The central theme of our latest article is to discuss the impact of the chromatin context on HIV latency. One of the most important findings was to show that HIV expression is a case of position effect: the viruses integrated close to endogenous enhancers have higher expression compared to those which integrates far from enhancers. Before this work, it was unclear whether the expression of HIV can be influenced by the location where it is inserted. The first article that studied this question was published by Albert Jordan. They found some heterogeneity in HIV expression from 34 Jurkat clonal cell lines, each containing a single integration. Consistently, we also found that HIV which integrates in different locations in a chromosome exhibits different levels of expression. Furthermore, we pointed out that latent HIV integrates slightly further from active endogenous enhancers compared to the active one.
Another key result of in this article is that latency-reversing agents have different effects towards different latent proviruses. The current strategy of antiretroviral therapies, called “shock and kill”, is to reactivate latent viruses so that infected cells containing activated HIV can be purged by the immune response. The first drug used in clinical trials for reactivation therapy is a histone deacetylase (HDAC) inhibitor called vorinostat. We wanted to test if HDAC inhibitors have the same effect on all latent proviruses regardless of their integration site, so we tested the efficacy of vorinostat on latent proviruses. B-HIVE allowed us to trace the latent proviruses that can be reactivated by the drug, along with their expression fold-change. Unexpectedly, we found that latent proviruses are not equally susceptible to vorinostat. More specifically, the strongest responders tend to be inserted closer to active enhancers.
This result has important consequences: it implies that “shock and kill” stands a chance only if we can develop cocktails of complementary drugs. B-HIVE paves the way to find optimal “shock and kill” cocktails.
The story of B-HIVE
Whether the chromatin context influences HIV latency has been a long-standing question. Due to the lack of a proper technology, there was practically no progress since the question was raised. At the end of 2013, Guillaume and me came up with the idea to create a technology to answer this question.
Hope sees the invisible, feels the intangible, and achieves the impossible.– Helen Keller
The main research interests in the laboratory is to understand chromatin. HIV is in fact a good model because its life cycle is strongly linked to human chromatin: during the course of infection, it integrates in the host genome. At this stage, a small fraction of the viruses enter a silent infection model called latency. As of today, latency is believed to be the main roadblock to the development of a cure of HIV. However, it is not clear how important the human chromatin context is for entry and exit from latency.
The B-HIVE technology inherits the central theme of TRIP, a genome-wide method to study position effects. We thought that one of the reasons that impedes the progression of investigating HIV latency is due to the lack of proper biological models and tools. At that moment, we still did not have a technology to map each HIV integration and measure its expression at the same time. B-HIVE was the technology to solve this problem.
The principle of B-HIVE is to tag individual HIV genomes with a unique barcode of 20 nucleotides to track the viral transcripts produced by each provirus of the infected cell population. The barcodes are randomly generated during the library preparation; we do not know the sequence of each barcode until the analysis stage. Like other high throughput technologies, B-HIVE also requires a lot of work at the computer for the analysis. Eduard, one of the authors in this article tackled many difficulties while analyzing B-HIVE data and together with all members involved in the project, we succeeded to make a step forward.
The future of B-HIVE
It is possible to fly without motors, but not without knowledge and skill.– Wilbur Wright
It is still a long way to fight against HIV/AIDS because what we know is still too little. In this article we provided a new technology to visualize those invisible latent proviruses in the immortalized cell line model. These results have important implications indicating that the chromatin context may be considered as a target for curing HIV as well. Although at present B-HIVE has limitations to be used in vivo and in the clinic, we are eager to increase the possibilities of B-HIVE in the near future. We believe that together with our knowledge in chromatin and HIV as well as B-HIVE, soon we will bring more benefits to the HIV community.
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