Transcriptome Profiling of Human Monocyte-Derived Macrophages Upon CCL2 Neutralization Reveals an Association Between Activation of Innate Immune Pathways and Restriction of HIV-1 Gene Expression

Abstract

Macrophages are key targets of human immunodeficiency virus type 1 (HIV-1) infection and main producers of the proinflammatory chemokine CC chemokine ligand 2 (CCL2), whose expression is induced by HIV-1 both in vitro and in vivo. We previously found that CCL2 neutralization in monocyte-derived macrophages (MDMs) strongly inhibited HIV-1 replication affecting post-entry steps of the viral life cycle. Here, we used RNAsequencing to deeply characterize the cellular factors and pathways modulated by CCL2 blocking in MDMs and involved in HIV-1 replication restriction. We report that exposure to CCL2 neutralizing antibody profoundly affected the MDM transcriptome. Functional annotation clustering of up-regulated genes identified two clusters enriched for antiviral defense and immune response pathways, comprising several interferonstimulated, and restriction factor coding genes. Transcripts in the clusters were enriched for RELA and NFKB1 targets, suggesting the activation of the canonical nuclear factor κB pathway as part of a regulatory network involving miR-155 up-regulation. Furthermore, while HIV-1 infection caused small changes to the MDM transcriptome, with no evidence of host defense gene expression and type I interferon signature, CCL2 blocking enabled the activation of a strong host innate response in infected macrophage cultures, and potently inhibited viral genes expression. Notably, an inverse correlation was found between levels of viral transcripts and of the restriction factors APOBEC3A (apolipoprotein B mRNA editing enzyme catalytic polypeptide-like 3 A),

Toll-Like Receptor (TLR) Signaling Enables Cyclic GMP-AMP Synthase (cGAS) Sensing of HIV-1 Infection in Macrophages

“…2 ) highlights a relative lack of HIV-1 by itself to cause cGAS-dependent IFN responses. Thus, overall, our data are consistent with some of the earlier reports showing that incoming HIV-1 particles are not a strong inducer for a type I IFN response that depends on cGAS sensing of HIV-1 DNA ( 11 , 31 , 42 , 47 , 60 , 84 – 86 ). It should be noted, however, that the early phase is not the only period during which HIV-1 can be sensed, as multiple lines of evidence point to innate immune responses that are elicited by late events of the viral replication cycle ( 13 , 15 , 32 , 33 , 35 , 51 , 87 , 88 ).…”

Host Restriction Factors Modulating HIV Latency and Replication in Myeloid Cells

“…Although A3A was not initially included among those, we [66] and others [67,68] have collected evidence of its potential role as restriction factor for HIV-1 infection in monocytes and macrophages, as later discussed. Of interest, an IFNindependent regulation of A3A expression has been observed in association with the downregulation of endogenously released chemokine CCL2/MCP-1 [69]. In the same study, CCL2 downregulation led to NF-KB mediated upregulation of the microRNA miR-155 that modulates the expression of several genes, including chemokines and their receptors [69].…”

“…Of interest, an IFNindependent regulation of A3A expression has been observed in association with the downregulation of endogenously released chemokine CCL2/MCP-1 [69]. In the same study, CCL2 downregulation led to NF-KB mediated upregulation of the microRNA miR-155 that modulates the expression of several genes, including chemokines and their receptors [69].…”

Host Restriction Factors Modulating HIV Latency and Replication in Macrophages

“…Although A3A was not initially included among those, we [ 85 ] and others [ 86 , 87 ] have reported its potential role as a restriction factor for HIV-1 infection in monocytes and macrophages, as later discussed. Of interest, the antibody (Ab)-mediated downregulation of endogenously released chemokine CCL2/Monocyte Chemotactic Protein-1 (MCP-1) leads to an IFN-independent upregulation of A3A expression [ 88 ]. In the same study, CCL2 downregulation led to an NF-KB mediated upregulation of the microRNA miR-155 that modulated the expression of several genes, including chemokines and their receptors [ 88 ].…”

“…Of interest, the antibody (Ab)-mediated downregulation of endogenously released chemokine CCL2/Monocyte Chemotactic Protein-1 (MCP-1) leads to an IFN-independent upregulation of A3A expression [ 88 ]. In the same study, CCL2 downregulation led to an NF-KB mediated upregulation of the microRNA miR-155 that modulated the expression of several genes, including chemokines and their receptors [ 88 ].…”