Data_Sheet_2_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.zip

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 RNA-sequencing 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 interferon-stimulated, 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), ISG15, and MX1. These findings highlight an association between activation of innate immune pathways and HIV-1 restriction upon CCL2 blocking and identify this chemokine as an endogenous factor contributing to the defective macrophage response to HIV-1. Therapeutic targeting of CCL2 may thus strengthen host innate immunity and restrict HIV-1 replication.

巨噬细胞是人类免疫缺陷病毒1型（HIV-1）感染的关键靶点，同时也是促炎趋化因子C-C趋化因子配体2（CCL2）的主要产生者。CCL2的表达在体外和体内均由HIV-1诱导。我们先前研究发现，在单核细胞衍生的巨噬细胞（MDMs）中，CCL2的中和能够强烈抑制HIV-1的复制，影响病毒生命周期中的后期步骤。在本研究中，我们利用RNA测序技术，对由CCL2阻断所调控的MDMs中的细胞因子和通路进行了深度表征，并确定了与HIV-1复制限制相关的因素。我们发现，CCL2中和抗体暴露对MDM转录组产生了深远的影响。上调基因的功能注释聚类识别出两个富含抗病毒防御和免疫反应通路的簇，其中包括多个干扰素激活和限制因子编码基因。这些簇中的转录本富含RELA和NFKB1靶点，表明经典核因子κB通路的激活是涉及miR-155上调的调控网络的一部分。此外，虽然HIV-1感染对MDM转录组仅有轻微的影响，没有宿主防御基因表达和I型干扰素特征的证据，但CCL2阻断能够激活感染巨噬细胞培养中的强宿主先天免疫反应，并有效抑制病毒基因的表达。值得注意的是，病毒转录本水平与限制因子APOBEC3A（载脂蛋白BmRNA编辑酶催化多肽样3A）、ISG15和MX1的水平呈负相关。这些发现突显了CCL2阻断后，先天免疫通路激活与HIV-1限制之间的关联，并将此趋化因子认定为一种内源性因素，它参与了巨噬细胞对HIV-1反应缺陷的贡献。因此，针对CCL2的治疗性靶向可能增强宿主先天免疫并限制HIV-1的复制。