Background
HIV elite control in the absence of therapy is marked by a highly clonal integration site landscape. However, the underlying mechanisms remain elusive, impeding the design of therapies that could replicate this exceptional HIV control. We previously demonstrated that elite controller CD8+ T cells reduced HIV integration site diversity, decreased genic integrations, and enriched for integrations in specific gene pathways in a xenograft mouse model. Here we deciphered how varying levels of CD8+ T cell pressure shape HIV integration site characteristics, hypothesizing that the strength of CD8+ T cell response correlates with latency-associated patterns of viral control.
Methods
NSG mice were engrafted with memory CD4+ T cells from three human HLA*B27:05 male elite controllers and injected with HIVJRCSF, and either kept untreated (control) or engrafted with autologous memory CD8+ T cells. After monitoring blood cell counts by flow cytometry and qPCR viral load for 8 weeks, spleens were harvested, and total DNA was subjected to linker-mediated PCR for integration site sequencing, analyzed via the AAvengeR pipeline, Reactome pathway analysis, and correlation analysis between integration distributions and immune response.
Results
In 57 xenograft mice, CD8+ T cell responses produced varied viral load and cell population outcomes. A strong positive correlation was observed between total CD8+ T cell counts, CD4+ T cell counts, and HLA*B27:05-KK10 tetramer-reactive cells (p.adj.<0.001). Elite controller CD8+ T cells reduced viral load by a median of three orders of magnitude. Decreases in viral load correlated with reductions in total and non-clonal integrations (p.adj.<0.05), while inversely correlating with integrations in repeats (p.adj.<0.05), indicating the preferential persistence of clonal integrations in repetitive genomic loci. The genic integrations persisting in the presence of CD8+ T cells were preferentially associated with functions in chromatin organization, SUMOylation, and transcriptional activation (p.adj.<0.05).
Conclusions
Inter- and intra-individual diversity in viral and immune trajectories and integration sites revealed key associations. Similar patterns, including increased HIV reservoir clonality and reduced genic integrations, have been observed in individuals on long-term antiretroviral therapy. These links between CD8+ T cell control and proviral landscape variables suggest the potential to use integration site patterns as a readout of CD8+ T cell strength over time.