Gene editing snips out HIV-infected cells

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For the first time, researchers have used a gene-editing technique already used to produce cells resistant to HIV infection to target HIV-infected cells. They have managed to remove HIV genes completely from infected cells, as shown by reductions in the cells’ overall rate of HIV production. In cells not already infected, the therapy has itself become part of their genome, producing cells that are resistant to infection for a prolonged period.

The therapy produced significant reductions in the ability of CD4 cells to be infected with HIV and to produce it. It produced positive results in a laboratory-generated CD4-cell analogue and in actual CD4 cells, both HIV-uninfected ones grown in the laboratory, and HIV-infected ones taken from four patients with HIV. This gene-editing technique has so far only been used on cells in the laboratory dish, but this study takes us one step closer to a therapy that could be administered as an injection and work within the body.

HIV is very difficult to cure because, as a retrovirus, it inserts its DNA – its genes, the “instructions” for making more HIV – into our own DNA inside the cells of our immune system. The HIV infection within cells that are not actively producing HIV is invisible to the part of the immune system that would normally destroy virally-infected cells. It persists even when people take HIV treatment, and even on treatment, a smouldering infection continues from one cell to another that maintains the size of this so-called “reservoir”.

Several ways of eliminating the viral reservoir have been suggested by scientists. The one most advanced in research has been the “shock and kill” strategy; this involves using HDAC inhibitors, immune-stimulant drugs that reactivate the reservoir cells, making them visible to the immune system. There are several problems with this strategy; only a small proportion of all HIV-infected reservoir cells are activated and to activate more, a damaging amount of stimulus to the whole immune system might be required; the natural immune response does not seem to be strong enough to destroy the cells even when they are activated; and any reactivation runs the risk of setting off a renewed cycle of HIV infection that only ‘re-seeds’ the cellular reservoir.

Another method in early research is to do the opposite and try to maintain the immune system in a permanent state of lockdown, using PD-1 inhibitors, drugs that stall the development and maturation of immune cells. Until recently, however, it was thought these might have to be taken as a regular therapy and therefore could not be a cure, although one study suggested it might be possible to induce reservoir cells into a state of permanent quiescence with a novel tat inhibitor drug.

The third method, a therapy that actively penetrates the immune system and removes the HIV content of infected cells, has always been one of the most promising ideas but has appeared very technically difficult. It would need to be both highly specific (it only removes HIV material and not human genes) and highly sensitive (i.e. it is able to detect a high proportion of infected cells). With this current research, scientists have moved closer to developing such a specific and sensitive therapy.

The scientists in this study used a genetic “missile” that combined two different modules. The first is a probe consisting of two pieces of so-called ‘guide RNA’ (gRNA). Their job is to sensitively detect and home in on the two ends of the HIV genome, the so-called long terminal repeats (LTRs) that act as the viral genome’s ‘frame’.

The second is a nuclease, an enzyme called Cas9 that removes the viral genetic material and rejoins the two cut ends of the human DNA together. In the process, it adds some “filler” DNA of its own.

Cas9 is a development of CRISPR, an enzyme already used in another HIV cure approach, to extract and “re-engineer” CD4 cells outside the body to make them immune to HIV and then re-introduce them; continued research into this strategy is also underway, though so far it has proved difficult to turn the HIV-resistant cells into the majority of immune cells once they are re-introduced.

The present team used a lentiviral vector – the shell of a virus of the same family as HIV, containing the gRNA/Cas9 as a ring or plasmid of nucleic acid – to infect T-lymphocyte cells (of which CD4 cells are a subset) in the test tube.
In the first set of experiments they used 2D10 cells, laboratory-created immune cells containing a specially engineered ‘fake’ HIV genetic sequence consisting of the HIV genome with most of its replication genes removed and a fluorescence gene inserted. These cells therefore, instead of HIV viral particles, spit out green fluorescent protein (GFP) when stimulated, which shows up in microphotographs. The 2D10 cells were infected with the vector and then stimulated with an HDAC inhibitor to see if they expressed GFP. Cells infected only with the Cas9 nuclease produced one unit of GFP unstimulated but 94 units of GFP when stimulated, while ones infected with the full gRNA/Cas9 probe produced less than one unit of GFP whether stimulated or not.

One of the issues with HIV infection is that the virus inserts its genome at random into the human genome, wherever it will fit, though some sites are more likely than others. Genetic analysis of cells used in the study found a complete HIV genome, consisting of 6130 base pairs (units of the DNA chain) on chromosome 1 of the cell’s 23 chromosomes, and a near-complete genome of 5467 base pairs in chromosome 16. In the gRNA/Cas9-treated cells, these had been replaced by smaller DNA ‘fillers’ consisting of 909 and 759 base pairs respectively. These “fillers” were not just inactive DNA: they acted as genes and actively expressed the gRNA and Cas9 nucleic acid sequences.

The researchers then investigated whether the infection of the cells by the gRNA/Cas9 vector had any adverse effects on other genes in chromosomes 1 and 16 and on cellular health in general. They found no indication of significant mutations in other genes, or in the viability or lifespan of cells.

