Using LARA model and OMICS sequencing to identify the role of cytokines in HIV integration and chromatin remolding during latency
The generation of a small pool of latently infected cells harboring replication competent HIV occurs very early after HIV infection. The precise mechanisms responsible for the establishment of this small pool of latently infected CD4+ T cells are not fully elucidated. Cytokines may contribute to this phenomenon, as the steep rise in the HIV viral load coincides with a large burst of inflammatory cytokines during acute HIV infection. IFN-α and IL-15 are the first cytokines elevated within 5 days after detection of viremia, followed by TNF-α, CXCL10, and IFN-γ, and then by IL-12. Following this initial burst of proinflammatory cytokines, an anti-inflammatory response is observed with a delayed peak of IL-10 production, along with the upregulation of the TGF-β，IL-1 receptor antagonist (IL-1RA). The development of this anti-inflammatory response, which characterizes the transition from the acute to the chronic phase of the infection, contribute to the generation of a reservoir of long lived latently infected cells.
So here we will use the latency and reversion assay (LARA) model to simulate such “infection – integration - latency” process, and integrate some OMICs sequencing methods including single cell RNA-seq, assay for transposase-accessible chromatin using sequencing (ATAC-seq) and HIV integration sequence analysis to try to address several critical issues:
① How do inflammatory cytokines, which occur during acute HIV infection, impact HIV integration? ② How do anti-inflammatory cytokines including IL-10 and TGF-β drive HIV latency in host cells including the change of chromatin status? ③How do the HIV integration sites influence the host gene expression and inversely impact HIV integration?
Currently, we have already established platforms of single cell RNA-seq and ATAC-seq and are evaluating the roles of some cytokines including IL-10 and TGF-β in the change of chromatin status and host cell transcription. In further studies, we will establish HIV integration analysis platform as well and integrate the three platforms into one Multi-OMICS analysis platform for the research of HIV latency.