Activation of ATF3 via the Integrated Stress Response Pathway Regulates Innate Immune Response to Restrict Zika Virus

Abstract

Zika virus (ZIKV) is a re-emerging mosquito-borne flavivirus that can have devastating health consequences. The developmental and neurological effects from a ZIKV infection arise in part from the virus triggering cellular stress pathways and perturbing transcriptional programs. To date, the underlying mechanisms of transcriptional control directing viral restriction and virus-host interaction are understudied. Activating Transcription Factor 3 (ATF3) is a stress-induced transcriptional effector that modulates the expression of genes involved in a myriad of cellular processes, including inflammation and antiviral responses, to restore cellular homeostasis. While ATF3 is known to be upregulated during ZIKV infection, the mode by which ATF3 is activated and the specific role of ATF3 during ZIKV infection is unknown. In this study, we show via inhibitor and RNA interference approaches that ZIKV infection initiates the integrated stress response pathway to activate ATF4 which in turn induces ATF3 expression. Additionally, by using a CRISPR-Cas9 system to deplete ATF3, we found that ATF3 acts to limit ZIKV gene expression in A549 cells. In particular, the ATF3-dependent anti-ZIKV response occurred through regulation of innate immunity and autophagy pathways. We show that ATF3 differentially regulates the expression of innate immune response genes and suppresses the transcription of autophagy related genes to influence autophagic flux. Our study therefore highlights an important role for the integrated stress response pathway and ATF3 in establishing an antiviral effect during ZIKV infection.

ATF4 Signaling in HIV-1 Infection: Viral Subversion of a Stress Response Transcription Factor

“…Microarray and RNAseq analyses have shown that the levels of ATF5 transcripts increase in cells infected with viruses such as ZIKV or dengue [ 214 ]. ZIKV infection also increases ATF4 transcript and protein levels [ 38 , 39 , 285 ]. In the context of HIV-1 infection, ATF5 transcript levels are up-regulated in Th1Th17 vs. Th1 cells [ 286 ].…”

The Dual Roles of Activating Transcription Factor 3 (ATF3) in Inflammation, Apoptosis, Ferroptosis, and Pathogen Infection Responses

“…In addition to cellular antiviral signaling, autophagy has also been demonstrated to inhibit JEV replication [154]. ATF3 regulates viral infection by stimulating and inhibiting immune responses [20,140,155]. ATF3 has been reported to inhibit cellular antiviral signaling and autophagy by binding to the promoter regions of STAT1, IRF9, ISG15, and ATG5, thereby promoting JEV virus replication [120].…”

“…Interestingly, compared to its response to JEV infection, ATF3 exhibits a different function in hosts infected with the Zika virus (ZIKV). Research found that ATF3 inhibits ZIKV infection by differentially regulating the transcription of specific innate immune response and autophagy genes [140]. During the infection with ZIKV of A549 cells, ATF3 promotes the transcription of the RIG-I, STAT1, IRF9, and ISG15 genes while simultaneously inhibiting the transcription levels of IFNβ and IFIT2 [140].…”

“…Research found that ATF3 inhibits ZIKV infection by differentially regulating the transcription of specific innate immune response and autophagy genes [140]. During the infection with ZIKV of A549 cells, ATF3 promotes the transcription of the RIG-I, STAT1, IRF9, and ISG15 genes while simultaneously inhibiting the transcription levels of IFNβ and IFIT2 [140]. In addition to modulating ER stress and innate immune responses, ZIKV also disrupts the autophagy pathway in the early stages of infection, thus facilitating viral replication [156,157].…”

Zika virus infection in a cell culture model reflects the transcriptomic signatures in patients

“…To determine if the transcriptomic events observed in ZIKV infected cell lines are similar to those in the pediatric patients we infected an A549 cell line with a contemporary ZIKV isolate namely PRVABC59 isolated from Puerto Rico [56] at a high multiplicity of infection and prepared samples for RNA-seq analysis 48 hours post-infection. Although A549 cells are derived from human lung adenocarcinoma, the cell line has an intact immune response and has been used for studies investigating the molecular virology and virus-host interactions of flaviviruses [82]. Moreover, infants with congenital Zika syndrome showed lung disease [83], and high viral titers were reported in the lung of mice infected with ZIKV [68,69].…”