
also unable to grow any HIV from her T-cells.
Although the investigators say cautiously
that “the logic of scientific discovery
does not allow us to confirm that [this patient]
has achieved a sterilising cure of HIV infection
through natural immune-mediated mechanisms,
it is notable that we have failed to falsify
this hypothesis”. In other words, this patient,
who has been identified by the New York Times
as Loreen Willenberg, a 66-year-old Californian
who was profiled as an elite controller last
year, has managed to clear all intact viral
material from her system in what could truly
be called a self-cure.
New York Times that since it was written they
have found a couple more people that could
qualify as cures. And the team is now contacting
people who have been on stable ART for more
than 20 years to find out if they too, have
managed to exile their virus to a genetic
version of Siberia.
Elite controllers are people who maintain
low or undetectable viral loads for many years
without needing to take antiretroviral therapy
and make up less than 0.5% of the HIV-positive
population. Previous studies have suggested
that a lucky combination of several different
characteristics – including defective HIV,
a hypervigilant and specific immune response
to HIV, and cells that are unusually resistant
to infection may all have a part to play.
Elite controllers, as indicated above, may
not be unique – there may also be a larger
population of people on long-term ART who
would qualify as “post-treatment controllers”
– but the only way to find out would be
to take them off ART.
Gene deserts
What the new study adds is, firstly, that
elite controllers not only have less HIV genetic
material integrated into their own DNA, but
that it is unusually located within it. HIV
carries its own transcription factors with
it such as the tat protein, but it also needs
to be integrated into lengths of human DNA
that contain genes themselves, because it
depends on the ‘switching on’ of other
genes, often in response to infection or damage,
to stimulate viral transcription. In other
words, HIV needs fertile genetic soil in which
to grow.
The researchers found that in elite controllers,
HIV genes are more often found in what they
call “gene deserts” – barren areas of
chromatin, the DNA-plus-protein complex that
actually makes up the nuclear 'stuff' inside
the nuclei of cells, and which it packages
into 23 pairs of chromosomes during the process
of cell division.
These gene deserts occur in places where chromatin
takes a densely-packed form which 'blocks
and locks' genetic activity. Locations typical
of this include the centromere, the knot of
protein that 'ties together' pairs of chromosomes
during division, and zinc fingers, areas where
DNA is bound to charged atoms of the element
zinc that bind it into a stable form. In addition,
the HIV genes were generally further away
from sites of genetic activity.
The investigators suggest that this is not
an accident. Elite controllers are not people
whose HIV has fallen on stony nuclear ground
by chance; nor do they have DNA that 'attracts'
HIV genes to these barren areas, perhaps by
allowing easier integration there.
It is rather that the DNA picture we see is
the archaeological evidence of a battle that
HIV usually wins against the immune system
but which, in elite controllers, the immune
system has won: HIV has been nipped out of
all the sites where it landed in fertile ground
by the killing of cells that contain these
areas, leaving only cells containing inactive
viral DNA.
Evidence for this is found in the fact that
up to 60% of the elite controllers’ HIV
genetic material was found in these areas
even though they may contain as few as 0.12%
of the 'integration sites' where HIV is physically
able to plant its genes.
Characterising elite controllers
The study compared 64 elite controllers with
41 chronically-infected people on ART. They
had the same average age (56) and the same
proportion were women (about 20%). They had
also been infected for the same length of
time on average (17 years) and, interestingly,
had been virally undetectable for the same
length of time (9 years) – this is a reminder
that elite controllers don’t always maintain
total viral undetectability but may instead
maintain low but detectable viral loads off
therapy for part of the time.
The elite controllers had somewhat higher
CD4 counts than those on ART (908 versus 726),
and more of them (27% versus 9%) had one of
two subtypes of the HLA set of genes that
recognise foreign material and pathogens.
One of these subtypes, HLA-B*57, causes allergy
to the HIV drug abacavir, but people with
it and another subtype, HLA-B*27, tend to
maintain lower HIV viral loads off treatment.
The people on ART had roughly 20 times as
many T-cells containing proviral HIV DNA as
the elite controllers. However a lot of the
integrated proviral HIV DNA is junk – it’s
just degraded HIV sequences that would not
be able to issue the instructions for making
new viruses.
The elite controllers (with one exception)
had a higher proportion of proviral DNA that
was intact – it could make new viruses and
did so if cultivated in a lab dish. About
17% of the proviral DNA in elite controllers
was intact compared with 8% in people on ART,
even though they had less proviral DNA overall.
Indeed in two elite controllers, 100% of the
proviral DNA they had was replication-competent.
This may sound bad, but if the proviral DNA
is in locations within the genome where it
cannot activate, then this does not mean HIV
replication is likely in the future. In addition,
it is evidence that the proviral DNA seen
in elite controllers is reproduced purely
clonally, which means it is purely due to
DNA copying itself when cells divide. This
reproduces the HIV material faithfully. If
proviral DNA within cells is instead being
‘reseeded’ by new waves of active viral
replication, then this is a more error-prone
process and one would expect more mutations.
The exception mentioned above was Loreen Willenberg.
The investigators failed to find a single
piece of replication-competent proviral HIV
DNA in 1.5 billion of her T-lymphocytes and
also failed to cultivate any HIV from 340
million of her CD4 cells in what is called
a viral outgrowth assay. What they did find
was 19 proviral sequences of HIV that were
incapable of replication – proof that she
had indeed had HIV (she has also had a single
detectable viral load of 93 copies/ml in 36
viral load tests over 24 years).
They also found another patient with a similar
viral load history (one detectable viral load
of 56 copies/ml in 12 years) in whom they
at first failed to find any HIV but eventually
found one cell in 1.02 billion that had a
single sequence of replication-competent proviral
DNA in it.
Could this help develop an immune therapy?
This is all very well, but what implication
does it have for the rest of us? The investigators
reference in passing a study, by the same
team, of three HIV patients last year on long-term
ART, using similar tools. It suggests that
the same processes – a gradual pruning of
HIV in sites favouring replication, so that
intact proviral DNA becomes, over time, more
likely to be located in parts of the genome
that don’t activate – are found in people
on long-term ART, if to a lesser degree.
In a commentary on the study, HIV cure expert
Nicolas Chomont from Montréal University
in Canada says that this shows that “such
selection, over years, could result in a reservoir
[of HIV-containing quiescent immune cells]
made entirely of proviruses that are unlikely
to be reactivated.” The only reason we didn’t
realise this was happening before was that
we lacked the sophisticated assays that show
that not all intact HIV proviral DNA is capable
of giving rise to new viruses.
This might be a long-term process in people
on ART. But it does hold out the possibility,
Chomont comments, that immune therapies including
novel ones like CAR T-cells – genetically
altered T-cells that have been induced to
be ‘hyper-aware’ of HIV and mount an intensified
response to it – could help this process
on its way, so that perhaps more of us can
become viral controllers.
