N6-methyladenosine modification of HIV-1 RNA suppresses type-I interferon induction in differentiated monocytic cells and primary macrophages

TL;DR

This study shows that N6-methyladenosine (m6A) modifications in HIV-1 RNA help the virus avoid triggering antiviral immune responses in myeloid cells.

Contribution

The study reveals a novel mechanism by which HIV-1 RNA m6A modifications suppress type-I interferon induction in monocytic cells and macrophages.

Findings

HIV-1 RNA with m6A modifications suppresses type-I interferon (IFN-I) expression in differentiated monocytic cells and macrophages.

Reduced m6A levels in HIV-1 RNA enhance IFN-I expression, indicating m6A's role in evading innate immune sensing.

m6A-modified HIV-1 RNA escapes RIG-I-mediated sensing and activation of IRF3 and IRF7 transcription factors.

Abstract

N6-methyladenosine (m6A) is a prevalent RNA modification that plays a key role in regulating eukaryotic cellular mRNA functions. RNA m6A modification is regulated by two groups of cellular proteins, writers and erasers that add or remove m6A, respectively. HIV-1 RNA contains m6A modifications that modulate viral infection and gene expression in CD4+ T cells. However, it remains unclear whether m6A modifications of HIV-1 RNA modulate innate immune responses in myeloid cells that are important for antiviral immunity. Here we show that m6A modification of HIV-1 RNA suppresses the expression of antiviral cytokine type-I interferon (IFN-I) in differentiated human monocytic cells and primary monocyte-derived macrophages. Transfection of differentiated monocytic U937 cells with HIV-1 RNA fragments containing a single m6A-modification significantly reduced IFN-I mRNA expression relative to their unmodified RNA counterparts. We generated HIV-1 with altered m6A levels of RNA by manipulating the expression of the m6A erasers (FTO and ALKBH5) or pharmacological inhibition of m6A addition in virus-producing cells, or by treating HIV-1 RNA with recombinant FTO in vitro. HIV-1 RNA transfection or viral infection of differentiated U937 cells and primary macrophages demonstrated that HIV-1 RNA with decreased m6A levels enhanced IFN-I expression, whereas HIV-1 RNA with increased m6A modifications had opposite effects. Our mechanistic studies indicated that m6A of HIV-1 RNA escaped retinoic acid-induced gene I (RIG-I)-mediated RNA sensing and activation of the transcription factors IRF3 and IRF7 that drive IFN-I gene expression. Together, these findings suggest that m6A modifications of HIV-1 RNA evade innate immune sensing in myeloid cells.

HIV-1 is known as a weak inducer of antiviral cytokines including IFN-I, but it is unclear how HIV-1 evades innate immunity. Different types of RNA modifications including m6A within the HIV-1 genome modulate viral replication; however, the role of m6A modifications of HIV-1 RNA in regulating innate immune responses remains elusive. Myeloid cells including macrophages are HIV-1 target cells and critical for generating antiviral immunity. In this study, we aimed to investigate the role of m6A modifications of HIV-1 RNA in regulating innate immune responses in myeloid cells. We found that m6A-modified HIV-1 RNA suppresses IFN-I expression in differentiated monocytic cells and primary macrophages. Our data suggest that the cellular protein RIG-I contributes to innate sensing of m6A-defective HIV-1 RNA in differentiated monocytic cells. Our findings provide new insights into the functions and mechanisms of m6A modifications of HIV-1 RNA in regulating innate immune sensing and responses in myeloid cells.

Figures