Project description:BCN02 was an exploratory, single arm study designed to evaluate a kick-and-kill therapeutic vaccine strategy in early-treated HIV infected individuals. The participants in the study received a MVA.HIVconsv vaccination before and after three cycles of infusion of romidepsin (RMD), an inhibitor of histone deacetylases that acts as a viral latency reversing agent. The inclusion of a monitored antiretroviral pause (MAP) identified 8 individuals with an early viral rebound (pVL > 2,000 HIV RNA copies/mL, < 4 weeks of MAP initiation) and 4, with a late viral rebound (pVL > 2,000 HIV RNA copies/mL, > 4 weeks of MAP initiation). In the present study, a systems biology analysis was conducted to identify the pathways modulated at transcriptomic and epigenetic level during the clinical intervention, involving vaccination and RMD, and to identify biomarkers predictive of HIV viral rebound during MAP. To this end, we studied gene expression and whole-genome DNA methylation in longitudinal PBMC samples prior and after the intervention. The main impact on host transcriptional and epigenetic signatures was observed after vaccination and RMD infusion (Vacc+RMD) with multiple pathways related to HIV infection and immune response showing changes at gene expression and DNA methylation level. Analysis of an independent cohort of individuals treated with RMD alone, showed that these changes were mainly driven by CD4 T cells. DNA methylation patterns in full PBMC obtained after full intervention (Vacc+RMD) allowed to discriminate individuals with an Early versus Late viral rebound. These individuals also showed a differential enrichment on chromatin accessibility and transcription factor binding sites. Intriguingly, 30 of the DMPs between Early and Late rebounders at Vacc+RMD were present already at baseline and were more accentuated after RMD infusion. Overall, this study provides with a deeper understanding of the mechanisms modulated during the BCN02 study and highlights the importance of DNA methylation profiles in HIV cure.

Project description:Recently, several neutralizing anti-HIV antibodies have been isolated from memory B cells of HIV-infected individuals. However, despite extensive evidence of B-cell dysfunction in HIV disease, little is known about the cells from which these rare HIV-specific antibodies originate. Accordingly, HIV envelope gp140 and CD4 or co-receptor (CoR) binding site (bs) mutant probes were used to evaluate HIV-specific responses in the peripheral blood B cells of individuals at various stages of infection. In contrast to non-HIV responses, HIV-specific responses against gp140 were enriched within abnormal B cells, namely activated and exhausted memory subsets, which are largely absent in the blood of uninfected individuals. Responses against the CoRbs (a poorly-neutralizing epitope) arose early whereas those against the CD4bs (a well-characterized neutralizing epitope) were delayed and infrequent. Enrichment of the HIV-specific response within resting memory B cells, the predominant subset in uninfected individuals, did occur in certain infected individuals who maintained low levels of plasma viremia and immune activation with or without antiretroviral therapy. These findings were corroborated by transcriptional profiles. Taken together, our findings provide valuable insight into virus-specific B-cell responses in HIV infection and demonstrate that memory B-cell abnormalities may contribute to the ineffectiveness of the antibody response in infected individuals. HIV-specific responses against gp140 were enriched within abnormal B cells, namely activated (AM) and exhausted (tissue-like; TLM) memory subsets, which are largely absent in the blood of uninfected individuals. These responses are highest during the early stage of HIV infection, significantly decreased following the initiation of antiretroviral therapy (ART), and most importantly, enriched in normal resting memory B cells (RM) when HIV viremia and immune activation are controlled either naturally or as a result of ART. These HIV-specific B cells (AM and TLM) and resting memory B cells (RM) were sorted from peripheral blood mononuclear cells (PBMCs) of 6 HIV infected individuals. In addition, gp140-specific IgG+ B cells were sorted from individuals with either a strong (n= 6) or weak (n= 6) pro-resting memory profile. TaqMan gene expression assay was performed on these HIV-specific B cells and B cell subset. The array consisted of 29 genes.

Dataset Information

Effect of HIV infection and antiretroviral therapy initiation on genome-wide DNA methylation patterns.

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