They next looked at whether it was possible to infect T-cells with HIV if they had already been infected with the gRNA/Cas9 vector. They infected HIV-negative T-cells with the vector, and selected four clonal lines of T-cells. One line produced gRNA but not Cas9, one Cas9 but not gRNA, and two both, one of which expressed more Cas9 than the other.

When these cells were cultivated with HIV, the cells expressing either gRNA or Cas9 could be infected, with 20-50% infected in the lab dish, but cells expressing both were more resistant to infection, with 3-4% of cells with the lower level of Cas9 infected and only 1% of cells with the higher level.

Two different strains of HIV were in fact used. With one the reduction in infections in cells expressing both gRNA and Cas9 was 48%; but with the other strain the reduction was 100% and no HIV replication was seen at all. The researchers found that the expression of the gRNA and Cas9 products by cells diminished over time and eventually disappeared, but that as long as they were integrated within the cell, the cells were protected from infection.

The researchers then looked at the ability of the gRNA/Cas9 vector to suppress replication in cells taken from people with HIV. They took T-cells from four patients who were all on antiretroviral therapy (ART) but had different responses: case one had a low viral load and high CD4 count but a low CD4 percentage (11%); cases two and three had undetectable viral loads and high CD4 counts, and case four a low but detectable viral load and a low CD4 count (53 cells/mm3).

Their CD4 cells were cultured in the test tube without ART and with the gRNA/Cas9 vector. Four days after the vector was introduced, they tested lab dish fluid and individual cells for HIV viral loads. Cells cultured with the gRNA/Cas9 vector had lower levels of the p24 HIV protein (71, 62, 39 and 54% less than control cells from the four patients respectively); cases one and two also had levels of the HIV gag protein measured too and this decreased by 92% and 56% respectively.

This is the first study to show that a combined HIV gene locator and remover removed HIV genes and repaired the genome of cells infected with HIV; inhibited HIV infection in treated laboratory cells; and reduced viral production by infected cells taken from people with HIV. It also shows that this gene therapy is safe and does not affect non-viral DNA.

Clearly not all HIV-infected cells were repaired, or completely repaired, by the gRNA/Cas9 therapy, as although infection and replication was reduced, only in one case was it stopped completely. This may mean that the therapy did not get into all cells, but it may also mean that it did efficiently infect cells but may not have removed and replaced the DNA in different individuals exactly as predicted, and residual viral DNA may have been left.

The researchers also found that in cells taken from patients, the exact sequences removed and replaced in the DNA did not always match their expectations, showing that genetic variations between individuals and viral strains may influence the function and effect of the therapy. This suggests it may have to be individualised to match people’s genetic makeup.

This study looked at the effect of the gRNA/Cas9 therapy on cells taken off antiretroviral therapy, in order to measure reductions in viral production. But given that the primary interest is to see if it can alter the genome and reduce the amount of HIV in non-productive reservoir cells, the researchers say that their next step will be to see if the gRNA/Cas9 therapy directly reduces the amount of HIV DNA in cells treated with ART, taken from both ART-treated and drug-naïve patients.

The study does show that a genetic “probe” is capable of targeting a high proportion of HIV-infected cells and efficiently and safely snipping out the entire HIV genome without damaging surrounding DNA. In addition, it integrates into non-infected cells, rendering them resistant to infection. But, as the researchers note, “some formidable challenges remain before this type of strategy can be implemented.” The biggest barrier will be HIV’s genetic diversity, which will require a variety of different gRNAs and CRISPR nucleases to be devised, possibly down to the level of personalising them individually. And secondly, although clearly high levels of cells were infected by the therapy vector, significant levels of viral replication remained, showing that some cells remained unaffected.

Animal studies will be required before the therapy is introduced into humans. Given its mode of action, however, it may eventually be possible with this combined therapy to clear HIV out of infected cells and make non-infected cells resistant by means of an injection rather than by cultivating cells in a lab dish and then reintroducing them.

We are a long way from that yet. Nonetheless, this study shows that a technical feat which a few years ago might have been thought impossible – the removal of pro-viral HIV DNA from the midst of a human cell’s genome – can be done efficiently, safely, and with significant positive effects on HIV infection and replication.

Abstract
We employed an RNA-guided CRISPR/Cas9 DNA editing system to precisely remove the entire HIV-1 genome spanning between 5′ and 3′ LTRs of integrated HIV-1 proviral DNA copies from latently infected human CD4+ T-cells. Comprehensive assessment of whole-genome sequencing of HIV-1 eradicated cells ruled out any off-target effects by our CRISPR/Cas9 technology that might compromise the integrity of the host genome and further showed no effect on several cell health indices including viability, cell cycle and apoptosis. Persistent co-expression of Cas9 and the specific targeting guide RNAs in HIV-1-eradicated T-cells protected them against new infection by HIV-1. Lentivirus-delivered CRISPR/Cas9 significantly diminished HIV-1 replication in infected primary CD4+ T-cell cultures and drastically reduced viral load in ex vivo culture of CD4+ T-cells obtained from HIV-1 infected patients. Thus, gene editing using CRISPR/Cas9 may provide a new therapeutic path for eliminating HIV-1 DNA from CD4+ T-cells and potentially serve as a novel and effective platform toward curing AIDS.

Aidsmap material
Nature Scientific Reports abstract


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