SREBP2-dependent lipid gene transcription enhances the infection of human dendritic cells by Zika virus

Abstract

The emergence of Zika virus (ZIKV) as a global health threat has highlighted the unmet need for ZIKV-specific vaccines and antiviral treatments. ZIKV infects dendritic cells (DC), which have pivotal functions in activating innate and adaptive antiviral responses; however, the mechanisms by which DC function is subverted to establish ZIKV infection are unclear. Here we develop a genomics profiling method that enables discrete analysis of ZIKV-infected versus neighboring, uninfected primary human DCs to increase the sensitivity and specificity with which ZIKV-modulated pathways can be identified. The results show that ZIKV infection specifically increases the expression of genes enriched for lipid metabolism-related functions. ZIKV infection also increases the recruitment of sterol regulatory element-binding protein (SREBP) transcription factors to lipid gene promoters, while pharmacologic inhibition or genetic silencing of SREBP2 suppresses ZIKV infection of DCs. Our data thus identify SREBP2-activated transcription as a mechanism for promoting ZIKV infection amenable to therapeutic targeting.

Introduction

Zika virus (ZIKV) is an arthropod-borne member of the Flaviviridae family of RNA viruses, which includes dengue virus (DENV), West Nile virus, and Japanese encephalitis virus. Outbreaks of ZIKV in many parts of the world, including the Americas, led the World Health Organization to declare ZIKV a public health emergency of global concern in 2016. Although most ZIKV infections cause short-lived and mild symptoms, they can also lead to severe complications with devastating consequences, particularly Guillain–Barré syndrome in adults^1,2 and congenital Zika syndrome in infants born to ZIKV-infected mothers^3,4,5,6,7,8. Despite intense research on ZIKV pathogenesis, the mechanisms by which the virus productively infects target cells remain unclear.

Dendritic cells (DCs) play crucial roles in detecting viral pathogens and orchestrating short- and long-term antiviral responses through both the innate and adaptive immune systems. DCs exist as multiple subsets, including plasmacytoid DCs, classical DCs, and monocyte-derived DCs (moDCs), with diverse ontogeny, phenotypes, and functions. Upon viral infection, DCs activate vigorous antiviral responses focused on the production of and response to type I interferons (IFNs), and they then undergo maturation to become potent antigen-presenting cells for virus-specific T cells. However, many viruses have evolved mechanisms to subvert DC function, thereby suppressing host defenses.

ZIKV can infect multiple DC subsets, including moDCs^9,10,11. Analysis of ZIKV-infected moDCs and primary myeloid DCs from infected individuals have shown that ZIKV suppresses the antiviral response, including production of type I IFN, as well as DC maturation and activation^9,12. However, little is known about the molecular mechanisms and pathways by which ZIKV enables productive infection of DCs. Previous studies have analyzed the transcriptional programs activated in cells infected with ZIKV, but it has proven difficult to identify transcription factors (TFs) responsible for changes in gene expression^13,14,15,16. Therefore, in the present study, we employed a highly sensitive approach recently developed by our laboratory to deconvolute the genomic profiles of purified ZIKV-infected and bystander uninfected cells, thereby facilitating the identification of key regulatory TFs that control DC responses specifically during ZIKV infection^17,18,19.

Here we identify transcriptional programs regulated by ZIKV by comparing genome-wide transcriptional profiles of highly purified ZIKV-infected and uninfected bystander moDCs with mock-infected cells. Notably, ZIKV infection is associated with increased expression of genes enriched in lipid metabolism-related functions. Chromatin immunoprecipitation sequencing (ChIP-seq) analyses reveals that sterol regulatory element-binding proteins (SREBPs), the master regulatory TFs of lipid metabolism, are preferentially recruited to the promoters of lipid metabolism-related genes, and capped small RNA-seq (csRNA-seq) analysis demonstrates increased transcription initiation of these genes. Further mechanistic investigation demonstrates that SREBP2 activity promotes ZIKV infection of moDCs. These findings identify a novel mechanism by which ZIKV creates a favorable environment for replication in moDCs and also suggest that SREBP2-dependent lipid metabolism is a potential therapeutic target to suppress ZIKV infection.

Results

ZIKV productively infects human moDCs

To investigate ZIKV–moDC interactions that determine the outcome of infection, we established a moDC model in which primary human monocytes were differentiated to moDCs in culture and then infected for various lengths of times with the Asian lineage ZIKV strain SD001¹⁷ at a multiplicity of infection (MOI) of 0.5. Viral infection was monitored by flow cytometry of cells stained with 4G2, a pan flavivirus envelope (E) protein-specific monoclonal antibody (mAb). …