Transcriptional and Posttranscriptional Regulation of Cytokine Gene Expression in HIV-1 Antigen-Specific CD8⁺T Cells That Mediate Virus Inhibition

Abstract

The ability of CD8 ؉ T cells to effectively limit HIV-1 replication and block HIV-1 acquisition is determined by the capacity to rapidly respond to HIV-1 antigens. Understanding both the functional properties and regulation of an effective CD8 ؉ response would enable better evaluation of T cell-directed vaccine strategies and may inform the design of new therapies. We assessed the antigen specificity, cytokine signature, and mechanisms that regulate antiviral gene expression in CD8؉ T cells from a cohort of HIV-1-infected virus controllers (VCs) (<5,000 HIV-1 RNA copies/ml and CD4؉ lymphocyte counts of >400 cells/l) capable of soluble inhibition of HIV-1. Gag p24 and Nef CD8؉ T cell-specific soluble virus inhibition was common among the VCs and correlated with substantial increases in the abundance of mRNAs encoding the antiviral cytokines macrophage inflammatory proteins MIP-1␣, MIP-1␣P (CCL3L1), and MIP-1␤; granulocyte-macrophage colony-stimulating factor (GM-CSF); lymphotactin (XCL1); tumor necrosis factor receptor superfamily member 9 (TNFRSF9); and gamma interferon (IFN-␥). The induction of several of these mRNAs was driven through a coordinated response of both increased transcription and stabilization of mRNA, which together accounted for the observed increase in mRNA abundance. This coordinated response allows rapid and robust induction of mRNA messages that can enhance the CD8 ؉ T cells' ability to inhibit virus upon antigen encounter. IMPORTANCEWe show that mRNA stability, in addition to transcription, is key in regulating the direct anti-HIV-1 function of antigen-specific memory CD8 ؉ T cells. Regulation at the level of RNA helps enable rapid recall of memory CD8 ؉ T cell effector functions for HIV-1 inhibition. By uncovering and understanding the mechanisms employed by CD8 ؉ T cell subsets with antigen-specific anti-HIV-1 activity, we can identify new strategies for comprehensive identification of other important antiviral genes. This will, in turn, enhance our ability to inhibit virus replication by informing both cure strategies and HIV-1 vaccine designs that aim to reduce transmission and can aid in blocking HIV-1 acquisition.

N6-methyladenosine is required for the hypoxic stabilization of specific mRNAs

“…Decay rates were calculated by the natural log of one minus the RNA input normalized ratio of labeled over unlabeled RNA. All half-lives were normalized to GAPDH half-life which was defined as 8 h based on previous publications and our unpublished data (Payne et al 2014). …”

Uniquely altered transcripts are associated with immune preservation in HIV infection

“…XCL1 was recently reported to inhibit HIV-1 at an early step of the viral replication cycle via the blockade of viral attachment and entry into host cells [27]. Our results seem to be consistent with a recent observation that described substantial increases in the abundance of mRNAs encoding lymphotactin (XCL1); the antiviral cytokines macrophage inflammatory proteins MIP-1α, MIP-1αP (CCL3L1), and MIP-1β; granulocyte-macrophage colony-stimulating factor (GM-CSF); tumor necrosis factor receptor superfamily member 9 (TNFRSF9); and gamma interferon (IFN-γ) in Gag p24- and Nef-specific CD8 + T cells from HIV-1-infected virus controllers (VCs) (less than 5,000 HIV-1 RNA copies/mL and CD4 + lymphocyte counts of higher than 400 cells/mm 3 ) [28]. The recent demonstration that there is an association between CD8 + T cells and primary human CD141 + DCs should also be considered.…”

c-Myc Represses Transcription of the Epstein-Barr Virus Latent Membrane Protein 1 Early After Primary B Cell Infection

“…Subsequently, three populations of RNA were reverse transcribed into cDNA using the High Capacity cDNA kit (Applied Biosystems): total RNA (T), unlabeled RNA (U), and nascent RNA (N). Quantitative real-time PCR was then performed on these three populations to discover total RNA abundance, relative transcription rates, and mRNA half-life as previously described (53). In brief, the abundance of mRNA was represented by the measurement of the total RNA sample ( T ).…”